Contacts of the helix formed by residues 109 - 122 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.1 14.5 - - + +
56A ILE* 5.4 1.6 - - + -
57A ALA* 4.5 13.7 - - + -
60A VAL* 4.1 24.2 - - - -
67A PRO* 5.2 0.4 - - - -
105A ILE 3.0 13.9 + - - +
106A SER* 3.6 4.7 + - - -
108A GLY* 1.3 79.0 - - - +
110A ALA* 1.3 67.5 + - - +
111A SER* 3.8 12.1 - - - -
112A THR* 3.3 34.5 + - - +
113A GLY 3.1 17.2 + - - -
380A ARG* 5.1 2.0 - - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A SER* 3.6 14.2 + - - +
109A CYS* 1.3 72.6 - - - +
111A SER* 1.3 61.5 + - - +
113A GLY* 3.3 1.9 + - - -
114A VAL* 3.1 17.7 + - - +
233A ILE* 4.1 7.0 - - + -
278A GLN* 3.1 14.3 + - - +
282A ILE* 4.0 20.6 - - + -
380A ARG* 5.5 2.4 - - - +
384A ASP* 3.3 41.1 + - + +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.1 5.0 - - - +
61A ASP* 6.0 0.2 - - - -
67A PRO* 5.3 1.1 - - - -
109A CYS* 3.2 12.1 - - - -
110A ALA* 1.3 74.8 - - - +
112A THR* 1.3 65.9 + - - +
114A VAL* 3.2 11.9 + - - +
115A ILE* 3.1 30.2 + - - +
233A ILE* 3.1 18.5 - - - -
234A ARG 3.4 0.7 + - - -
235A GLY* 3.1 39.1 + - - -
236A SER 3.8 5.6 - - - -
384A ASP* 5.3 0.3 + - - -
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.9 15.9 - - + +
56A ILE* 5.1 0.2 - - - +
67A PRO* 3.5 20.4 - - - +
70A GLN* 5.1 1.0 - - + +
71A VAL* 5.1 6.0 - - + +
74A MET* 3.0 40.8 - - + +
105A ILE* 3.5 9.4 - - + -
109A CYS* 3.3 24.6 + - - +
111A SER* 1.3 77.8 - - - +
113A GLY* 1.3 61.8 + - - +
115A ILE* 3.5 11.2 + - - +
116A MET* 3.1 22.9 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A MET* 3.2 19.6 - - - +
105A ILE* 3.8 10.1 - - - +
106A SER* 3.5 23.6 - - - -
109A CYS 3.1 11.3 + - - -
110A ALA 3.3 2.9 + - - -
111A SER 3.1 0.4 - - - -
112A THR* 1.3 76.8 - - - +
114A VAL* 1.3 56.6 + - - +
116A MET* 3.3 1.4 + - - +
117A SER* 2.9 23.9 + - - -
278A GLN* 4.9 1.1 - - - -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA 3.1 12.7 + - - +
111A SER* 3.2 17.3 - - - +
113A GLY* 1.3 72.2 - - - +
115A ILE* 1.3 65.1 + - - +
117A SER* 4.2 4.5 - - - -
118A VAL* 2.9 32.0 + - + +
187A THR* 4.2 13.9 - - + +
233A ILE* 4.1 9.4 - - + -
236A SER* 3.8 26.5 - - - +
275A ILE* 4.5 9.4 - - + -
278A GLN* 3.8 8.1 - - - +
391A TYR* 3.2 39.0 - - + +
392A GLU* 5.7 0.2 - - - +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.6 27.4 - - + -
67A PRO* 3.7 24.9 - - + -
71A VAL* 4.1 18.2 - - + -
80A LEU* 5.2 1.3 - - + -
111A SER 3.1 23.6 + - - +
112A THR* 3.8 6.3 - - - +
114A VAL* 1.3 76.5 - - - +
116A MET* 1.3 61.9 + - - +
118A VAL 3.5 0.2 + - - -
119A ASN* 3.3 19.8 + - - +
149A ILE* 3.9 22.2 - - + -
188A ASN* 3.6 31.8 + - - +
235A GLY 4.1 6.7 - - - +
236A SER* 4.0 11.7 - - - -
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Residues in contact with MET 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MET* 3.7 27.1 - - + -
79A LEU* 3.1 28.3 - - + +
80A LEU* 4.0 14.3 - - + +
82A MET* 3.9 20.2 - - - -
98A TYR* 4.3 4.3 - - + -
101A ALA* 4.0 15.9 - - + -
102A MET* 3.9 23.6 - - - +
105A ILE* 3.8 17.9 - - + -
112A THR 3.1 17.6 + - - +
113A GLY 3.6 2.2 - - - +
115A ILE* 1.3 75.8 - - - +
117A SER* 1.3 60.2 + - - +
119A ASN* 3.4 2.0 + - - +
120A ASN* 2.9 46.8 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 2.7 23.6 + - - -
102A MET* 3.9 12.1 - - - -
113A GLY 2.9 17.4 + - - -
114A VAL* 3.2 7.8 + - - -
116A MET* 1.3 75.3 - - - +
118A VAL* 1.3 61.7 + - - +
121A SER* 2.8 34.7 + - - -
122A LEU* 5.2 0.7 - - - -
271A GLY 4.3 1.9 + - - -
274A GLY* 3.5 19.4 - - - -
275A ILE* 4.0 15.2 + - - +
392A GLU* 4.9 2.6 + - - -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 2.9 27.2 + - + +
117A SER* 1.3 74.4 - - - +
119A ASN* 1.3 64.4 + - - +
122A LEU* 3.0 33.8 + - + -
123A TYR 2.9 22.0 + - - -
150A GLY 3.8 10.5 - - - +
151A CYS* 3.9 15.5 - - - -
152A PHE* 4.5 1.6 - - + +
187A THR* 3.7 31.4 - - + +
188A ASN* 3.6 21.1 - - - +
392A GLU* 5.3 2.9 - - - +
501A FAD 4.9 2.9 - - - +
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.0 33.8 + - + +
115A ILE 3.3 13.8 + - - +
116A MET* 3.9 4.3 - - - +
117A SER 3.3 0.2 - - - -
118A VAL* 1.3 81.3 - - - +
120A ASN* 1.3 56.4 + - - +
123A TYR* 3.9 9.5 - - - -
124A LEU* 2.9 40.9 + - - +
143A PHE* 3.2 23.2 + - - +
149A ILE* 3.3 21.8 - - + +
150A GLY* 2.8 32.5 + - - +
188A ASN* 4.5 0.4 - - - +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU 2.8 24.8 + - - -
80A LEU 3.4 13.5 + - - +
81A ALA* 3.6 0.9 - - - -
82A MET* 2.9 33.3 + - - +
83A ASP* 4.5 2.3 + - - +
95A TYR* 4.5 4.4 + - + +
98A TYR* 3.5 30.1 - - + -
116A MET* 2.9 34.3 + - - +
119A ASN* 1.3 76.8 - - - +
121A SER* 1.3 60.2 + - - +
124A LEU* 3.6 6.5 - - - +
125A GLY* 3.0 23.4 + - - -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 2.9 23.1 + - - -
98A TYR* 2.8 25.4 + - - -
117A SER* 2.8 18.4 + - - -
120A ASN* 1.3 76.6 - - - +
122A LEU* 1.3 59.7 + - - +
125A GLY* 3.3 20.0 - - - -
126A PRO* 3.4 4.3 - - - +
267A THR* 3.5 7.8 - - - +
270A MET* 3.6 11.5 + - - +
271A GLY* 3.6 26.7 - - - -
274A GLY* 4.6 0.2 - - - -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A SER 4.6 0.2 - - - +
118A VAL* 3.0 31.5 + - + +
121A SER* 1.3 79.5 - - - +
123A TYR* 1.3 60.4 + - - +
126A PRO* 3.1 18.9 - - - +
152A PHE* 3.3 51.8 - - + +
196A VAL* 4.2 2.3 - - - +
267A THR* 3.7 20.4 - - + +
268A LEU* 4.6 7.6 - - + -
271A GLY* 3.9 14.6 - - - -
392A GLU* 3.7 40.6 - - + +
501A FAD 4.9 7.4 - - + +
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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