Contacts of the strand formed by residues 146 - 157 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A HIS 3.1 14.6 - - - -
13A PHE* 3.5 15.1 - - - -
101A ALA* 5.4 0.2 - - - -
102A GLN 5.5 0.3 + - - -
140A PHE* 3.8 4.2 + - - -
141A THR* 3.6 25.0 - - - +
144A GLN* 3.4 2.3 - - - -
145A GLU* 1.3 83.1 + - - +
147A ILE* 1.3 69.5 + - - +
138B LEU* 4.0 7.8 - - - +
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Residues in contact with ILE 147 (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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10A VAL* 3.3 6.4 - - - +
11A HIS* 2.9 47.1 + - + +
13A PHE* 3.4 23.1 - - + -
38A GLY 4.9 3.8 - - - +
40A VAL* 3.9 23.1 - - + +
99A ILE* 5.4 5.4 - - + -
100A ILE 3.8 8.7 - - - +
101A ALA* 3.8 22.7 - - + -
102A GLN 5.5 0.9 - - - +
140A PHE* 4.7 0.2 - - - -
141A THR* 3.9 3.6 - - - -
146A GLY* 1.3 82.2 - - - +
148A ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 148 (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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8A PHE* 4.0 14.1 - - + -
9A ASP 3.1 11.7 - - - +
10A VAL* 3.7 14.4 - - + -
40A VAL* 3.6 8.0 - - - +
99A ILE* 3.8 2.4 - - - +
100A ILE* 2.9 39.5 + - + +
140A PHE* 4.4 3.8 - - + -
141A THR* 3.9 12.7 - - + +
147A ILE* 1.3 76.5 - - - +
149A CYS* 1.3 66.2 + - - +
170A ACY 5.1 2.5 - - + -
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Residues in contact with CYS 149 (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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8A PHE* 3.2 9.4 - - - -
9A ASP 2.9 30.2 + - - -
40A VAL* 3.0 33.9 - - + +
41A ALA* 3.6 15.5 - - - -
44A ALA* 3.6 4.0 - - - +
97A ILE* 3.4 33.4 - - - -
98A THR 3.4 14.4 - - - -
99A ILE* 4.0 5.8 - - - -
100A ILE* 4.4 2.9 - - - +
148A ALA* 1.3 73.4 - - - +
150A GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 150 (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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6A HIS* 3.0 23.4 + - + +
7A GLY 3.3 4.5 - - - +
8A PHE* 4.4 11.2 - - + -
44A ALA* 4.3 0.2 - - - -
98A THR* 2.8 34.8 + - - +
100A ILE* 4.5 13.3 - - + +
149A CYS* 1.3 81.1 - - - +
151A ALA* 1.3 64.2 + - - +
6B HIS* 4.6 0.3 + - - -
150B GLU* 2.7 40.3 - - - +
6C HIS* 3.3 24.4 + - + +
8C PHE* 5.0 2.4 - - - -
150C GLU* 2.8 24.9 - - - +
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Residues in contact with ALA 151 (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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6A HIS* 3.3 4.7 - - - -
7A GLY 2.7 34.7 + - - +
44A ALA* 3.9 6.1 - - + +
45A LEU* 3.8 34.1 - - + +
48A ALA* 4.1 3.1 - - + -
96A ASP 3.5 11.4 - - - +
97A ILE* 4.1 11.7 - - + -
150A GLU* 1.3 79.4 - - - +
152A VAL* 1.3 68.4 + - - +
6C HIS* 5.7 1.3 - - - -
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY 3.2 10.8 - - - +
6A HIS* 4.5 10.5 - - + -
45A LEU* 5.2 0.3 - - - +
48A ALA* 4.3 1.3 - - - -
95A VAL* 3.5 3.5 - - - +
96A ASP* 3.1 40.5 + - + +
151A ALA* 1.3 80.2 - - - +
153A ALA* 1.3 63.3 + - - +
152B VAL* 4.8 6.5 - - + -
4C ILE* 3.9 27.8 - - + +
5C GLY 4.2 1.8 - - - -
6C HIS* 3.8 40.6 - - + +
152C VAL* 4.8 11.2 - - + -
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Residues in contact with ALA 153 (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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3A ARG 3.6 0.5 - - - +
4A ILE* 3.3 8.1 - - - +
5A GLY 2.8 31.5 + - - -
45A LEU* 4.9 0.4 - - + -
48A ALA* 4.0 18.2 - - + +
49A ILE* 4.0 21.8 - - + -
52A ALA* 4.4 1.3 - - + +
94A ASN 3.8 4.9 - - - -
95A VAL* 3.8 18.2 - - + -
152A VAL* 1.3 77.5 - - - +
154A LEU* 1.3 63.1 + - - +
155A LEU* 5.2 2.9 - - + -
4C ILE* 4.2 4.0 - - - -
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Residues in contact with LEU 154 (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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2A ILE* 3.8 23.1 - - + -
3A ARG 3.2 11.9 - - - +
4A ILE* 4.0 22.0 - - + -
92A ILE* 4.2 1.0 - - - +
93A GLY* 2.7 33.4 + - - -
94A ASN* 3.0 28.8 + - - +
153A ALA* 1.3 74.9 - - - +
155A LEU* 1.3 58.4 - - - +
156A ILE* 5.3 3.4 - - + -
154B LEU* 5.0 4.5 - - + -
2C ILE* 3.5 50.5 - - + +
4C ILE* 3.9 16.8 - - + +
154C LEU* 4.7 5.4 - - + -
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Residues in contact with LEU 155 (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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2A ILE* 3.3 5.0 - - - +
3A ARG* 2.6 37.9 + - + +
49A ILE* 3.8 31.9 - - + +
52A ALA* 3.9 17.0 - - + +
53A ALA* 3.8 15.9 - - + +
85A VAL* 3.7 31.6 - - + -
90A TYR* 4.0 17.5 - - + -
91A LYS 3.7 12.1 - - - +
92A ILE* 4.2 18.4 - - + -
153A ALA* 5.2 2.0 - - + -
154A LEU* 1.3 76.8 - - - +
156A ILE* 1.3 70.7 + - - +
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Residues in contact with ILE 156 (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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1A LEU 3.5 13.0 - - - +
2A ILE* 4.7 7.2 - - + -
90A TYR* 3.2 9.3 - - - -
91A LYS* 2.8 50.1 + - + +
92A ILE 5.2 0.2 - - - -
93A GLY* 3.8 23.8 - - - -
154A LEU* 4.8 2.2 - - + +
155A LEU* 1.3 81.9 - - - +
157A ARG* 1.3 75.3 + - - +
0C SER* 6.4 2.0 - - - -
1C LEU 6.1 2.0 - - - +
2C ILE* 4.4 22.4 - - + +
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Residues in contact with ARG 157 (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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0A SER 3.0 40.1 + - - +
1A LEU* 3.4 20.7 + - + +
88A LYS* 3.4 26.4 + - - +
89A GLY* 2.9 25.3 + - - -
90A TYR* 3.7 24.6 + - + -
91A LYS* 4.8 1.7 - - - -
156A ILE* 1.3 86.2 - - + +
158A GLN* 1.3 61.9 + - - +
126B GLU* 5.9 0.8 + - - -
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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