Contacts of the helix formed by residues 109 - 122 (chain G) in PDB entry 2VIG
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 CYS 109 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G LEU* 4.0 17.6 - - + +
56G ILE* 5.3 2.5 - - + -
57G ALA* 4.5 13.9 - - + -
60G VAL* 4.1 32.1 - - - -
105G ILE 2.9 16.3 + - - +
106G SER* 3.6 4.1 - - - -
108G GLY* 1.3 77.3 - - - +
110G ALA* 1.3 66.7 + - - +
111G SER* 3.2 5.3 + - - -
112G THR* 3.7 30.0 - - - +
113G GLY 3.1 18.2 + - - -
380G ARG* 5.4 2.2 - - - +
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G SER* 3.5 13.9 + - - +
109G CYS* 1.3 72.5 - - - +
111G SER* 1.3 56.7 + - - +
113G GLY* 3.5 0.9 + - - -
114G VAL* 3.2 13.0 + - - +
233G ILE* 4.0 7.0 - - + -
278G GLN* 2.9 24.9 + - - +
282G ILE* 3.9 22.4 - - + -
380G ARG* 5.5 3.2 - - - +
384G ASP* 3.4 39.7 + - + +
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Residues in contact with SER 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G VAL* 4.2 5.7 - - - +
61G ASP* 6.0 0.3 - - - -
67G PRO* 5.5 0.7 - - - -
109G CYS* 3.2 11.2 - - - -
110G ALA* 1.3 75.7 - - - +
112G THR* 1.3 65.0 + - - +
114G VAL* 3.2 11.5 - - - +
115G ILE* 2.9 31.1 + - - +
233G ILE* 3.2 17.9 - - - -
234G ARG 3.5 0.9 + - - -
235G GLY* 3.1 27.1 + - - -
236G SER 3.7 17.7 - - - -
384G ASP* 5.4 0.5 + - - -
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Residues in contact with THR 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G LEU* 3.9 15.4 - - + +
67G PRO* 3.5 21.0 - - - +
70G GLN* 5.1 0.9 - - + +
71G VAL* 5.1 6.7 - - + +
74G MET* 3.0 41.5 - - + +
105G ILE* 3.6 10.3 - - + -
109G CYS* 3.4 23.2 + - - -
111G SER* 1.3 77.9 - - - +
113G GLY* 1.3 57.2 + - - +
115G ILE* 3.3 10.4 + - - +
116G MET* 2.9 29.5 + - - +
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Residues in contact with GLY 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G MET* 3.3 18.8 - - - +
105G ILE* 3.7 10.2 - - - +
106G SER* 3.4 23.6 - - - -
109G CYS 3.1 11.4 + - - -
110G ALA 3.7 3.4 - - - -
111G SER 3.2 0.2 - - - -
112G THR* 1.3 76.0 - - - +
114G VAL* 1.3 55.6 + - - +
116G MET* 3.2 2.4 + - - +
117G SER* 2.8 25.3 + - - -
278G GLN* 4.7 0.2 - - - -
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Residues in contact with VAL 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ALA 3.2 12.9 + - - +
111G SER* 3.2 13.9 - - - +
113G GLY* 1.3 70.8 - - - +
115G ILE* 1.3 68.3 + - - +
117G SER* 4.1 4.9 - - - -
118G VAL* 2.9 38.1 + - + +
187G THR* 4.3 7.0 - - + +
233G ILE* 4.2 9.4 - - + -
236G SER* 3.8 25.1 - - - +
275G ILE* 4.5 7.6 - - + -
278G GLN* 3.6 7.9 - - - +
391G TYR* 3.2 40.8 - - + +
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Residues in contact with ILE 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G PHE* 3.6 21.5 - - + -
67G PRO* 3.7 24.7 - - + -
71G VAL* 3.9 23.6 - - + -
74G MET* 6.4 0.2 - - + -
80G LEU* 5.5 2.2 - - + -
111G SER 2.9 27.7 + - - +
112G THR* 3.5 6.5 - - - +
114G VAL* 1.3 76.1 - - - +
116G MET* 1.3 62.9 + - - +
118G VAL* 5.2 0.2 - - - -
119G ASN* 3.2 21.2 + - + +
149G ILE* 4.0 18.4 - - + -
187G THR* 5.2 0.2 - - - -
188G ASN* 3.5 33.9 + - - +
235G GLY 4.2 6.5 - - - +
236G SER* 4.0 10.5 - - - -
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Residues in contact with MET 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G MET* 3.8 26.9 - - + -
79G LEU* 3.4 23.8 - - + +
80G LEU* 4.0 11.7 - - + -
82G MET* 4.0 21.1 - - - -
98G TYR* 4.3 1.8 - - + -
101G ALA* 4.1 4.9 - - + -
102G MET* 3.8 37.9 - - + +
105G ILE* 3.8 20.6 - - + -
112G THR 2.9 16.6 + - - +
113G GLY 3.4 2.9 - - - +
115G ILE* 1.3 78.4 - - - +
117G SER* 1.3 61.9 + - - +
119G ASN* 3.2 2.3 + - - +
120G ASN* 3.0 42.2 + - - +
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Residues in contact with SER 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G TYR* 2.8 24.8 + - - -
102G MET* 3.8 11.7 - - - -
113G GLY 2.8 19.7 + - - -
114G VAL* 3.3 8.7 + - - -
116G MET* 1.3 71.0 - - - +
118G VAL* 1.3 58.9 + - - +
121G SER* 2.7 37.8 + - - -
122G LEU* 5.2 0.9 - - - -
271G GLY 4.4 1.9 + - - -
274G GLY* 3.5 19.2 - - - -
275G ILE* 4.0 14.3 + - - +
392G GLU* 4.8 2.9 + - - -
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Residues in contact with VAL 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL* 2.9 31.3 + - + +
117G SER* 1.3 71.2 - - - +
119G ASN* 1.3 64.9 + - - +
122G LEU* 3.0 35.3 + - + -
123G TYR 2.9 22.9 + - - -
150G GLY 3.8 11.4 - - - +
151G CYS* 4.0 14.8 - - - -
152G PHE* 4.4 2.9 - - + +
187G THR* 3.8 30.3 - - + +
188G ASN* 3.6 20.6 - - - +
275G ILE* 6.3 0.2 - - + -
392G GLU* 5.3 1.8 - - - +
501G FAD 4.9 2.0 - - - +
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Residues in contact with ASN 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LEU* 2.9 34.7 + - + +
115G ILE 3.2 12.6 + - - +
116G MET* 3.2 7.6 + - - +
118G VAL* 1.3 80.8 - - - +
120G ASN* 1.3 57.1 + - - +
123G TYR* 3.6 8.7 - - - +
124G LEU* 2.9 43.4 + - - +
143G PHE 3.1 22.9 + - - +
149G ILE* 3.4 19.1 - - + +
150G GLY* 2.9 33.6 + - - +
188G ASN* 4.6 0.2 - - - +
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Residues in contact with ASN 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G LEU 2.8 25.4 + - - -
80G LEU* 3.5 11.1 - - - +
81G ALA* 3.4 4.0 + - - -
82G MET* 2.9 31.2 + - - +
83G ASP 4.5 2.1 + - - -
84G VAL* 5.6 0.9 - - - +
95G TYR* 4.5 4.2 + - + +
98G TYR* 3.4 30.6 - - + -
116G MET* 3.0 31.8 + - - +
119G ASN* 1.3 77.6 - - - +
121G SER* 1.3 58.6 + - - +
124G LEU* 3.8 6.9 - - - +
125G GLY* 3.1 23.2 + - - -
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Residues in contact with SER 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G TYR* 3.2 15.3 + - - -
98G TYR* 2.7 36.6 + - - -
117G SER* 2.7 18.2 + - - -
120G ASN* 1.3 73.1 - - - +
122G LEU* 1.3 62.2 + - - +
125G GLY* 3.5 5.8 - - - -
126G PRO* 3.5 8.8 - - - +
267G THR* 3.4 16.3 - - - +
270G MET* 3.6 7.7 + - - +
271G GLY* 3.4 29.7 - - - -
274G GLY* 4.6 0.2 - - - -
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G SER 4.6 0.2 - - - +
118G VAL* 3.0 32.2 + - + +
121G SER* 1.3 80.4 - - - +
123G TYR* 1.3 60.2 + - - +
126G PRO* 3.3 13.7 - - - +
152G PHE* 3.0 55.9 - - + +
196G VAL* 4.5 1.7 - - - +
267G THR* 3.6 27.1 - - + +
268G LEU* 4.4 11.0 - - + -
271G GLY* 4.1 3.1 - - - -
392G GLU* 3.3 39.5 - - + +
501G FAD 4.9 5.4 - - + +
502G COS 4.6 7.0 - - - -
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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