Contacts of the helix formed by residues 90 - 114 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 5.6 7.4 - - + +
78A TYR* 3.6 26.6 - - + -
81A ARG* 2.9 48.5 + - - +
82A LYS* 4.7 8.3 - - - +
88B GLU 4.1 0.4 + - - -
89B THR* 1.3 72.0 - - - +
91B GLU* 1.3 61.8 + - - +
93B LYS* 4.5 4.7 - - - +
94B ILE* 3.1 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 3.2 21.4 + - - +
90B GLU* 1.3 75.0 - - - +
92B GLU* 1.3 80.2 + - + +
94B ILE* 3.0 31.9 - - + +
95B ARG* 3.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY* 4.0 2.5 - - - -
88B GLU* 3.5 16.2 - - - +
89B THR* 2.7 47.6 + - - +
91B GLU* 1.3 88.0 - - + +
93B LYS* 1.3 63.9 + - - +
95B ARG* 3.3 2.4 + - - +
96B VAL* 3.0 28.3 + - - +
148B VAL* 3.2 29.4 - - + +
149B GLY* 5.9 0.8 - - - -
151B LYS* 3.0 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.5 35.3 - - - +
86B CYS* 5.4 3.4 - - + -
87B GLY* 3.8 32.8 + - - +
88B GLU 3.7 19.7 + - - -
89B THR 2.8 13.4 + - - +
90B GLU* 3.9 3.1 - - - +
92B GLU* 1.3 77.1 - - - +
94B ILE* 1.3 61.1 + - - +
96B VAL* 3.1 6.2 + - + +
97B ASP* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 4.5 16.4 - - + -
69A ILE* 4.4 21.1 - - + -
74A ALA 6.0 0.2 - - - +
78A TYR* 4.2 12.8 - - + -
81A ARG* 3.3 24.2 - - - +
90B GLU* 3.1 24.9 + - + +
91B GLU* 3.0 28.9 - - + +
93B LYS* 1.3 72.4 - - - +
95B ARG* 1.3 65.1 + - + +
97B ASP* 3.2 7.9 + - - +
98B ILE* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 3.9 13.1 + - - -
91B GLU* 3.0 27.7 + - - +
92B GLU* 3.7 6.3 - - - +
94B ILE* 1.3 82.6 - - + +
96B VAL* 1.3 60.8 + - - +
98B ILE* 4.1 3.1 - - - -
99B LEU* 3.2 26.9 + - - +
139B GLN 5.6 0.4 + - - -
140B PHE* 3.0 61.2 + - + +
144B ARG* 2.8 35.2 - - - +
147B PHE 3.1 20.4 + - - -
148B VAL* 4.1 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B CYS* 5.1 0.9 - - + -
87B GLY* 4.1 17.9 - - - +
92B GLU 3.0 20.1 + - - +
93B LYS* 3.3 11.7 - - + +
94B ILE 3.1 0.2 - - - -
95B ARG* 1.3 77.9 - - - +
97B ASP* 1.3 57.2 + - - +
100B GLU* 2.8 35.3 + - - +
148B VAL* 3.7 17.0 - - + -
153B THR* 4.5 5.6 - - + +
154B PHE* 3.2 37.2 - - + -
155B VAL* 3.4 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.8 22.3 - - + +
77A CYS* 3.7 19.2 - - + +
81A ARG* 2.6 33.3 + - - -
93B LYS* 2.9 17.7 + - - +
94B ILE* 3.6 5.4 - - - +
96B VAL* 1.3 79.4 - - - +
98B ILE* 1.3 65.8 + - - +
100B GLU* 3.1 19.2 - - - +
101B ASN* 2.7 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.5 1.8 - - + +
56A PHE* 3.6 36.3 - - + -
68A LYS 5.3 1.6 - - - +
69A ILE* 4.1 26.7 - - + -
70A THR* 4.0 25.1 - - - +
71A GLN* 3.7 5.5 - - + +
74A ALA* 3.9 17.9 - - + -
94B ILE* 2.9 36.7 + - + +
95B ARG* 4.1 5.8 - - - +
97B ASP* 1.3 78.2 - - - +
99B LEU* 1.3 66.7 + - - +
101B ASN 3.2 0.2 + - - -
102B GLN* 2.9 23.9 + - + +
140B PHE* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.4 12.1 - - + -
95B ARG 3.2 16.2 + - - +
96B VAL 3.9 2.2 - - - +
98B ILE* 1.3 82.6 - - - +
100B GLU* 1.3 55.2 + - - +
102B GLN* 4.0 3.8 - - + -
103B ALA* 2.7 43.2 + - + +
137B PHE* 4.3 22.0 - - + -
140B PHE* 4.3 9.2 - - + -
147B PHE* 3.5 47.3 - - + +
148B VAL* 6.3 0.2 - - + -
155B VAL* 4.0 31.4 - - + +
158B LEU* 6.0 0.2 - - + -
159B ALA* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.3 0.7 - - - +
100A GLU* 4.1 14.8 - - - +
101A ASN* 4.6 0.2 + - - -
73B ASN* 2.9 40.7 + - - +
77B CYS* 5.5 3.1 - - - -
96B VAL 2.8 24.1 + - - +
97B ASP* 3.1 14.4 - - - +
99B LEU* 1.3 76.3 - - - +
101B ASN* 1.3 84.7 + - - +
103B ALA* 3.4 3.8 + - - +
104B MET* 3.4 21.5 + - - +
154B PHE* 4.6 16.2 - - + -
155B VAL* 4.1 5.4 - - + +
158B LEU* 4.0 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.1 28.1 + - + +
73A ASN* 2.8 45.8 + - - +
74A ALA* 3.9 8.1 - - - +
73B ASN* 4.5 5.3 + - - +
97B ASP* 2.7 27.3 + - - +
98B ILE 3.2 0.6 + - - -
100B GLU* 1.3 103.2 + - - +
102B GLN* 1.3 58.5 + - - +
104B MET* 3.5 6.5 + - - +
105B ASP* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.2 54.7 - - + +
58A ASN* 5.3 5.2 - - - +
70A THR* 5.6 2.1 - - - -
71A GLN* 2.9 14.0 + - - +
98B ILE* 2.9 21.2 + - + +
99B LEU* 3.6 12.1 - - + +
101B ASN* 1.3 74.1 - - - +
103B ALA* 1.3 67.3 + - - +
105B ASP* 3.0 37.3 + - - +
106B VAL* 3.1 23.1 + - + +
137B PHE* 4.7 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 2.7 27.8 + - + +
100B GLU 3.6 4.3 - - - +
102B GLN* 1.3 74.9 - - - +
104B MET* 1.3 64.1 + - - +
106B VAL* 3.0 13.0 + - - +
107B SER* 3.0 24.6 + - - +
137B PHE* 5.0 6.3 - - + -
158B LEU* 3.9 37.7 - - + +
159B ALA* 5.0 1.3 - - - +
162B VAL* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.8 23.8 - - + -
72B SER* 3.6 30.5 - - - +
73B ASN* 3.8 24.7 - - - +
76B LEU* 6.0 0.4 - - - -
100B GLU 3.4 13.0 + - - +
101B ASN* 3.9 8.7 - - - +
102B GLN 3.3 0.2 - - - -
103B ALA* 1.3 79.2 - - - +
105B ASP* 1.3 62.0 + - - +
107B SER* 3.8 12.5 - - - -
108B ASN* 3.0 30.9 + - - +
158B LEU* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 5.9 2.6 - - - -
71A GLN* 3.5 15.7 + - - +
101B ASN 2.9 15.7 + - - +
102B GLN* 3.0 32.6 + - - +
104B MET* 1.3 78.1 - - - +
106B VAL* 1.3 55.6 + - - +
108B ASN* 3.6 3.8 + - - +
109B GLN* 3.0 38.7 + - - +
112B ARG* 4.3 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 3.1 21.5 + - + +
103B ALA 3.0 18.2 + - - +
105B ASP* 1.3 76.3 - - + +
107B SER* 1.3 65.3 + - - +
109B GLN* 3.6 12.2 - - - +
110B LEU* 3.2 19.4 + - - +
126B TYR* 3.6 7.5 + - - +
133B MET* 4.3 30.5 - - + -
137B PHE* 4.1 25.8 - - + -
162B VAL* 3.3 22.7 - - + -
166B HIS* 4.6 5.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 6.2 3.4 - - - -
103B ALA 3.0 18.3 + - - -
104B MET* 3.8 16.2 - - - -
106B VAL* 1.3 77.8 - - - +
108B ASN* 1.3 65.8 + - - +
110B LEU* 3.3 6.2 + - - +
111B ALA* 3.0 21.2 + - - +
158B LEU* 6.0 1.0 - - - +
161B ASP* 5.0 3.6 + - - -
162B VAL* 3.3 21.6 - - - +
165B LEU* 4.6 14.2 - - - +
208B TYR* 4.3 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 4.5 12.9 - - - +
12B LEU* 4.9 13.3 - - - +
104B MET* 3.0 19.0 + - - +
105B ASP* 3.7 3.4 - - - +
107B SER* 1.3 79.9 - - - +
109B GLN* 1.3 66.0 + - - +
111B ALA* 2.9 9.9 + - - +
112B ARG* 2.9 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 3.0 32.1 + - - +
106B VAL* 3.6 14.3 - - - +
108B ASN* 1.3 76.1 - - - +
110B LEU* 1.3 62.1 + - - +
112B ARG* 3.3 21.8 + - - +
113B VAL* 3.5 24.8 + - - +
126B TYR* 3.8 26.8 - - + -
129B GLU* 5.3 4.5 - - - +
133B MET* 4.4 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL 3.2 9.2 + - - +
107B SER* 3.6 8.3 - - - +
108B ASN 3.2 0.6 - - - -
109B GLN* 1.3 77.2 - - - +
111B ALA* 1.3 63.9 + - - +
113B VAL* 3.5 7.5 + - + +
114B CYS* 3.1 21.7 + - + +
126B TYR* 3.5 32.1 + - + +
165B LEU* 4.2 29.8 - - + +
166B HIS* 3.5 24.9 - - + +
169B PHE* 3.9 32.3 - - + -
207B LEU* 6.6 0.2 - - + -
208B TYR* 3.3 16.9 + - + +
214B TRP* 5.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER 3.0 12.9 + - - +
108B ASN* 2.9 17.4 + - - +
110B LEU* 1.3 74.5 - - - +
112B ARG* 1.3 55.7 + - + +
114B CYS 2.9 2.4 + - - -
115B TYR* 2.7 49.5 + - + +
208B TYR* 3.2 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 4.6 7.1 + - - -
112A ARG* 4.1 34.0 - - - +
105B ASP* 4.3 9.3 + - - -
108B ASN* 2.9 48.6 + - + +
109B GLN* 3.3 40.6 - - - +
111B ALA* 1.3 74.5 - - + +
113B VAL* 1.3 64.0 + - + +
115B TYR* 3.3 14.8 + - - -
116B SER* 3.4 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLN 3.5 13.2 + - - +
110B LEU* 3.5 10.5 + - + +
111B ALA 3.2 0.6 - - - -
112B ARG* 1.3 77.0 - - + +
114B CYS* 1.3 60.7 + - - +
116B SER* 3.5 21.0 + - - +
119B PHE* 3.8 20.8 - - + +
122B LEU* 4.1 39.7 - - + +
123B LYS* 4.2 16.8 - - - +
126B TYR* 4.8 22.4 - - + -
169B PHE* 5.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.1 18.0 + - + +
111B ALA 2.9 5.1 + - - +
113B VAL* 1.3 74.0 - - - +
115B TYR* 1.3 59.7 + - - +
116B SER 3.2 5.2 - - - -
119B PHE* 4.4 7.2 - - - -
169B PHE* 5.2 1.8 - - - -
208B TYR* 3.7 18.4 - - + +
212B ALA* 4.1 0.9 - - - -
213B VAL* 3.0 34.4 + - - +
214B TRP* 3.1 68.0 - - - -
----------------------------------------------------------
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