Contacts of the helix formed by residues 103 - 117 (chain B) in PDB entry 1GQC
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 ARG 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 5.4 2.5 - - - +
101B MET 4.1 8.5 + - - +
102B ILE* 1.3 82.9 - - - +
104B PRO* 1.3 61.7 - - + +
105B ARG* 4.4 6.1 - - + +
106B ASP* 2.6 66.2 + - - +
107B VAL* 3.3 4.5 + - - +
218B ALA* 2.9 44.5 + - - +
219B ALA 3.1 18.0 + - - -
220B THR* 4.1 8.4 - - - +
221B GLY 4.9 4.0 - - - +
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Residues in contact with PRO 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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36B ARG* 3.6 35.4 - - + +
39B GLN* 3.9 36.3 - - + +
40B VAL* 3.9 14.6 - - + +
102B ILE* 3.6 9.1 - - + +
103B ARG* 1.3 83.4 - - + +
105B ARG* 1.3 62.7 + - + +
107B VAL* 3.1 7.8 + - + +
108B GLU* 2.9 29.3 + - - +
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Residues in contact with ARG 105 (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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103B ARG* 2.9 7.0 + - + -
104B PRO* 1.3 80.6 - - + +
106B ASP* 1.3 65.6 + - - +
108B GLU* 3.2 27.8 + - - +
109B THR* 3.1 24.4 + - - -
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 4.6 7.2 - - + +
103B ARG* 2.6 62.1 + - + +
105B ARG* 1.3 76.6 - - - +
107B VAL* 1.3 59.9 + - - +
109B THR* 3.2 11.4 + - - -
110B LEU* 3.2 19.4 + - - +
125B LEU* 4.1 22.6 - - + +
217B VAL* 3.7 29.6 - - + +
218B ALA 5.2 0.2 + - - -
220B THR* 4.2 6.6 - - - +
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Residues in contact with VAL 107 (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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5B ILE* 4.5 5.8 - - + -
40B VAL* 3.7 30.9 - - + +
93B ILE* 4.0 31.1 - - + +
95B LEU* 4.0 13.5 - - + -
102B ILE* 3.9 32.3 - - + -
103B ARG 4.0 3.8 - - - +
104B PRO* 3.1 8.6 + - + +
106B ASP* 1.3 75.3 - - - +
108B GLU* 1.3 57.1 + - - +
110B LEU* 3.4 10.7 - - + +
111B LEU* 3.1 24.6 + - - +
125B LEU* 5.5 0.9 - - - -
175B ILE* 4.9 3.6 - - + -
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Residues in contact with GLU 108 (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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39B GLN 3.7 9.5 - - - +
40B VAL* 3.8 10.9 - - + -
41B ALA* 3.0 36.7 + - - +
104B PRO* 2.9 18.6 + - - +
105B ARG* 3.4 32.6 + - - +
106B ASP 3.2 0.2 - - - -
107B VAL* 1.3 73.4 - - - +
109B THR* 1.3 56.7 + - - +
111B LEU* 3.1 7.6 + - - +
112B GLN* 2.8 40.9 + - + +
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Residues in contact with THR 109 (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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105B ARG 3.1 11.2 + - - -
106B ASP* 3.3 13.8 + - - +
108B GLU* 1.3 80.1 - - - +
110B LEU* 1.3 56.6 + - - +
112B GLN* 3.2 7.7 + - - +
113B GLY* 3.0 25.5 + - - -
125B LEU* 4.9 0.7 - - + -
215B PHE* 4.1 30.9 - - + -
216B GLU 5.3 2.7 - - - +
217B VAL* 4.9 12.6 - - + +
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Residues in contact with LEU 110 (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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93B ILE* 4.5 11.0 - - + -
106B ASP 3.2 8.2 + - - +
107B VAL* 3.4 13.0 - - + +
109B THR* 1.3 78.9 - - - +
111B LEU* 1.3 64.6 + - - +
113B GLY* 3.3 10.2 + - - -
114B MET* 3.3 15.5 + - - +
123B ALA* 3.7 11.0 - - + +
124B THR* 3.6 43.3 - - - +
125B LEU* 4.0 11.9 - - + +
175B ILE* 3.7 30.3 - - + -
176B TYR 4.1 7.6 - - - +
177B ALA* 3.8 22.7 - - + -
215B PHE* 4.5 5.8 - - + -
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Residues in contact with LEU 111 (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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3B ALA* 4.0 8.1 - - + -
40B VAL* 4.8 2.5 - - + -
41B ALA 3.6 22.2 - - - +
42B GLY 4.0 3.6 - - - +
43B VAL* 4.0 20.2 - - + -
91B ILE* 4.0 20.2 - - + -
93B ILE* 3.8 19.9 - - + +
107B VAL 3.1 9.8 + - - +
108B GLU* 3.1 8.9 + - - +
110B LEU* 1.3 76.3 - - - +
112B GLN* 1.3 66.1 + - - +
114B MET* 3.1 7.2 + - - +
115B ARG* 3.0 60.7 + - - +
177B ALA* 5.6 0.4 - - - -
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Residues in contact with GLN 112 (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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108B GLU* 2.8 22.8 + - + +
109B THR* 3.5 8.5 - - - +
111B LEU* 1.3 72.8 - - + +
113B GLY* 1.3 57.8 + - - +
115B ARG* 3.3 12.3 + - - +
116B ASP* 2.8 74.2 + - - +
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Residues in contact with GLY 113 (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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109B THR 3.0 9.9 + - - -
110B LEU 3.3 3.1 + - - -
111B LEU 3.1 0.6 - - - -
112B GLN* 1.3 79.3 - - - +
114B MET* 1.3 61.4 + - - +
116B ASP* 4.1 6.7 - - - +
117B ASP* 3.5 15.8 + - - +
120B LEU* 3.9 11.8 - - - +
213B ARG* 5.3 0.5 + - - -
215B PHE* 3.5 35.5 - - - -
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Residues in contact with MET 114 (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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91B ILE* 4.0 23.1 - - + -
110B LEU 3.3 12.9 + - - +
111B LEU* 3.1 9.7 + - - +
113B GLY* 1.3 76.8 - - - +
115B ARG* 1.3 56.1 + - - +
117B ASP 2.8 26.9 - - - +
120B LEU* 3.8 15.5 - - - +
121B PRO 3.6 21.5 - - - +
123B ALA* 3.6 26.0 - - + -
177B ALA* 3.7 20.6 - - + +
178B TYR 3.7 8.3 - - - -
179B ARG* 3.0 47.9 + - - +
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Residues in contact with ARG 115 (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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1B SER* 2.7 44.8 + - - +
3B ALA* 3.6 12.9 - - - +
42B GLY* 3.1 36.2 + - - -
91B ILE* 4.3 10.2 - - + +
111B LEU* 3.0 43.1 + - - +
112B GLN* 3.9 13.7 - - - +
114B MET* 1.3 74.7 - - - +
116B ASP* 1.3 65.6 + - - +
117B ASP 3.1 2.9 + - - -
118B PRO* 3.8 13.4 - - - +
179B ARG* 4.7 2.7 - - - +
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Residues in contact with ASP 116 (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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112B GLN* 2.8 57.4 + - - +
113B GLY* 4.1 6.7 + - - +
114B MET 3.4 0.2 - - - -
115B ARG* 1.3 74.7 - - - +
117B ASP* 1.3 59.4 + - + +
118B PRO* 3.8 4.9 - - - +
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Residues in contact with ASP 117 (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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113B GLY 3.5 7.0 + - - +
114B MET 2.8 13.5 + - - +
115B ARG 3.1 0.4 - - - -
116B ASP* 1.3 81.6 - - + +
118B PRO* 1.3 60.8 - - - +
119B ALA* 2.9 26.7 + - - +
120B LEU* 3.1 23.0 + - + +
179B ARG* 3.2 2.3 + - - -
213B ARG* 2.8 38.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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