Contacts of the strand formed by residues 146 - 157 (chain B) in PDB entry 1VHA
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 GLY 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B HIS 3.2 13.9 - - - -
13B PHE* 3.6 14.1 - - - -
101B ALA* 5.4 0.2 - - - -
102B GLN 5.6 0.2 + - - -
140B PHE* 3.6 4.8 + - - -
141B THR* 3.5 26.2 - - - +
144B GLN* 3.2 2.7 - - - -
145B GLU* 1.3 81.9 - - - +
147B ILE* 1.3 68.7 + - - +
138C LEU* 4.0 8.4 - - - +
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Residues in contact with ILE 147 (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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10B VAL* 3.4 6.3 - - - +
11B HIS* 3.0 45.0 + - + +
13B PHE* 3.8 21.5 - - + -
38B GLY 4.6 8.5 - - - +
40B VAL* 3.6 25.9 - - + +
99B ILE* 5.5 4.0 - - + -
100B ILE 3.8 7.0 - - - +
101B ALA* 3.6 25.4 - - + -
102B GLN 5.5 0.4 - - - +
106B MSE 5.5 7.9 - - + -
140B PHE* 4.9 0.2 - - - -
141B THR* 4.2 3.1 - - - -
146B GLY* 1.3 77.1 - - - +
148B ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 148 (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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8B PHE* 4.1 14.4 - - + -
9B ASP 3.2 12.8 - - - +
10B VAL* 4.0 13.2 - - + -
40B VAL* 3.5 8.5 - - - +
99B ILE* 3.8 3.3 - - - +
100B ILE* 2.9 40.0 + - + +
140B PHE* 4.5 4.0 - - + -
141B THR* 4.1 12.1 - - + +
147B ILE* 1.3 75.4 - - - +
149B CYS* 1.3 64.9 + - - +
171B ACY 4.8 2.9 - - + -
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Residues in contact with CYS 149 (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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8B PHE* 3.1 9.5 - - - -
9B ASP 3.0 30.0 + - - -
40B VAL* 3.4 27.8 - - + +
41B ALA* 3.7 14.4 - - - -
44B ALA* 3.6 6.1 - - + +
97B ILE* 3.5 30.1 - - - -
98B THR 3.4 17.0 - - - -
99B ILE* 4.0 4.3 - - - -
100B ILE* 4.4 2.4 - - - +
148B ALA* 1.3 79.1 - - - +
150B GLU* 1.3 69.4 + - - +
151B ALA* 5.1 0.2 - - - -
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Residues in contact with GLU 150 (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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6A HIS* 3.4 28.3 + - + +
8A PHE* 4.6 4.5 - - - -
150A GLU* 2.7 27.4 - - - +
6B HIS* 3.1 21.1 + - + +
7B GLY 3.2 2.9 - - - +
8B PHE* 4.2 13.2 - - + -
96B ASP 4.2 0.2 - - - +
98B THR* 2.9 35.8 + - - +
100B ILE* 4.4 14.7 - - + +
149B CYS* 1.3 77.1 - - - +
151B ALA* 1.3 62.6 + - - +
150C GLU* 2.5 33.4 - - - +
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Residues in contact with ALA 151 (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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6A HIS* 5.7 0.9 - - - -
6B HIS* 3.3 6.1 - - - -
7B GLY 2.8 33.4 + - - +
44B ALA* 3.9 29.6 - - + +
45B LEU* 3.9 12.8 - - + +
48B ALA* 4.1 3.1 - - + -
96B ASP 3.4 10.1 - - - +
97B ILE* 4.1 13.2 - - + -
150B GLU* 1.3 77.3 - - - +
152B VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 152 (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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4A ILE* 4.0 27.8 - - + +
5A GLY 4.2 2.5 - - - +
6A HIS* 3.7 37.9 - - + +
152A VAL* 4.8 10.1 - - + -
5B GLY 3.2 10.3 - - - +
6B HIS* 4.5 10.8 - - + -
45B LEU* 5.1 0.2 - - - +
48B ALA* 4.2 1.1 - - - -
95B VAL* 3.5 4.2 - - - +
96B ASP* 3.1 45.0 + - + +
151B ALA* 1.3 80.8 - - - +
153B ALA* 1.3 62.8 + - - +
152C VAL* 5.0 4.5 - - + -
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Residues in contact with ALA 153 (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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4A ILE* 4.3 4.0 - - - -
3B ARG 3.7 0.5 - - - +
4B ILE* 3.3 5.9 - - - +
5B GLY 2.8 33.3 + - - +
45B LEU* 5.0 0.4 - - + -
48B ALA* 4.0 17.7 - - + +
49B ILE* 3.9 22.7 - - + -
52B ALA* 4.3 2.3 - - + +
94B ASN 3.8 4.7 - - - -
95B VAL* 3.8 17.9 - - + -
152B VAL* 1.3 76.6 - - - +
154B LEU* 1.3 62.5 + - - +
155B LEU* 4.1 2.5 - - + -
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Residues in contact with LEU 154 (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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2A ILE* 3.6 47.8 - - + +
3A ARG 4.6 0.4 - - - -
4A ILE* 3.7 24.8 - - + +
154A LEU* 5.0 2.5 - - + -
2B ILE* 3.5 25.4 - - + -
3B ARG 3.2 18.6 - - - +
4B ILE* 4.5 8.7 - - + -
92B ILE* 4.2 1.0 - - - +
93B GLY* 2.8 24.8 + - - -
94B ASN* 3.0 24.0 + - - +
153B ALA* 1.3 74.6 - - - +
155B LEU* 1.3 64.9 + - - +
156B ILE* 4.9 6.3 - - + -
154C LEU* 4.9 5.6 - - + -
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Residues in contact with LEU 155 (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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2B ILE* 3.3 6.8 - - - +
3B ARG* 2.7 38.9 + - + +
49B ILE* 3.9 22.4 - - + +
52B ALA* 3.9 26.2 - - + -
53B ALA* 4.2 8.3 - - + +
85B VAL* 3.2 34.3 - - + -
90B TYR* 3.9 18.8 - - + -
91B LYS 3.6 14.4 - - - +
92B ILE* 4.2 20.2 - - + -
95B VAL* 6.3 0.2 - - + -
153B ALA* 5.3 2.0 - - + -
154B LEU* 1.3 79.4 - - - +
156B ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 156 (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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0A SER* 5.7 6.5 - - - +
1A LEU 6.2 0.9 - - - +
2A ILE* 4.7 20.0 - - + +
1B LEU* 3.3 12.1 - - + +
2B ILE* 5.0 6.5 - - + -
90B TYR* 3.5 5.6 - - - -
91B LYS* 3.0 56.5 + - - +
93B GLY* 3.6 24.8 - - - +
154B LEU* 4.9 7.0 - - + -
155B LEU* 1.3 78.8 - - - +
157B ARG* 1.3 77.4 + - - +
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Residues in contact with ARG 157 (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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0B SER 2.9 26.0 + - - +
1B LEU* 2.5 35.4 + - + +
88B LYS 3.8 17.9 + - - -
89B GLY* 3.4 17.8 + - - -
90B TYR* 3.8 21.4 + - - -
91B LYS* 4.8 3.2 - - - -
156B ILE* 1.3 83.3 - - - +
158B GLN* 1.3 66.5 + - - +
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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