Contacts of the helix formed by residues 107 - 121 (chain B) in PDB entry 2GAO
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.5 29.6 - - + +
34B ASP* 3.0 48.4 + - - +
35B ASN* 4.1 8.3 - - - +
76B LEU 5.7 0.2 + - - -
104B ASP* 2.9 35.1 + - + +
105B HIS 3.2 0.6 - - - -
106B SER* 1.3 85.5 - - - +
108B LEU* 1.3 57.2 + - - +
109B VAL 3.3 2.2 - - - -
110B GLU* 3.3 38.6 + - - +
111B SER* 2.9 26.4 + - - -
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Residues in contact with LEU 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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100B VAL* 3.5 31.9 - - + -
101B ASP 3.8 10.8 - - - +
102B CYS* 4.6 3.4 - - - +
104B ASP 3.5 9.6 + - - +
105B HIS* 3.5 28.2 + - + +
107B ARG* 1.3 77.6 - - - +
109B VAL* 1.3 58.6 + - + +
111B SER* 3.3 5.0 + - - -
112B LYS* 2.8 30.0 + - - +
142B ILE* 3.9 34.8 - - + -
150B ILE* 3.8 34.8 - - + -
151B PHE* 4.0 10.1 - - + -
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Residues in contact with VAL 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 HIS 4.9 2.8 + - - +
106B SER 4.7 5.1 + - - +
107B ARG 3.3 0.4 - - - -
108B LEU* 1.3 77.8 - - + +
110B GLU* 1.3 58.2 + - - +
112B LYS* 3.3 15.5 + - + +
113B VAL* 3.0 33.9 + - + +
150B ILE* 5.5 7.2 - - + -
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Residues in contact with GLU 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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33B LEU* 3.8 20.6 - - + +
106B SER 5.2 2.0 + - - +
107B ARG* 3.3 49.1 + - - +
109B VAL* 1.3 77.5 - - - +
111B SER* 1.3 64.5 + - - +
113B VAL* 3.3 18.1 + - + +
114B GLU* 3.4 18.9 + - - +
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Residues in contact with SER 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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33B LEU* 3.4 23.4 - - - +
98B PHE* 3.4 30.2 - - - -
99B LEU 4.6 1.0 + - - -
100B VAL* 3.9 14.0 - - - +
101B ASP 6.0 0.2 - - - -
107B ARG 2.9 17.3 + - - -
108B LEU* 3.6 7.2 - - - -
110B GLU* 1.3 72.3 - - - +
112B LYS* 1.3 66.7 + - - +
114B GLU* 3.1 11.2 + - - +
115B LEU* 3.1 10.4 + - - +
151B PHE* 3.5 12.8 - - - -
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU 2.8 17.0 + - - +
109B VAL* 3.3 19.1 - - + +
111B SER* 1.3 73.5 + - - +
113B VAL* 1.3 58.5 + - + +
115B LEU* 3.2 2.6 + - - +
116B ASN* 2.9 59.0 + - - +
150B ILE* 3.2 27.6 - - + +
151B PHE* 3.5 44.1 + - + -
152B GLY* 5.0 1.6 - - - -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 3.0 22.5 + - + +
110B GLU* 3.5 12.1 - - - +
111B SER 3.3 0.4 - - - -
112B LYS* 1.3 76.5 - - + +
114B GLU* 1.3 68.6 - - - +
116B ASN* 3.5 8.5 + - - +
117B ALA* 2.9 28.4 + - + +
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Residues in contact with GLU 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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33B LEU* 4.0 17.0 - - + +
76B LEU* 3.9 47.5 - - + +
98B PHE* 4.1 9.2 - - + -
110B GLU* 3.4 14.4 + - - +
111B SER* 3.1 8.1 + - - +
113B VAL* 1.3 84.5 - - - +
115B LEU* 1.3 65.4 + - - +
117B ALA* 3.4 12.7 + - - +
118B LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 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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98B PHE* 3.9 38.1 - - + -
111B SER 3.1 8.0 + - - +
112B LYS 3.8 5.8 - - - +
114B GLU* 1.3 72.5 - - - +
116B ASN* 1.3 61.0 + - - +
118B LEU* 3.1 9.8 + - + +
119B MET* 2.9 57.7 + - + +
129B ILE* 4.2 20.4 - - + -
131B ILE* 3.9 26.0 - - + -
151B PHE* 3.4 30.3 - - + -
153B LEU* 4.5 3.8 - - + -
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Residues in contact with ASN 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 LYS* 2.9 55.6 + - - +
113B VAL* 3.8 7.6 - - - +
115B LEU* 1.3 76.4 - - - +
117B ALA* 1.3 58.7 + - - +
119B MET* 2.8 33.8 - - - +
120B THR* 2.8 36.3 + - + +
151B PHE* 4.4 3.1 - - - +
156B GLN* 5.5 0.3 + - - -
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Residues in contact with ALA 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 VAL* 2.9 17.6 + - + +
114B GLU* 3.5 19.5 - - - +
115B LEU 3.2 0.4 - - - -
116B ASN* 1.3 75.6 - - - +
118B LEU* 1.3 60.9 + - + +
120B THR* 3.6 6.2 + - - -
121B ASP* 3.2 24.4 + - - +
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Residues in contact with LEU 118 (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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31B LEU* 3.7 23.8 - - + -
76B LEU* 4.0 6.1 - - + -
86B TRP* 3.5 33.2 - - + -
96B ILE* 4.2 13.7 - - + -
98B PHE* 3.7 30.7 - - + -
114B GLU 3.1 16.6 + - - +
115B LEU* 3.1 12.5 + - + +
117B ALA* 1.3 76.2 - - + +
119B MET* 1.3 62.6 + - - +
120B THR 3.4 0.7 + - - -
121B ASP* 3.4 14.3 + - - +
124B ILE* 3.8 29.7 - - + +
129B ILE* 4.8 13.0 - - + +
171B ARG* 4.2 5.6 + - - -
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Residues in contact with MET 119 (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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115B LEU* 2.9 36.4 + - + +
116B ASN* 2.8 41.7 - - - +
118B LEU* 1.3 75.6 - - - +
120B THR* 1.3 62.7 + - + +
121B ASP 3.6 1.0 - - - +
125B SER* 5.9 0.5 - - - -
129B ILE* 4.3 6.3 - - + -
151B PHE* 4.9 1.8 - - + +
153B LEU* 4.6 5.8 - - + -
156B GLN* 4.6 20.6 - - - +
171B ARG* 3.3 24.4 + - - +
173B MET* 3.6 37.0 - - - +
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Residues in contact with THR 120 (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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116B ASN* 2.8 26.6 + - + +
117B ALA* 3.6 6.8 + - - -
119B MET* 1.3 83.9 - - + +
121B ASP* 1.3 62.5 + - - +
122B GLU* 3.3 5.9 + - - +
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Residues in contact with ASP 121 (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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86B TRP* 5.5 0.9 - - - -
87B LYS* 3.7 23.6 + - - +
90B LEU* 5.1 1.7 - - - +
117B ALA 3.2 17.2 + - - +
118B LEU* 3.4 9.9 + - - +
119B MET 5.1 0.9 - - - +
120B THR* 1.3 76.0 - - - +
122B GLU* 1.3 61.7 + - - +
123B THR* 2.7 36.5 + - - +
124B ILE* 3.2 30.0 + - + +
125B SER* 3.7 7.3 + - - -
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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