Contacts of the helix formed by residues 90 - 114 (chain H) in PDB entry 4GTU
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 GLU 90 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G HIS* 5.0 9.2 - - + +
78G TYR* 4.8 7.4 - - + -
81G ARG* 2.8 51.4 + - - +
82G LYS* 4.6 12.1 - - - +
89H THR* 1.3 73.5 - - - +
91H GLU* 1.3 58.6 + - - +
93H LYS* 3.4 11.1 + - - +
94H ILE* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G HIS* 5.5 7.5 + - + +
89H THR* 2.6 25.2 + - - +
90H GLU* 1.3 75.4 - - - +
92H GLU* 1.3 85.6 + - - +
94H ILE* 3.1 10.3 + - - +
95H ARG* 2.9 40.0 + - + +
148H VAL 4.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H CYS 3.5 3.2 - - - +
87H GLY* 3.8 7.0 - - - -
88H GLU* 2.9 43.7 + - - +
89H THR* 2.8 24.6 + - - +
91H GLU* 1.3 89.6 + - - +
93H LYS* 1.3 58.8 + - - +
96H VAL* 3.1 24.6 + - - +
148H VAL* 3.1 32.9 - - + +
151H LYS* 3.3 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ARG* 3.3 40.5 + - + +
87H GLY* 4.0 31.6 - - - +
88H GLU 4.7 5.3 + - - -
89H THR 2.7 21.5 + - - +
90H GLU* 3.5 13.8 + - - +
92H GLU* 1.3 76.0 - - - +
94H ILE* 1.3 59.2 + - - +
96H VAL* 2.8 10.3 + - + +
97H ASP* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G HIS* 3.4 34.1 - - + +
68G LYS 6.2 0.4 - - - -
69G ILE* 4.2 17.0 - - + -
78G TYR* 3.7 22.4 - - + -
81G ARG* 3.6 20.6 - - - +
90H GLU* 2.9 23.2 + - + +
91H GLU* 3.6 7.2 - - - +
93H LYS* 1.3 76.1 - - - +
95H ARG* 1.3 59.6 + - + +
97H ASP* 3.8 2.5 - - - +
98H ILE* 3.0 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ASP* 5.6 2.0 + - - -
91H GLU* 2.9 27.3 + - + +
92H GLU 4.0 0.2 - - - -
94H ILE* 1.3 79.3 - - + +
96H VAL* 1.3 60.6 - - - +
98H ILE* 4.4 0.7 - - + -
99H LEU* 3.3 27.7 + - - +
139H GLN 5.5 0.6 + - - -
140H PHE* 3.0 60.6 + - + +
144H ARG* 3.2 36.5 - - - +
147H PHE 2.7 29.5 + - - -
148H VAL* 3.4 36.3 - - + +
155H VAL* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H CYS* 4.4 4.3 - - - -
87H GLY* 4.0 22.7 - - - +
92H GLU 3.1 19.5 + - - +
93H LYS* 2.8 16.7 + - + +
95H ARG* 1.3 78.0 - - - +
97H ASP* 1.3 64.8 + - - +
100H GLU* 2.9 34.5 + - - +
148H VAL* 4.1 11.2 - - + -
153H THR* 4.3 9.2 - - + +
154H PHE* 3.7 28.9 - - + -
155H VAL* 3.8 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ILE* 5.8 0.7 - - + -
74G ALA* 3.6 21.7 - - + +
77G CYS* 3.1 36.6 - - - +
81G ARG* 2.6 30.6 + - - +
93H LYS* 2.8 11.2 + - - +
94H ILE* 3.2 6.7 + - - +
96H VAL* 1.3 78.2 - - - +
98H ILE* 1.3 66.2 + - + +
100H GLU* 3.2 13.8 + - - +
101H ASN* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ASP* 3.8 20.9 - - - +
56G PHE* 3.6 32.1 - - + -
68G LYS 4.6 0.4 - - - +
69G ILE* 4.5 8.5 - - + -
70G THR* 3.7 46.9 - - - +
71G GLN* 4.0 0.7 - - - +
74G ALA* 4.0 0.9 - - - -
94H ILE* 3.0 37.3 + - + +
95H ARG 4.7 1.6 - - - +
97H ASP* 1.3 78.5 - - + +
99H LEU* 1.3 53.6 + - - +
101H ASN* 3.1 2.1 + - - +
102H GLN* 2.7 37.4 + - + +
140H PHE* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G PHE* 5.0 4.7 - - + -
95H ARG 3.3 17.9 + - - +
96H VAL 4.3 0.9 - - - +
97H ASP 3.5 0.2 - - - -
98H ILE* 1.3 79.2 - - - +
100H GLU* 1.3 57.1 + - - +
102H GLN* 4.1 5.4 - - - -
103H ALA* 2.7 47.0 + - + +
137H PHE* 3.9 27.8 - - + -
140H PHE* 4.7 6.3 - - + -
147H PHE* 3.4 50.5 - - + -
148H VAL 5.3 0.2 - - - +
155H VAL* 3.6 26.9 - - + +
158H LEU* 5.4 0.9 - - + -
159H ALA* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G GLU* 5.3 5.2 - - - +
101G ASN* 4.5 8.1 + - - -
73H ASN* 3.2 39.7 + - - +
77H CYS* 5.4 5.8 - - - -
96H VAL* 2.9 22.5 + - - +
97H ASP* 3.4 17.1 - - - +
98H ILE 3.1 0.2 + - - -
99H LEU* 1.3 78.9 - - - +
101H ASN* 1.3 74.9 + - - +
104H MET* 3.3 19.2 + - - +
154H PHE* 4.1 26.9 - - + -
155H VAL* 4.7 3.3 - - + +
158H LEU* 3.8 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G GLN* 3.5 31.1 + - + +
73G ASN* 3.2 34.1 + - - +
74G ALA* 3.8 15.9 - - - +
77G CYS* 6.1 1.4 - - - -
100G GLU* 5.0 0.6 + - - +
73H ASN* 5.1 2.4 + - - +
97H ASP* 2.8 26.9 + - - +
98H ILE 3.1 2.2 + - - +
100H GLU* 1.3 93.3 + - - +
102H GLN* 1.3 65.0 + - - +
104H MET* 3.2 7.5 - - - +
105H ASP* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G PHE* 3.8 40.3 + - + +
58G ASN* 5.1 9.6 + - - +
70G THR* 3.7 14.2 - - - +
71G GLN* 2.8 29.5 + - - +
98H ILE* 2.7 28.0 + - + +
99H LEU* 4.0 4.0 - - - +
101H ASN* 1.3 68.5 - - - +
103H ALA* 1.3 63.8 + - - +
104H MET 2.9 5.1 + - - -
105H ASP* 2.6 44.9 + - - +
106H VAL* 3.3 12.7 + - + +
137H PHE* 4.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H LEU* 2.7 36.4 + - + +
102H GLN* 1.3 75.0 - - - +
104H MET* 1.3 62.0 + - - +
106H VAL* 3.3 22.8 - - - +
107H SER* 3.7 4.5 + - - -
137H PHE* 4.5 6.7 - - + -
158H LEU* 4.4 23.9 - - + +
159H ALA* 4.6 4.0 - - - +
162H VAL* 3.4 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASN* 5.2 8.1 - - - +
104G MET* 6.3 2.9 - - + -
108G ASN* 5.5 6.3 - - - +
12H LEU* 5.9 7.2 - - - -
73H ASN* 4.1 20.6 - - - +
100H GLU 3.3 14.5 + - - +
101H ASN* 3.2 13.9 + - - +
102H GLN 2.9 0.4 - - - -
103H ALA* 1.3 80.6 - - - +
105H ASP* 1.3 63.5 + - - +
107H SER* 3.6 3.1 + - - -
108H ASN* 3.1 38.6 + - + +
158H LEU* 5.0 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G GLN* 2.9 26.5 + - - +
101H ASN 3.1 8.2 + - - +
102H GLN* 2.6 32.2 + - - +
104H MET* 1.3 79.5 - - - +
106H VAL* 1.3 60.1 + - - +
108H ASN* 3.1 9.8 + - - +
109H GLN* 2.6 56.4 + - - +
112H ARG* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H GLN* 3.8 12.6 - - + +
103H ALA* 3.3 19.1 - - - +
105H ASP* 1.3 86.6 + - - +
107H SER* 1.3 59.5 + - - +
109H GLN* 3.3 14.1 - - - +
110H LEU* 3.0 27.0 + - - +
126H TYR* 4.0 4.9 + - - -
133H MET* 4.5 16.8 - - + -
137H PHE* 4.1 22.7 - - + -
162H VAL* 3.3 31.2 - - + -
166H HIS* 4.1 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 6.1 4.9 - - - -
103H ALA 4.0 5.8 - - - -
104H MET* 3.6 4.3 + - - -
105H ASP 3.3 0.2 - - - -
106H VAL* 1.3 77.9 - - - +
108H ASN* 1.3 59.8 + - - +
109H GLN 3.1 0.2 - - - -
110H LEU* 3.4 6.0 + - - +
111H ALA* 3.0 30.7 + - - +
161H ASP* 4.8 4.1 + - - -
162H VAL* 3.1 28.9 + - - +
165H LEU* 3.7 24.4 - - - +
166H HIS* 5.0 2.0 - - - -
208H TYR* 4.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ASN* 4.7 6.9 - - - +
112G ARG* 3.5 24.0 + - - +
12H LEU* 6.4 2.0 - - + +
104H MET* 3.1 34.5 + - - +
105H ASP* 3.1 10.1 + - - +
107H SER* 1.3 76.4 - - - +
109H GLN* 1.3 59.4 + - - +
111H ALA* 4.1 6.3 - - - +
112H ARG* 3.0 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ASP* 2.6 38.6 + - - +
106H VAL* 3.3 9.6 - - - +
108H ASN* 1.3 74.3 - - - +
110H LEU* 1.3 65.0 + - - +
112H ARG* 3.3 27.8 + - - +
113H VAL* 3.9 8.8 + - - +
126H TYR* 3.5 14.3 + - + -
133H MET* 3.0 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H VAL 3.0 16.7 + - - +
107H SER 3.8 3.8 - - - +
109H GLN* 1.3 73.9 - - - +
111H ALA* 1.3 67.3 + - - +
113H VAL* 2.9 32.1 + - + +
114H CYS* 3.2 19.3 + - - -
126H TYR* 3.8 26.9 + - + +
165H LEU* 4.4 16.2 - - + +
166H HIS* 3.6 32.5 - - + +
169H PHE* 4.0 25.8 - - + -
208H TYR* 3.4 20.2 - - + +
214H TRP* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H SER 3.0 18.4 + - - +
108H ASN* 4.2 8.7 - - - +
110H LEU* 1.3 76.7 - - - +
112H ARG* 1.3 62.6 + - - +
114H CYS* 3.7 4.3 - - - -
115H TYR* 3.1 41.2 + - + +
208H TYR* 3.7 29.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ARG* 3.1 44.6 - - - +
105H ASP 5.2 0.6 + - - -
108H ASN* 3.0 45.3 + - - +
109H GLN* 3.3 24.8 + - - +
110H LEU 3.0 0.2 - - - -
111H ALA* 1.3 78.7 - - - +
113H VAL* 1.3 64.5 + - + +
115H TYR* 3.9 3.7 + - - +
116H SER* 3.4 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H GLN 4.2 9.6 - - - +
110H LEU* 2.9 34.9 + - + +
112H ARG* 1.3 77.7 - - + +
114H CYS* 1.3 60.4 + - - +
115H TYR 3.1 4.7 - - - -
116H SER* 3.0 27.4 + - - +
119H PHE* 3.4 27.0 - - + +
122H LEU* 4.1 34.3 - - + +
123H LYS* 5.7 0.9 - - - -
125H GLU* 6.0 0.9 - - - +
126H TYR* 4.8 23.6 - - + -
169H PHE* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H LEU* 4.0 27.6 - - - +
111H ALA* 3.1 10.1 + - - +
113H VAL* 1.3 79.5 - - - +
115H TYR* 1.3 60.6 + - + +
119H PHE* 3.9 21.5 - - - -
169H PHE* 4.0 1.3 - - - -
208H TYR* 4.2 15.0 - - + -
212H ALA* 3.6 3.1 - - - +
213H VAL* 2.9 27.7 + - - +
214H TRP* 3.2 44.6 + - - +
----------------------------------------------------------
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