Contacts of the helix formed by residues 109 - 122 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.1 15.4 - - + +
56D ILE* 5.4 1.6 - - + -
57D ALA* 4.4 16.8 - - + -
60D VAL* 4.3 21.8 - - - -
105D ILE 2.8 17.0 + - - +
106D SER* 3.6 4.6 + - - -
108D GLY* 1.3 76.7 - - - +
110D ALA* 1.3 66.7 + - - +
111D SER* 3.3 12.5 + - - -
112D THR* 3.4 33.9 - - - +
113D GLY 3.1 16.5 + - - -
380D ARG* 5.3 2.7 - - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D SER* 3.6 12.9 + - - +
109D CYS* 1.3 73.4 - - - +
111D SER* 1.3 57.3 + - - +
113D GLY* 3.3 2.1 + - - -
114D VAL* 3.1 22.5 + - - +
233D ILE* 4.1 3.4 - - + -
278D GLN* 3.1 17.8 + - - +
282D ILE* 3.8 28.7 - - + -
380D ARG* 5.5 2.8 - - - +
384D ASP* 3.2 35.4 + - + +
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Residues in contact with SER 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 4.3 4.6 - - - +
61D ASP* 6.0 0.2 - - - -
67D PRO* 5.3 0.7 - - - -
109D CYS* 3.3 11.4 - - - -
110D ALA* 1.3 73.7 - - - +
112D THR* 1.3 67.4 + - - +
114D VAL* 3.2 11.8 + - - +
115D ILE* 3.0 30.4 + - - +
233D ILE* 3.2 18.2 - - - +
234D ARG 3.5 0.5 + - - -
235D GLY* 3.0 26.6 + - - -
236D SER 3.6 18.4 - - - -
384D ASP* 5.6 0.2 + - - -
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.6 21.9 - - + +
67D PRO* 3.5 16.5 - - - +
70D GLN* 5.5 0.9 - - + -
71D VAL* 4.8 7.4 - - + +
74D MET* 3.1 39.2 - - + +
105D ILE* 3.7 9.2 - - + -
109D CYS* 3.4 23.1 + - - -
111D SER* 1.3 75.1 - - - +
113D GLY* 1.3 57.0 + - - +
115D ILE* 3.4 11.9 + - - +
116D MET* 3.0 29.3 + - - +
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Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D MET* 2.7 36.5 - - - +
105D ILE* 3.8 9.0 - - - +
106D SER* 3.7 13.0 - - - -
109D CYS 3.1 11.4 + - - -
110D ALA 3.4 5.4 - - - -
111D SER 3.1 0.4 - - - -
112D THR* 1.3 74.8 - - - +
114D VAL* 1.3 61.8 + - - +
116D MET* 3.3 1.8 + - - +
117D SER 3.0 10.9 + - - -
278D GLN* 4.7 0.9 - - - -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA 3.1 11.4 + - - +
111D SER* 3.3 17.0 - - - +
113D GLY* 1.3 73.3 - - - +
115D ILE* 1.3 57.2 + - - +
117D SER* 3.1 4.7 + - - -
118D VAL* 2.8 38.0 + - + +
187D THR* 4.0 15.0 - - + +
233D ILE* 4.4 9.9 - - + -
236D SER* 3.6 28.0 - - - +
275D ILE* 4.5 8.1 - - + -
278D GLN* 3.9 6.8 - - - +
391D TYR* 3.3 40.8 - - + +
392D GLU* 5.8 0.4 - - - +
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D PHE* 3.7 22.4 - - + -
67D PRO* 3.7 28.0 - - + -
71D VAL* 4.2 22.9 - - + -
80D LEU* 5.4 1.7 - - + +
111D SER 3.0 23.3 + - - +
112D THR* 3.6 7.0 - - - +
114D VAL* 1.3 77.3 - - - +
116D MET* 1.3 63.4 + - - +
118D VAL 3.6 0.2 + - - -
119D ASN* 3.2 21.7 + - - +
149D ILE* 4.1 20.4 - - + -
188D ASN* 3.5 31.3 + - - +
236D SER* 4.1 17.0 - - - +
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Residues in contact with MET 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D MET* 3.6 28.0 - - + -
79D LEU* 3.3 31.4 - - + +
80D LEU* 4.1 12.6 - - + -
82D MET* 4.1 10.1 - - - -
98D TYR* 4.3 8.3 - - + -
101D ALA* 4.0 27.8 - - + -
102D MET* 4.0 24.5 - - - +
105D ILE* 3.8 17.0 - - - -
112D THR 3.0 16.7 + - - +
113D GLY 3.7 3.8 - - - +
115D ILE* 1.3 76.8 - - - +
117D SER* 1.3 56.4 + - - +
119D ASN* 3.6 1.7 + - - +
120D ASN* 2.7 37.4 + - - +
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TYR* 2.8 23.4 + - - -
102D MET* 3.6 12.1 - - - -
113D GLY 3.0 17.7 + - - -
114D VAL* 3.7 7.6 - - - -
116D MET* 1.3 75.4 - - - +
118D VAL* 1.3 61.1 + - - +
121D SER* 2.9 34.3 + - - -
122D LEU* 4.6 1.5 - - - +
271D GLY 4.4 2.3 + - - -
274D GLY* 3.4 19.4 - - - -
275D ILE* 4.1 13.2 + - - +
392D GLU* 4.9 2.3 + - - -
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D VAL* 2.8 30.5 + - + +
117D SER* 1.3 72.7 - - - +
119D ASN* 1.3 59.3 + - - +
122D LEU* 3.0 34.1 + - + -
123D TYR* 2.9 26.3 + - - +
150D GLY 3.8 11.2 - - - +
151D CYS* 3.9 15.0 - - - -
152D PHE* 4.4 2.7 - - + +
187D THR* 3.7 31.6 - - + +
188D ASN* 3.6 20.9 - - - +
392D GLU* 5.2 2.7 - - - +
501D FAD 4.9 1.8 - - - +
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 2.7 38.4 + - + +
115D ILE 3.2 15.3 + - - +
116D MET* 4.0 4.3 - - - +
118D VAL* 1.3 79.7 - - - +
120D ASN* 1.3 58.8 + - - +
123D TYR* 4.0 11.3 - - - -
124D LEU* 2.9 43.5 + - - +
143D PHE* 3.1 22.6 + - - +
149D ILE* 3.4 20.7 - - + +
150D GLY 3.0 28.8 + - - +
188D ASN* 4.5 0.6 - - - +
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Residues in contact with ASN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU 2.8 24.0 + - - -
80D LEU* 3.5 14.4 - - - +
81D ALA* 3.5 2.6 + - - -
82D MET* 2.9 34.3 + - - +
83D ASP* 4.5 1.9 + - - +
84D VAL* 5.8 0.7 - - - +
95D TYR* 4.6 4.8 + - + +
98D TYR* 3.6 26.8 - - + +
116D MET* 2.7 34.9 + - - +
119D ASN* 1.3 78.0 - - - +
121D SER* 1.3 59.1 + - - +
124D LEU* 3.6 6.9 - - - +
125D GLY* 3.1 22.0 + - - -
128D LEU* 5.8 0.7 - - - +
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TYR* 2.6 26.4 + - - -
98D TYR* 2.9 23.0 + - - -
117D SER* 2.9 17.0 + - - -
120D ASN* 1.3 73.2 - - - +
122D LEU* 1.3 65.6 + - - +
125D GLY* 3.5 6.9 - - - -
126D PRO* 3.4 14.6 - - - +
267D THR* 3.5 8.0 - - - +
270D MET* 3.6 10.8 + - - +
271D GLY* 3.6 25.6 - - - -
274D GLY* 4.8 0.2 - - - -
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D SER 4.6 0.2 - - - +
118D VAL* 3.0 32.2 + - + +
121D SER* 1.3 78.8 - - - +
123D TYR* 1.3 59.7 + - - +
126D PRO* 3.0 19.7 - - - +
152D PHE* 3.3 51.0 - - + +
196D VAL* 4.5 1.2 - - - +
267D THR* 3.7 19.1 - - + +
268D LEU* 4.6 10.5 - - + -
271D GLY* 4.0 11.0 - - - -
392D GLU* 3.5 42.4 - - + +
501D FAD 4.8 8.3 - - + +
502D 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