Contacts of the helix formed by residues 94 - 109 (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 ASP 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D HIS* 3.1 25.7 + - - -
82D MET* 5.0 1.4 - - - +
83D ASP* 3.6 13.9 - - - +
93D LEU* 1.3 79.7 - - - +
95D TYR* 1.3 59.0 + - - +
96D LEU* 3.3 3.3 + - - +
97D ALA* 2.9 23.2 + - - +
98D TYR* 3.1 24.3 + - - +
336D ASP* 3.4 25.0 - - + +
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Residues in contact with TYR 95 (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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83D ASP* 3.6 30.5 + - + -
94D ASP* 1.3 70.7 - - - +
96D LEU* 1.3 57.5 + - - +
98D TYR* 3.5 32.9 - + + +
99D ALA* 3.0 23.4 + - - +
120D ASN* 4.6 4.0 + - + -
121D SER* 2.6 33.3 + - - -
125D GLY* 5.7 0.9 - - - -
270D MET* 3.6 26.7 - - + +
273D ILE* 4.1 19.1 - - + -
332D ALA* 3.5 21.0 - - + +
335D LYS* 3.1 43.4 + - + -
336D ASP* 2.7 21.5 + - - +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 4.2 12.6 - - + -
35D PRO* 4.8 8.5 - - + -
38D HIS* 3.7 22.2 - - + +
94D ASP* 3.3 6.7 + - - +
95D TYR* 1.3 76.2 - - - +
97D ALA* 1.3 62.6 + - - +
99D ALA* 3.3 2.5 + - - +
100D ILE* 3.1 34.3 + - + +
329D TRP* 3.8 45.3 - - + +
332D ALA* 3.8 7.6 - - + +
333D MET* 4.4 26.0 - - + -
336D ASP* 3.1 16.8 + - - +
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Residues in contact with ALA 97 (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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38D HIS* 3.6 15.7 + - + +
41D LEU* 3.3 32.7 - - + +
82D MET* 4.5 1.6 - - + -
93D LEU* 3.9 23.1 - - + -
94D ASP* 2.9 21.1 + - - +
96D LEU* 1.3 74.0 - - - +
98D TYR* 1.3 60.0 + - - +
100D ILE* 3.4 2.2 + - - +
101D ALA* 3.0 27.6 + - - +
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Residues in contact with TYR 98 (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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82D MET* 3.9 22.6 - - + -
83D ASP* 5.7 0.4 - - + -
94D ASP 3.1 14.4 + - - +
95D TYR* 3.5 45.8 - + + +
97D ALA* 1.3 77.5 - - - +
99D ALA* 1.3 55.3 + - - +
101D ALA* 3.4 0.9 + - - +
102D MET* 2.8 53.4 + - + +
116D MET* 4.3 4.0 - - + -
117D SER* 2.8 34.7 + - - -
120D ASN* 3.6 34.7 - - + +
121D SER* 2.9 25.6 + - - -
273D ILE* 5.3 1.3 - - + -
274D GLY* 3.7 17.8 - - - -
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Residues in contact with ALA 99 (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 3.0 16.9 + - - +
96D LEU 3.3 5.1 + - - +
98D TYR* 1.3 77.8 - - - +
100D ILE* 1.3 57.5 + - - +
102D MET* 4.1 0.4 - - - -
103D GLU* 3.0 27.7 + - - +
273D ILE* 4.4 9.2 - - + -
277D SER* 3.0 31.2 + - - +
280D LEU* 5.7 0.9 - - + +
328D THR* 4.2 15.0 - - + -
329D TRP* 4.6 12.8 - - + +
332D ALA* 4.6 3.8 - - + -
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Residues in contact with ILE 100 (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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34D LEU* 3.5 37.9 - - + -
38D HIS* 4.0 20.0 - - + +
41D LEU* 4.7 3.1 - - + -
42D LEU* 3.7 45.3 - - + +
96D LEU* 3.1 20.8 + - + +
97D ALA* 3.6 7.2 - - - +
98D TYR 3.3 0.2 - - - -
99D ALA* 1.3 73.6 - - - +
101D ALA* 1.3 64.7 + - - +
103D GLU* 3.4 8.0 + - - +
104D GLU* 3.1 23.4 + - - +
329D TRP* 4.0 23.1 - - + +
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Residues in contact with ALA 101 (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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41D LEU* 4.5 3.8 - - + -
45D CYS* 3.6 30.7 - - - -
79D LEU* 4.0 2.7 - - + -
82D MET* 3.7 23.1 - - - -
97D ALA 3.0 17.5 + - - +
98D TYR 3.8 0.4 - - - +
100D ILE* 1.3 75.9 - - - +
102D MET* 1.3 59.1 + - - +
104D GLU* 3.3 1.9 + - - +
105D ILE* 2.9 34.5 + - - +
116D MET* 4.0 8.3 - - + -
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Residues in contact with MET 102 (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 30.4 + - + +
99D ALA 3.6 4.9 - - - +
100D ILE 3.2 0.2 - - - -
101D ALA* 1.3 77.8 - - - +
103D GLU* 1.3 58.0 + - - +
105D ILE* 3.6 1.4 + - - +
106D SER* 2.6 45.1 + - - +
113D GLY* 2.7 44.2 - - - +
114D VAL 4.2 0.2 - - - +
116D MET* 4.0 26.0 - - + +
117D SER* 3.6 23.1 - - - -
274D GLY* 3.6 19.5 - - - +
277D SER* 3.6 8.5 - - - -
278D GLN* 3.8 14.6 - - + +
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Residues in contact with GLU 103 (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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99D ALA 3.0 17.5 + - - +
100D ILE* 3.6 7.0 - - - +
102D MET* 1.3 73.6 - - - +
104D GLU* 1.3 76.3 + - - +
106D SER 3.4 0.3 + - - -
107D ARG* 3.0 27.2 + - + +
277D SER* 3.4 11.6 + - - +
280D LEU* 3.7 17.4 - - + +
281D GLY* 3.4 24.0 - - - +
284D GLN* 4.2 11.7 - - + +
325D ARG* 2.9 48.1 + - - +
329D TRP* 4.8 6.4 + - - -
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Residues in contact with GLU 104 (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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42D LEU* 3.8 40.3 - - + +
45D CYS* 3.6 26.0 - - + -
46D ARG* 3.4 33.6 - - - +
49D ALA* 3.5 12.0 - - - +
100D ILE 3.1 13.8 + - - +
101D ALA 3.3 2.2 + - - +
103D GLU* 1.3 87.9 - - - +
105D ILE* 1.3 64.4 + - - +
107D ARG* 3.4 22.3 + - - +
108D GLY 3.4 14.2 + - - -
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Residues in contact with ILE 105 (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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45D CYS* 4.5 15.5 - - + +
48D PHE* 3.9 20.0 - - + -
49D ALA* 4.7 0.4 - - + -
53D LEU* 3.6 19.2 - - + +
74D MET* 3.9 7.9 - - + -
79D LEU* 4.1 14.8 - - + -
101D ALA* 2.9 20.7 + - - +
102D MET* 4.0 3.8 - - - +
104D GLU* 1.3 77.2 - - - +
106D SER* 1.3 59.2 + - - +
108D GLY* 3.1 5.2 + - - -
109D CYS 2.8 23.6 + - - +
112D THR* 3.7 30.1 - - + -
113D GLY* 3.8 15.5 - - - +
116D MET* 3.8 20.6 - - + -
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Residues in contact with SER 106 (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* 2.6 34.4 + - - +
103D GLU 4.0 2.0 - - - -
104D GLU 3.3 0.2 - - - -
105D ILE* 1.3 74.0 - - - +
107D ARG* 1.3 65.7 + - - +
108D GLY 3.2 1.0 + - - -
109D CYS 3.6 16.5 + - - -
110D ALA* 3.6 13.2 + - - +
113D GLY* 3.7 3.5 - - - -
278D GLN* 3.3 43.6 - - - +
281D GLY* 4.1 7.2 - - - -
282D ILE* 4.3 6.1 + - - +
285D THR* 4.9 1.2 - - - +
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Residues in contact with ARG 107 (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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46D ARG* 4.2 12.1 + - - +
49D ALA* 5.6 1.0 - - - +
50D GLU* 3.5 25.4 + - - +
54D PHE* 3.3 28.5 - - + -
103D GLU* 3.0 19.5 + - - +
104D GLU* 3.4 32.0 + - - +
106D SER* 1.3 76.6 - - - +
108D GLY* 1.3 58.7 + - - +
281D GLY* 3.3 17.8 - - - +
284D GLN* 4.0 17.6 - - - +
285D THR* 3.3 40.0 + - - +
288D ASP* 3.1 27.6 + - - +
380D ARG* 5.9 0.5 + - - -
381D HIS* 5.4 1.4 - - - -
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Residues in contact with GLY 108 (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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49D ALA* 4.1 3.6 - - - -
53D LEU* 3.9 17.2 - - - +
54D PHE* 3.5 29.2 + - - -
57D ALA* 3.6 17.5 - - - +
104D GLU 3.4 4.2 + - - -
105D ILE 3.1 8.0 + - - -
107D ARG* 1.3 80.8 - - - +
109D CYS* 1.3 61.4 + - - +
380D ARG* 4.6 3.7 + - - -
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Residues in contact with CYS 109 (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* 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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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