Contacts of the helix formed by residues 109 - 122 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.9 13.7 - - + +
56F ILE* 5.3 2.5 - - + -
57F ALA* 4.6 14.1 - - + -
60F VAL* 4.2 22.2 - - - -
67F PRO* 5.2 0.2 - - - -
105F ILE 2.9 13.6 + - - +
106F SER* 3.5 6.0 + - - -
108F GLY* 1.3 79.0 - - - +
110F ALA* 1.3 61.9 + - - +
111F SER* 3.8 12.6 - - - -
112F THR* 3.3 35.2 + - - +
113F GLY 3.1 22.0 + - - -
380F ARG* 5.2 2.5 - - - +
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Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F SER* 3.6 12.9 + - - +
109F CYS* 1.3 70.4 - - - +
111F SER* 1.3 65.1 + - - +
113F GLY* 3.5 1.0 + - - -
114F VAL* 3.2 9.5 + - - +
233F ILE* 4.0 6.7 - - + +
278F GLN* 2.9 25.0 + - - +
282F ILE* 3.9 21.8 - - + -
380F ARG* 5.4 3.0 - - - +
384F ASP* 3.4 40.4 + - + +
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Residues in contact with SER 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F VAL* 4.0 13.6 - - - +
61F ASP* 6.0 0.2 - - - -
67F PRO* 5.3 1.1 - - - -
109F CYS* 3.8 3.5 - - - -
110F ALA* 1.3 76.3 - - - +
112F THR* 1.3 64.6 + - - +
114F VAL* 3.2 10.9 + - - +
115F ILE* 3.2 30.6 + - - +
233F ILE* 3.1 19.6 - - - +
234F ARG 3.3 0.5 + - - -
235F GLY* 2.9 39.6 + - - -
236F SER 3.9 4.5 - - - -
384F ASP* 5.2 0.4 + - - -
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Residues in contact with THR 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LEU* 3.8 14.9 - - + +
56F ILE* 5.1 0.2 - - - +
67F PRO* 3.4 23.7 - - - +
70F GLN* 5.0 0.8 - - + +
71F VAL* 4.9 6.5 - - + +
74F MET* 3.1 36.7 - - + +
105F ILE* 3.4 11.9 - - + -
109F CYS* 3.3 25.8 + - - +
111F SER* 1.3 78.4 - - - +
113F GLY* 1.3 62.3 + - - +
115F ILE* 3.5 9.8 + - - +
116F MET* 3.1 23.4 + - - +
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Residues in contact with GLY 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F MET* 3.2 20.9 - - - +
105F ILE* 3.8 9.4 - - - +
106F SER* 3.5 23.1 - - - -
109F CYS 3.1 11.2 + - - -
110F ALA 3.8 2.7 - - - -
111F SER 3.2 0.6 - - - -
112F THR* 1.3 78.8 - - - +
114F VAL* 1.3 56.3 + - - +
116F MET 3.6 0.2 + - - -
117F SER* 2.9 22.5 + - - -
278F GLN* 4.6 0.9 - - - -
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Residues in contact with VAL 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ALA 3.2 10.3 + - - +
111F SER* 3.2 15.2 + - - +
113F GLY* 1.3 72.5 - - - +
115F ILE* 1.3 60.2 + - - +
117F SER* 4.2 3.8 - - - -
118F VAL* 2.9 49.3 + - + +
187F THR* 4.4 6.7 - - + +
233F ILE* 4.1 9.4 - - + -
236F SER* 3.8 26.9 - - - +
275F ILE* 4.5 8.7 - - + -
278F GLN* 3.6 7.7 - - - +
391F TYR* 3.2 40.8 - - + +
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Residues in contact with ILE 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F PHE* 3.6 30.3 - - + -
67F PRO* 3.8 21.1 - - + -
71F VAL* 4.2 18.6 - - + -
80F LEU* 4.7 1.3 - - + -
111F SER 3.2 21.4 + - - +
112F THR* 3.8 5.4 - - - +
114F VAL* 1.3 77.5 - - - +
116F MET* 1.3 62.9 + - - +
118F VAL 3.4 0.3 + - - -
119F ASN* 3.2 21.1 + - - +
149F ILE* 3.9 22.2 - - + -
187F THR* 5.2 0.2 - - - -
188F ASN* 3.6 32.4 + - - +
235F GLY 4.2 7.4 - - - +
236F SER* 4.1 13.2 - - - -
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Residues in contact with MET 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F MET* 3.5 29.8 - - + -
79F LEU* 3.3 25.4 - - + +
80F LEU* 3.7 13.0 - - + -
82F MET* 4.0 8.3 - - - -
98F TYR* 4.3 1.1 - - + -
101F ALA* 4.0 27.4 - - + -
102F MET* 3.7 28.9 - - + +
105F ILE* 3.8 17.0 - - - -
112F THR 3.1 17.0 + - - +
113F GLY 3.8 2.5 - - - +
115F ILE* 1.3 78.1 - - - +
117F SER* 1.3 61.3 + - - +
119F ASN* 3.3 1.0 + - - +
120F ASN* 2.8 42.6 + - - +
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Residues in contact with SER 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F TYR* 2.8 23.3 + - - -
102F MET* 3.8 11.7 - - - -
113F GLY 2.9 18.9 + - - -
114F VAL* 3.3 8.0 + - - -
116F MET* 1.3 76.6 - - - +
118F VAL* 1.3 58.8 + - - +
121F SER* 2.9 33.1 + - - -
122F LEU* 4.5 1.5 - - - +
271F GLY 4.4 2.6 + - - -
274F GLY* 3.5 19.1 - - - -
275F ILE* 4.0 14.5 + - - +
392F GLU* 4.7 2.6 + - - -
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F VAL* 2.9 28.9 + - + +
115F ILE 3.8 0.2 - - - +
116F MET 3.4 0.2 - - - -
117F SER* 1.3 75.7 - - - +
119F ASN* 1.3 58.7 + - - +
122F LEU* 3.1 32.4 + - + +
123F TYR* 2.9 26.3 + - - +
150F GLY 4.0 9.4 - - - +
151F CYS* 4.0 14.1 - - - -
152F PHE* 4.5 3.1 - - + +
187F THR* 3.7 31.4 - - + +
188F ASN* 3.7 22.0 - - - +
392F GLU* 5.3 2.2 - - - +
501F FAD 4.9 2.2 - - - +
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Residues in contact with ASN 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU* 2.9 39.8 + - + +
115F ILE 3.2 16.3 + - - +
116F MET 3.8 3.4 - - - +
117F SER 3.3 0.2 - - - -
118F VAL* 1.3 78.1 - - - +
120F ASN* 1.3 57.2 + - - +
123F TYR* 4.0 9.4 - - - -
124F LEU* 2.9 42.1 + - - +
143F PHE* 3.1 22.6 + - - +
149F ILE* 3.4 18.0 - - + +
150F GLY* 2.9 31.0 + - - -
188F ASN* 4.7 0.6 - - - +
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Residues in contact with ASN 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F LEU 2.9 23.3 + - - +
80F LEU* 3.5 10.7 - - - +
81F ALA* 3.4 4.0 + - - -
82F MET* 3.2 31.2 + - - +
83F ASP 4.6 1.6 + - - -
84F VAL* 5.8 0.7 - - - +
95F TYR* 4.5 5.1 + - + +
98F TYR* 3.5 29.6 - - + -
116F MET* 2.8 34.6 + - - +
119F ASN* 1.3 76.8 - - - +
121F SER* 1.3 59.7 + - - +
124F LEU* 3.7 5.6 - - - +
125F GLY* 3.1 22.9 + - - -
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Residues in contact with SER 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F TYR* 2.7 24.8 + - - -
98F TYR* 2.9 22.1 + - - -
117F SER* 2.9 17.3 + - - -
120F ASN* 1.3 74.3 - - - +
122F LEU* 1.3 63.5 + - - +
123F TYR 3.6 0.2 - - - -
125F GLY* 3.3 19.7 - - - -
126F PRO* 3.5 3.6 - - - +
267F THR* 3.6 7.8 - - - +
270F MET* 3.5 11.3 + - - +
271F GLY* 3.6 25.2 - - - -
392F GLU* 5.6 0.2 - - - -
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F SER 4.5 0.2 - - - +
118F VAL* 3.1 30.9 + - + +
121F SER* 1.3 78.8 - - - +
123F TYR* 1.3 59.9 + - - +
126F PRO* 3.3 14.5 - - - +
152F PHE* 3.2 55.1 - - + +
196F VAL* 4.2 2.1 - - - +
267F THR* 3.7 20.4 - - + +
268F LEU* 4.5 9.4 - - + -
271F GLY* 3.8 14.1 - - - -
392F GLU* 3.5 41.1 - - + +
501F FAD 4.9 7.6 - - + +
502F COS 5.4 1.6 - - - -
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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