Contacts of the helix formed by residues 89 - 116 (chain A) in PDB entry 1C72
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 1.3 83.5 - - + +
90A GLU* 1.3 65.7 + - - +
91A VAL* 4.1 8.9 + - - +
92A GLU* 2.7 35.2 + - - +
93A LYS* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 1.3 72.0 - - - +
91A VAL* 1.3 63.5 + - + +
93A LYS* 3.3 6.1 + - - +
94A GLN* 2.9 55.2 + - - +
78B TYR* 3.6 15.8 - - + -
81B ARG* 2.6 51.8 + - - +
82B LYS* 6.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.2 8.6 + - - +
90A GLU* 1.3 77.5 - - + +
92A GLU* 1.3 63.4 + - + +
94A GLN* 3.1 19.3 + - + +
95A ARG* 3.0 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A CYS 5.2 0.2 - - - +
87A GLY* 3.8 3.2 - - - -
88A GLU* 3.3 30.6 + - - +
89A THR* 2.7 32.7 + - - +
90A GLU 3.3 0.2 - - - -
91A VAL* 1.3 79.6 - - + +
93A LYS* 1.3 56.2 + - - +
95A ARG* 3.3 7.0 + - - +
96A VAL* 3.0 32.6 + - - +
148A VAL* 3.4 37.8 - - + +
151A LYS* 3.4 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 6.0 1.6 - - - +
86A CYS* 5.1 8.9 - - - +
87A GLY* 3.8 28.9 + - - +
88A GLU 4.6 7.0 - - - +
89A THR 3.1 19.3 + - - +
90A GLU* 3.8 7.0 - - - +
91A VAL 3.3 0.2 - - - -
92A GLU* 1.3 72.1 - - - +
94A GLN* 1.3 64.6 + - - +
96A VAL* 3.7 6.2 - - - +
97A ASP* 3.0 32.7 + - - +
81B ARG* 3.8 33.6 - - - +
93B LYS* 6.0 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 2.9 44.1 + - - +
91A VAL* 3.1 19.9 + - + +
93A LYS* 1.3 75.2 - - - +
95A ARG* 1.3 63.1 + - + +
97A ASP* 3.5 1.7 + - - +
98A VAL* 3.1 27.9 + - - +
67B VAL* 3.7 34.4 - - - +
68B LYS 5.3 0.7 + - - -
69B LEU* 4.5 20.7 - - + +
78B TYR* 4.1 15.4 - - + -
81B ARG* 4.0 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.0 39.1 + - + +
92A GLU* 3.6 15.9 - - - +
94A GLN* 1.3 76.5 - - + +
96A VAL* 1.3 64.9 + - - +
98A VAL* 3.3 7.9 - - - +
99A LEU* 3.1 29.5 + - - +
140A PHE* 3.7 28.5 - - + -
144A ARG* 3.5 28.4 - - - +
147A PHE 4.0 8.7 - - - -
148A VAL* 2.6 46.0 + - + -
149A GLY* 4.2 4.0 - - - +
151A LYS* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.4 4.7 - - - +
86A CYS* 4.8 2.2 - - + -
87A GLY 4.1 19.7 - - - +
92A GLU 3.0 17.8 + - - +
93A LYS* 3.3 6.7 + - - +
95A ARG* 1.3 76.6 - - - +
97A ASP* 1.3 65.4 + - - +
100A GLU* 2.9 34.1 + - - +
148A VAL* 3.8 23.3 - - + -
153A THR* 4.8 4.7 - - - +
154A PHE* 3.4 35.4 - - + -
155A VAL* 3.4 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 2.8 40.2 + - - +
93A LYS* 3.0 17.4 + - - +
94A GLN* 4.1 2.7 - - - +
96A VAL* 1.3 80.4 - - - +
98A VAL* 1.3 61.2 + - - +
100A GLU* 3.9 0.5 - - - +
101A ASN* 3.1 30.6 + - - +
74B ALA* 3.6 20.9 - - + +
77B ARG* 3.5 21.6 - - - +
81B ARG* 2.5 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN 3.1 20.7 + - - +
95A ARG* 3.3 14.1 - - - +
97A ASP* 1.3 75.4 - - - +
99A LEU* 1.3 66.2 + - + +
101A ASN 3.3 1.6 + - - -
102A HIS* 2.8 31.1 + - + +
140A PHE* 5.0 4.7 - - + -
55B ASP* 6.1 0.9 - - + +
56B PHE* 4.1 23.3 - - + -
69B LEU* 5.0 7.4 - - + -
70B THR* 3.8 33.7 - - - +
71B GLN* 3.7 7.5 - - + +
74B ALA* 3.8 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG 3.1 15.6 + - - +
98A VAL* 1.3 80.4 - - + +
100A GLU* 1.3 65.2 + - - +
102A HIS* 4.2 5.8 - - + -
103A LEU* 2.9 44.3 + - + +
137A LEU* 4.2 16.8 - - + -
140A PHE* 3.6 18.2 - - + -
147A PHE* 3.6 34.3 - - + +
148A VAL* 4.9 2.2 - - + -
155A VAL* 3.5 26.9 - - + -
56B PHE* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.4 43.8 + - - +
77A ARG* 2.8 46.5 + - - +
96A VAL 2.9 20.2 + - - +
97A ASP 3.9 2.0 - - - +
99A LEU* 1.3 77.6 - - - +
101A ASN* 1.3 76.8 + - - +
103A LEU* 4.4 1.7 - - - +
104A MET* 3.5 18.2 + - - +
154A PHE* 4.2 10.3 - - + -
155A VAL* 4.6 8.2 - - + +
158A LEU* 4.5 13.4 - - + +
100B GLU* 4.3 11.2 - - - +
101B ASN* 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.6 2.4 + - - +
97A ASP* 3.1 21.2 + - - +
98A VAL 3.3 1.2 + - - -
99A LEU 3.2 0.4 - - - -
100A GLU* 1.3 92.5 + - - +
102A HIS* 1.3 65.5 + - - +
104A MET* 3.3 9.0 + - - +
105A ASP* 3.2 19.8 + - - +
71B GLN* 3.0 34.5 - - + +
73B ASN* 3.1 45.3 + - - +
74B ALA* 3.8 4.6 - - - +
100B GLU* 5.1 0.6 + - - -
104B MET* 5.1 3.6 - - - +
221B EPY 4.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 2.8 18.8 + - + +
99A LEU* 3.9 10.1 - - + +
101A ASN* 1.3 77.0 - - - +
103A LEU* 1.3 58.1 + - + +
105A ASP* 3.1 10.9 + - + +
106A LEU* 3.0 61.3 + - + +
133A LYS* 5.3 5.5 + - + +
136A GLN* 4.5 10.5 + - - -
137A LEU* 4.3 15.2 - - + +
56B PHE* 3.8 48.5 - + + +
58B ASN* 5.6 3.7 + - - -
71B GLN* 3.8 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 2.9 35.1 + - + +
100A GLU 4.4 2.2 - - - +
102A HIS* 1.3 75.6 - - + +
104A MET* 1.3 59.1 + - - +
106A LEU* 3.7 16.6 - - + +
107A ARG* 2.9 29.2 + - - +
137A LEU* 4.6 17.7 - - + -
155A VAL* 4.1 11.2 - - + +
158A LEU* 3.9 15.3 - - + -
159A ALA* 3.6 36.3 - - + +
162A VAL* 3.7 35.5 - - + +
163A LEU* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.0 10.8 - - + -
72A SER* 5.4 4.5 - - - +
73A ASN* 4.8 15.9 - - - +
100A GLU 3.5 14.2 + - - +
101A ASN* 3.3 12.9 + - - +
102A HIS 3.2 0.6 - - - -
103A LEU* 1.3 74.7 - - - +
105A ASP* 1.3 60.7 + - - +
107A ARG* 3.2 22.9 + - - +
108A MET* 2.8 62.9 + - + +
220A EPY 3.8 31.2 - - + +
101B ASN* 5.9 2.9 - - - +
105B ASP* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN 3.2 9.5 + - - +
102A HIS* 3.1 14.5 + - + +
104A MET* 1.3 76.5 - - - +
106A LEU* 1.3 62.6 + - + +
108A MET* 3.3 12.7 + - - +
109A ALA* 2.9 32.0 + - - +
112A ARG* 4.5 3.3 + - - +
58B ASN* 3.9 8.3 + - - -
71B GLN* 3.1 15.6 + - - -
221B EPY 3.0 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A HIS* 3.0 48.2 + - + +
103A LEU* 3.7 19.3 - - + +
105A ASP* 1.3 82.7 - - + +
107A ARG* 1.3 63.5 + - - +
109A ALA* 3.5 5.9 + - + +
110A PHE* 3.2 23.9 + - - +
126A TYR* 4.8 2.9 + - - -
130A LEU* 6.3 1.8 - - + -
133A LYS* 4.7 25.8 - - + -
134A LEU* 6.4 0.7 - - + -
137A LEU* 3.9 21.1 - - + -
162A VAL* 4.3 14.1 - - + -
166A GLN* 5.1 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY 3.5 17.4 + - - -
12A LEU* 3.4 36.5 + - - +
15A ALA* 5.1 2.6 - - - +
103A LEU 2.9 19.9 + - - +
104A MET* 3.3 20.9 - - - +
106A LEU* 1.3 77.0 - - - +
108A MET* 1.3 58.1 + - + +
110A PHE* 3.5 7.0 + - - +
111A ALA* 3.1 24.7 + - - +
158A LEU* 4.3 17.9 - - - +
161A ASP* 2.5 35.1 + - - +
162A VAL* 3.7 25.9 - - + +
165A GLN* 4.5 12.7 + - - +
166A GLN* 6.1 0.4 - - - +
220A EPY 2.5 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 2.8 55.0 + - + +
105A ASP* 3.9 13.0 - - - +
107A ARG* 1.3 72.2 - - + +
109A ALA* 1.3 60.8 + - - +
111A ALA* 3.6 8.7 - - + +
112A ARG* 3.0 62.9 + - - +
220A EPY 5.6 7.9 - - + -
104B MET* 6.2 3.8 - - + -
108B MET* 4.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP 2.9 17.5 + - - +
106A LEU* 3.9 7.2 - - + +
107A ARG 3.4 0.2 - - - -
108A MET* 1.3 76.2 - - - +
110A PHE* 1.3 60.9 + - - +
112A ARG* 3.5 21.8 - - - +
113A LEU* 3.4 19.6 + - - +
126A TYR* 4.3 15.1 - - + -
129A LEU* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 3.2 15.1 + - - +
107A ARG* 3.5 4.5 - - - +
109A ALA* 1.3 77.9 - - - +
111A ALA* 1.3 64.5 + - - +
113A LEU* 3.2 8.4 + - + +
114A CYS* 3.1 34.7 + - - -
126A TYR* 3.8 30.7 - + - +
165A GLN* 3.3 54.1 - - + -
166A GLN* 3.8 11.2 - - - +
169A PHE* 4.0 27.8 - + + -
207A ILE* 5.0 0.7 - - + -
208A PHE* 3.2 37.2 - + - -
214A TRP* 4.3 6.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG 3.1 14.3 + - - +
108A MET* 3.3 12.3 + - + +
110A PHE* 1.3 75.5 - - - +
112A ARG* 1.3 65.1 + - - +
114A CYS 3.1 1.4 + - - -
115A TYR* 3.0 42.3 + - + -
208A PHE* 3.9 12.3 - - + -
220A EPY 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 4.5 3.2 + - - +
108A MET* 3.0 48.6 + - + +
109A ALA* 3.5 33.2 - - - +
111A ALA* 1.3 76.9 - - - +
113A LEU* 1.3 62.5 + - - +
115A TYR* 4.0 3.2 - - - +
116A SER* 3.1 24.3 + - - -
122A LEU* 6.1 0.2 - - - -
108B MET* 4.7 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA 3.4 8.3 + - - +
110A PHE* 3.2 10.4 + - + +
112A ARG* 1.3 79.5 - - - +
114A CYS* 1.3 67.6 + - - +
116A SER* 3.2 20.1 + - - +
119A PHE* 3.2 56.0 - - + +
122A LEU* 3.8 25.4 - - + +
123A LYS* 3.9 9.4 - - - +
126A TYR* 3.8 39.0 - - + -
169A PHE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE* 3.1 45.8 + - - +
111A ALA 3.1 2.4 + - - +
113A LEU* 1.3 81.1 - - - +
115A TYR* 1.3 58.4 + - - +
119A PHE* 3.9 16.4 - - - -
169A PHE* 4.7 1.3 - - - -
208A PHE* 4.1 24.2 - - + -
212A ALA* 3.6 3.2 - - - +
213A LEU* 2.8 32.0 + - - +
214A TRP* 3.9 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 3.0 31.1 + - + +
112A ARG* 4.2 3.6 - - - +
114A CYS* 1.3 76.3 - - - +
116A SER* 1.3 64.0 + - - +
117A PRO* 3.5 7.4 - - - +
208A PHE* 3.7 12.3 - + - -
209A TRP* 3.0 30.7 + - + +
211A THR* 3.7 28.8 - - - +
212A ALA* 3.8 22.7 - - + +
213A LEU* 4.5 7.3 - - - +
220A EPY 3.0 55.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG 3.1 17.9 + - - -
113A LEU 3.2 7.4 + - - -
115A TYR* 1.3 75.8 - - - +
117A PRO* 1.3 66.3 - - - +
118A ASP* 3.4 14.1 + - - +
119A PHE* 3.0 28.3 + - - +
122A LEU* 3.5 25.2 - - - +
213A LEU* 3.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il