Contacts of the helix formed by residues 109 - 122 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C LEU* 4.0 14.9 - - + +
56C ILE* 5.4 1.3 - - + -
57C ALA* 4.6 13.9 - - + -
60C VAL* 4.1 24.0 - - - -
105C ILE 2.9 14.1 + - - +
106C SER* 3.5 4.8 - - - -
108C GLY* 1.3 77.9 - - - +
110C ALA* 1.3 65.5 + - - +
111C SER* 3.7 14.6 - - - -
112C THR* 3.3 35.9 - - - +
113C GLY 3.1 15.8 + - - -
380C ARG* 5.3 2.0 - - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C SER* 3.4 13.7 + - - +
109C CYS* 1.3 72.3 - - - +
111C SER* 1.3 57.4 + - - +
113C GLY* 3.2 1.4 + - - -
114C VAL* 3.0 14.4 + - - +
233C ILE* 4.2 3.1 - - + -
278C GLN* 2.9 26.3 + - - +
282C ILE* 4.0 21.8 - - + -
380C ARG* 5.4 3.4 - - - +
384C ASP* 3.3 39.2 + - + +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL* 4.2 5.4 - - - +
61C ASP* 6.1 0.2 - - - -
67C PRO* 5.4 0.4 - - - -
109C CYS* 3.2 11.9 - - - -
110C ALA* 1.3 74.7 - - - +
112C THR* 1.3 66.7 + - - +
114C VAL* 3.1 14.6 - - - +
115C ILE* 3.1 27.8 + - - +
233C ILE* 3.1 21.2 - - - +
234C ARG 3.4 0.2 + - - -
235C GLY* 3.0 29.1 + - - -
236C SER 3.8 14.6 - - - -
384C ASP* 5.2 0.4 + - - -
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 3.7 15.1 - - + +
67C PRO* 3.6 17.3 - - + +
70C GLN* 5.6 0.9 - - + -
71C VAL* 5.1 4.7 - - + -
74C MET* 3.2 33.7 - - - -
105C ILE* 3.6 12.3 - - + -
109C CYS* 3.3 30.1 + - - +
111C SER* 1.3 79.7 - - - +
113C GLY* 1.3 59.0 + - - -
115C ILE* 3.4 11.5 + - - +
116C MET* 3.1 22.7 + - - +
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C MET* 3.1 20.2 - - - +
105C ILE* 3.9 10.0 - - - +
106C SER* 3.6 21.3 - - - -
109C CYS 3.1 12.2 + - - -
110C ALA 3.2 5.6 + - - -
111C SER 3.2 0.2 - - - -
112C THR* 1.3 76.8 - - - +
114C VAL* 1.3 56.3 + - - +
116C MET* 3.4 1.4 + - - -
117C SER 2.9 23.7 + - - -
278C GLN* 4.5 0.9 - - - -
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ALA 3.0 9.4 + - - +
111C SER* 3.1 19.3 - - - +
113C GLY* 1.3 75.0 - - - +
115C ILE* 1.3 56.2 + - - +
117C SER* 4.2 4.5 - - - -
118C VAL* 2.9 36.4 + - + +
187C THR* 4.2 13.9 - - + +
233C ILE* 4.3 7.6 - - + -
236C SER* 3.7 26.7 - - - +
275C ILE* 4.6 7.2 - - + -
278C GLN* 3.7 8.8 - - - +
391C TYR* 3.2 40.6 - - + +
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Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 3.7 22.9 - - + -
67C PRO* 3.8 24.9 - - + -
71C VAL* 4.1 22.7 - - + -
80C LEU* 5.0 2.0 - - + -
111C SER 3.1 22.7 + - - +
112C THR* 3.7 5.8 - - - +
113C GLY 3.2 0.2 - - - -
114C VAL* 1.3 76.0 - - - +
116C MET* 1.3 62.8 + - - +
118C VAL 3.5 0.3 + - - -
119C ASN* 3.2 21.8 + - - +
149C ILE* 4.1 17.0 - - + -
188C ASN* 3.6 35.7 + - - +
235C GLY 4.3 0.2 - - - +
236C SER* 3.9 17.5 - - - -
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Residues in contact with MET 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C MET* 3.5 24.9 - - + -
79C LEU* 3.5 23.8 - - + +
80C LEU* 3.8 19.5 - - + +
82C MET* 4.1 7.9 - - - -
98C TYR* 4.4 3.8 - - + -
101C ALA* 4.0 15.9 - - + -
102C MET* 3.7 41.7 - - + +
105C ILE* 3.8 15.5 - - + -
112C THR 3.1 15.7 + - - +
113C GLY 3.7 2.2 - - - +
115C ILE* 1.3 78.3 - - - +
117C SER* 1.3 63.1 + - - +
119C ASN* 3.3 1.4 + - - +
120C ASN* 2.8 37.2 + - - +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C TYR* 3.1 18.2 + - - -
102C MET* 3.7 14.8 - - - -
113C GLY 2.9 17.8 + - - -
114C VAL* 3.3 8.5 + - - -
116C MET* 1.3 79.0 - - - +
118C VAL* 1.3 60.8 + - - +
121C SER* 3.0 27.7 + - - -
122C LEU* 4.5 1.7 - - - +
271C GLY 4.3 3.1 + - - -
274C GLY* 3.6 17.8 - - - -
275C ILE* 4.0 14.1 + - - +
392C GLU* 4.5 2.9 + - - -
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C VAL* 2.9 28.3 + - + +
117C SER* 1.3 75.9 - - - +
119C ASN* 1.3 59.0 + - - +
122C LEU* 3.0 33.6 + - + -
123C TYR 2.9 25.6 + - - -
150C GLY 3.8 10.8 - - - +
151C CYS* 4.0 15.0 - - - -
152C PHE* 4.5 2.2 - - + +
187C THR* 3.7 30.3 - - + +
188C ASN* 3.7 21.3 - - - +
392C GLU* 5.4 2.5 - - - +
501C FAD 4.9 1.6 - - - +
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.0 37.6 + - + +
115C ILE 3.2 16.9 + - - +
116C MET 3.8 4.0 - - - +
117C SER 3.3 0.2 - - - -
118C VAL* 1.3 78.6 - - - +
120C ASN* 1.3 56.8 + - - +
123C TYR* 3.6 8.8 - - - +
124C LEU* 2.9 42.0 + - - +
143C PHE 3.1 22.7 + - - +
148C LYS 4.9 0.2 + - - -
149C ILE* 3.3 18.0 - - + +
150C GLY* 2.9 31.8 + - - +
188C ASN* 5.3 0.2 - - - +
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Residues in contact with ASN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU 2.9 22.2 + - - -
80C LEU* 3.5 14.0 - - - +
81C ALA* 3.6 0.7 - - - -
82C MET* 3.0 35.7 + - - +
83C ASP 4.5 1.6 + - - -
84C VAL* 5.8 0.2 - - - +
95C TYR* 4.4 6.4 + - + +
98C TYR* 3.5 28.2 - - + +
116C MET* 2.8 34.0 + - - +
119C ASN* 1.3 79.0 - - - +
121C SER* 1.3 59.1 + - - +
124C LEU* 3.8 6.2 - - - +
125C GLY* 3.1 23.9 + - - -
128C LEU* 6.1 0.2 - - - +
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TYR* 2.9 22.8 + - - -
98C TYR* 2.9 24.0 + - - -
117C SER* 3.0 13.1 + - - -
120C ASN* 1.3 77.9 - - - +
122C LEU* 1.3 64.0 + - - +
125C GLY* 3.6 5.7 - - - +
126C PRO* 3.5 8.1 - - - +
267C THR* 3.3 16.8 - - - +
270C MET* 3.6 11.1 + - - +
271C GLY* 3.5 27.2 - - - -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 3.0 33.3 + - + +
121C SER* 1.3 77.4 - - - +
123C TYR* 1.3 60.5 + - - +
126C PRO* 3.3 14.3 - - - +
152C PHE* 3.2 55.8 - - + +
196C VAL* 4.3 2.8 - - - +
267C THR* 3.7 20.9 - - + +
268C LEU* 4.7 8.5 - - + -
271C GLY* 3.9 25.1 - - - -
392C GLU* 3.7 27.6 - - + +
501C FAD 4.8 8.1 - - + +
502C COS 5.6 1.3 - - - -
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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