Contacts of the helix formed by residues 95 - 112 (chain B) in PDB entry 1VGX
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B TYR* 2.8 13.2 + - - +
71B LEU* 6.1 0.7 - - - +
93B GLU* 3.3 8.7 + - + +
94B PRO* 1.3 76.0 - - - +
96B GLU* 1.3 64.2 + - - +
97B GLN* 3.7 6.4 + - - +
98B GLY* 3.0 27.2 + - - -
99B VAL* 2.9 25.6 + - + +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 3.9 6.3 - - + +
23B ARG* 3.6 9.0 - - - +
24B LEU* 2.7 49.5 + - + +
39B TYR* 4.1 12.3 - - + -
94B PRO* 4.0 1.5 - - + -
95B ASP* 1.3 72.8 - - - +
97B GLN* 1.3 58.2 + - - +
99B VAL* 3.8 2.3 - - - +
100B MET* 2.9 30.5 + - - +
150B VAL* 3.5 33.0 - - + +
151B GLN 4.0 5.5 - - - +
152B GLU* 5.8 0.2 - - - -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 3.2 5.9 + - - +
96B GLU* 1.3 78.6 - - - +
98B GLY* 1.3 63.7 + - - +
100B MET* 3.2 22.0 + - - +
101B LYS* 3.0 53.7 + - + +
150B VAL* 4.1 11.7 - - + +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.9 5.4 - - - +
95B ASP* 3.0 27.1 + - - -
97B GLN* 1.3 77.7 - - - +
99B VAL* 1.3 57.7 + - - +
101B LYS* 3.4 8.0 + - - +
102B ALA* 3.0 27.5 + - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.7 17.3 - - + -
39B TYR* 3.5 37.5 - - + +
41B LEU* 4.1 7.6 - - + -
67B MET* 4.5 1.7 - - + +
71B LEU* 4.3 21.1 - - + -
88B MET* 3.9 22.0 - - + -
90B VAL* 5.0 1.1 - - + -
95B ASP* 2.9 22.4 + - + +
96B GLU 3.8 4.0 - - - +
98B GLY* 1.3 74.3 - - - +
100B MET* 1.3 61.0 + - - +
102B ALA* 3.3 6.4 + - - +
103B PHE* 2.8 28.9 + - - +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 3.9 20.9 - - + -
96B GLU 2.9 18.6 + - - +
97B GLN* 3.5 36.6 - - - +
99B VAL* 1.3 79.2 - - - +
101B LYS* 1.3 66.4 + - + +
103B PHE* 3.4 1.4 + - - +
104B GLU* 2.8 33.6 + - - +
148B LEU* 4.0 19.9 - - + +
149B LYS* 3.5 40.4 - - - -
150B VAL* 3.8 7.9 - - + +
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 3.0 42.6 + - + +
98B GLY* 3.7 7.9 - - - +
99B VAL 3.3 0.2 - - - -
100B MET* 1.3 83.2 - - + +
102B ALA* 1.3 64.3 + - - +
104B GLU* 3.4 27.1 + - - +
105B ALA* 3.1 22.9 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 4.3 7.6 - - + -
70B HIS* 3.6 35.4 - - + +
71B LEU* 3.9 19.1 - - + -
98B GLY 3.0 17.4 + - - +
99B VAL* 3.7 5.8 - - - +
101B LYS* 1.3 78.1 - - - +
103B PHE* 1.3 57.0 + - - +
105B ALA* 3.3 4.5 + - - +
106B ALA* 2.9 28.8 + - - +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR 4.5 3.4 - - - -
22B VAL* 3.5 23.3 - - + -
41B LEU* 3.9 32.8 - - + -
42B ARG 5.1 0.9 - - - -
43B PHE* 3.6 31.4 - + - -
63B LEU* 4.6 9.4 - - + -
67B MET* 3.7 25.2 - - + +
99B VAL 2.8 21.8 + - - +
100B MET 3.7 2.5 - - - +
102B ALA* 1.3 69.7 - - - +
104B GLU* 1.3 61.2 + - - +
106B ALA 3.2 0.7 + - - -
107B LEU* 2.8 60.9 + - + +
143B VAL* 4.8 1.8 - - + -
148B LEU* 3.7 32.8 - - + -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET* 2.8 22.6 + - - +
101B LYS* 3.6 29.4 + - - +
103B PHE* 1.3 76.8 - - - +
105B ALA* 1.3 61.7 + - - +
107B LEU* 3.3 3.3 + - - +
108B LYS* 3.0 49.7 + - - +
144B LEU* 3.9 19.9 - - + +
148B LEU* 4.1 24.8 + - + +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B HIS* 3.6 31.2 - - + +
101B LYS 3.1 14.0 + - - +
102B ALA* 3.6 7.6 - - - +
104B GLU* 1.3 75.8 - - - +
106B ALA* 1.3 58.9 + - - +
108B LYS* 3.2 14.4 + - - +
109B ASP* 3.0 30.8 + - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.0 6.5 - - + -
66B TYR* 3.6 26.7 - - + +
67B MET* 3.6 25.4 - - - +
70B HIS* 3.7 1.3 - - - -
102B ALA 2.9 16.9 + - - +
103B PHE 3.2 1.5 + - - +
105B ALA* 1.3 78.9 - - - +
107B LEU* 1.3 57.5 + - - +
109B ASP* 3.3 11.9 + - - +
110B THR* 2.8 32.9 + - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 3.8 20.9 - - + -
59B LEU* 5.5 0.4 - - + -
63B LEU* 4.7 7.9 - - + -
103B PHE* 2.8 53.8 + - + +
104B GLU 3.6 4.5 - - - +
105B ALA 3.2 0.2 - - - -
106B ALA* 1.3 73.3 - - - +
108B LYS* 1.3 61.8 + - - +
110B THR* 3.5 4.3 - - + -
111B ALA* 2.8 30.3 + - - +
140B ALA* 3.6 22.1 - - + +
143B VAL* 3.5 32.5 - - + -
144B LEU* 3.9 16.6 - - + +
148B LEU* 4.0 9.9 - - + -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU* 3.0 45.7 + - - +
105B ALA* 3.2 13.2 + - - +
107B LEU* 1.3 75.8 - - - +
109B ASP* 1.3 65.1 + - - +
111B ALA* 3.4 3.3 + - - +
112B GLY* 3.1 19.6 + - - -
141B ARG* 5.1 6.4 + - - +
144B LEU* 3.6 22.0 - - + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TYR* 3.5 39.6 + - + -
69B ASP* 4.6 1.4 - - - +
70B HIS* 2.8 34.4 + - - -
105B ALA 3.0 13.2 + - - +
106B ALA* 3.4 7.4 - - - +
108B LYS* 1.3 80.6 - - - +
110B THR* 1.3 60.5 + - - +
112B GLY* 3.4 3.7 + - - -
113B HIS* 3.2 22.0 + - - +
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.0 18.8 - - + -
62B LEU* 4.0 22.8 - - + +
63B LEU* 3.8 15.0 - - - +
66B TYR* 3.7 17.7 - - - -
106B ALA 2.8 23.6 + - - -
107B LEU* 3.3 7.6 + - + -
109B ASP* 1.3 76.3 - - - +
111B ALA* 1.3 64.6 + - - +
113B HIS* 3.1 14.9 + - - +
136B ALA 4.1 5.2 - - - +
137B ARG* 3.4 13.7 - - - +
140B ALA* 3.7 18.2 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 2.8 20.7 + - - +
108B LYS* 3.8 2.9 - - - +
110B THR* 1.3 73.3 - - - +
112B GLY* 1.3 53.8 + - - +
113B HIS 3.3 0.2 - - - -
137B ARG* 2.8 51.0 + - - +
140B ALA* 3.9 4.4 - - + +
141B ARG* 3.7 38.6 - - + +
144B LEU* 4.7 0.2 - - + -
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS 3.1 13.7 + - - -
109B ASP 3.5 6.7 - - - -
111B ALA* 1.3 76.8 - - - +
113B HIS* 1.3 55.7 + - - +
114B ASP* 3.0 17.3 + - - +
137B ARG* 3.8 8.6 + - - -
141B ARG* 5.5 0.4 - - - +
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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