Contacts of the helix formed by residues 89 - 106 (chain B) in PDB entry 1GG3
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 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 4.4 4.2 - - - +
38B GLU* 3.3 39.4 + - + +
39B GLU* 2.6 19.3 + - + +
87B LEU* 4.4 1.4 - - - +
88B THR* 1.3 86.8 - - + +
90B ASP* 1.3 65.0 + - - +
91B ILE* 3.4 28.4 - - + +
92B THR* 3.5 21.1 + - - +
93B ARG* 3.1 20.1 + - - +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 1.3 69.6 - - - +
91B ILE* 1.3 62.5 + - + +
92B THR 3.0 1.6 - - - -
93B ARG* 2.6 54.9 + - - +
94B TYR* 2.9 10.9 + - - +
171B ALA* 3.5 31.4 - - + +
174B ASP* 5.6 0.2 - - - +
175B LEU* 6.1 0.2 - - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN 4.4 8.3 - - - +
36B LEU* 3.9 25.8 - - + +
37B LEU* 4.4 4.5 - - + -
89B GLU* 3.4 36.6 - - + +
90B ASP* 1.3 76.7 - - + +
92B THR* 1.3 66.9 + - - +
94B TYR* 2.8 23.4 + - + +
95B TYR* 3.0 41.9 + - + +
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.8 21.4 - - + +
39B GLU* 2.9 41.4 + - + +
42B PHE* 5.1 3.4 - - + -
44B LEU* 4.4 15.3 - - + +
87B LEU* 3.7 23.3 - - + -
89B GLU* 3.5 19.0 + - - +
90B ASP 3.0 0.4 - - - -
91B ILE* 1.3 79.5 - - - +
93B ARG* 1.3 57.7 + - - +
95B TYR* 3.6 2.5 + - - +
96B LEU* 3.0 27.8 + - + +
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO 3.2 23.0 + - - +
85B ALA* 3.5 11.3 + - - +
87B LEU* 2.6 36.2 + - + -
88B THR 4.2 4.8 + - - -
89B GLU 3.1 20.3 + - - +
90B ASP* 2.6 44.6 + - - +
92B THR* 1.3 71.9 - - - +
94B TYR* 1.3 67.8 + - - +
96B LEU* 3.5 7.6 - - - +
97B CYS* 2.9 29.2 + - - -
171B ALA 5.6 2.0 - - - -
174B ASP* 4.7 7.4 - - + -
175B LEU* 3.8 30.6 - - - +
178B LEU* 3.4 25.4 - - + -
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 5.5 3.5 + - - +
90B ASP 2.9 6.9 + - - +
91B ILE* 2.8 19.9 + - + +
93B ARG* 1.3 80.1 - - - +
95B TYR* 1.3 89.7 + + - +
97B CYS* 3.1 11.3 + - + +
98B LEU* 3.1 45.7 + - + +
101B ARG* 5.8 0.7 - - - -
126B SER* 6.1 3.8 - - - -
127B GLU* 4.4 15.6 + - - -
174B ASP* 4.1 23.9 + - - +
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.7 23.2 - - + +
35B ASN* 3.0 54.6 + - - -
37B LEU* 3.6 29.2 - - + -
44B LEU* 4.6 11.4 - - + -
75B PHE* 5.1 0.4 - + - -
77B VAL* 4.9 1.6 - - - -
91B ILE* 3.0 36.7 + - + +
92B THR 4.2 2.5 - - - +
94B TYR* 1.3 96.6 - + - +
96B LEU* 1.3 63.5 + - - +
98B LEU* 3.1 18.2 + - + +
99B GLN* 2.9 23.9 + - - +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 5.6 0.4 - - - +
77B VAL* 4.1 26.9 - - + +
80B TYR* 4.3 14.6 - - + -
81B PRO* 3.7 38.1 - - + -
84B PRO* 3.8 12.3 - - + -
87B LEU* 4.4 6.5 - - + -
92B THR* 3.0 19.2 + - + +
93B ARG* 3.5 5.4 - - - +
94B TYR 3.2 0.2 - - - -
95B TYR* 1.3 77.7 - - - +
97B CYS* 1.3 57.4 + - - +
99B GLN* 3.4 1.4 + - - +
100B LEU* 3.0 37.0 + - + +
178B LEU* 3.5 28.5 - - + -
187B TYR* 4.0 6.5 - - - +
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Residues in contact with CYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ARG 2.9 19.7 + - - -
94B TYR* 3.3 10.1 - - + +
96B LEU* 1.3 74.5 - - - +
98B LEU* 1.3 56.6 + - + +
100B LEU* 2.9 9.4 + - - +
101B ARG* 2.6 44.0 + - + +
174B ASP* 3.7 40.4 - - - +
177B PHE* 3.7 30.0 - - + -
178B LEU* 3.9 7.9 - - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 39.9 - - + +
9B ASP* 4.3 13.5 - - + -
94B TYR* 3.1 50.8 + - + +
95B TYR* 3.1 16.6 + - + +
97B CYS* 1.3 75.6 - - + +
99B GLN* 1.3 64.2 + - - +
101B ARG* 3.2 36.1 + - - +
102B GLN* 2.8 26.7 + - - +
127B GLU* 5.1 2.2 - - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.5 12.9 - - + +
53B LYS* 6.0 0.4 - - - +
76B ASN* 3.1 32.4 + - - +
77B VAL* 2.8 48.6 + - + +
80B TYR* 3.4 24.9 - - + +
95B TYR 2.9 13.3 + - - +
96B LEU* 3.4 9.4 - - + +
98B LEU* 1.3 75.1 - - - +
100B LEU* 1.3 59.6 + - - +
102B GLN* 3.1 8.4 + - - +
103B ASP* 2.7 53.7 + - - +
108B ARG* 4.1 4.5 + - - -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TYR* 3.8 21.1 - - + -
96B LEU* 3.0 22.3 + - + +
97B CYS 2.9 7.5 + - - +
99B GLN* 1.3 74.7 - - - +
101B ARG* 1.3 66.2 + - - +
103B ASP* 3.0 8.5 + - - +
104B ILE* 2.8 28.9 + - - +
109B LEU* 4.2 17.0 - - + -
177B PHE* 3.7 22.4 - - + -
178B LEU* 3.7 28.0 - - + -
181B ALA* 3.9 12.1 - - + -
187B TYR* 3.7 30.7 - - + -
188B GLY 5.3 0.9 - - - +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 5.8 0.4 - - - -
97B CYS* 2.6 35.6 + - + +
98B LEU* 3.2 37.7 - - + +
100B LEU* 1.3 70.3 - - - +
102B GLN* 1.3 65.4 + - - +
104B ILE* 3.0 15.3 + - - +
105B VAL* 2.9 31.0 + - + +
123B THR* 3.2 45.1 - - - +
127B GLU* 4.1 24.2 + - - +
144B PHE* 4.4 10.7 - - - -
145B LYS* 4.9 17.2 + - - +
146B LEU* 5.4 1.3 - - - +
177B PHE* 4.6 6.9 - - + -
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU 4.8 0.3 - - - +
8B LEU* 2.8 38.0 + - + +
10B ASP* 3.1 30.7 + - - +
76B ASN* 6.1 2.0 - - - +
98B LEU 2.8 10.7 + - - +
99B GLN* 3.2 17.9 - - - +
101B ARG* 1.3 77.1 - - - +
103B ASP* 1.3 62.8 + - - +
105B VAL* 3.2 9.9 + - + +
106B ALA* 2.9 24.3 + - - +
108B ARG* 4.4 8.1 - - - +
145B LYS* 5.8 2.2 - - - +
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TYR* 2.8 30.4 + - - -
99B GLN* 2.7 39.2 + - - +
100B LEU* 3.2 14.5 - - - +
102B GLN* 1.3 71.8 - - - +
104B ILE* 1.3 59.9 + - - +
106B ALA 3.3 1.7 + - - -
107B GLY 3.3 2.3 + - - -
108B ARG* 2.7 71.9 + - - +
109B LEU* 3.4 20.7 + - + +
188B GLY 5.0 3.8 + - - -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU 2.8 19.4 + - - +
101B ARG* 3.0 11.0 + - - +
103B ASP* 1.3 70.7 - - - +
105B VAL* 1.3 62.2 + - + +
107B GLY* 2.9 18.7 + - - -
109B LEU* 3.4 34.3 - - + +
111B CYS* 5.4 3.4 - - - -
116B LEU* 4.0 14.8 - - + -
119B LEU* 3.6 32.3 - - + -
146B LEU 3.5 25.4 - - - +
147B ALA* 4.3 4.5 - - - -
148B PRO* 3.5 11.3 - - + +
177B PHE* 4.1 16.2 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 2.9 17.6 + - + +
102B GLN* 3.8 11.9 - - - +
104B ILE* 1.3 76.3 - - + +
106B ALA* 1.3 57.3 + - - +
107B GLY 2.9 10.5 + - - -
145B LYS* 4.0 42.6 - - + +
146B LEU 5.0 0.2 - - - -
147B ALA 4.8 8.3 - - - +
148B PRO* 3.6 23.2 - - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 2.9 13.8 + - + +
103B ASP 3.5 5.8 - - - +
104B ILE 3.2 0.2 - - - -
105B VAL* 1.3 76.3 - - - +
107B GLY* 1.3 61.9 + - - +
108B ARG* 2.8 41.7 + - - +
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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) + - + + + + + -
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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