Contacts of the strand formed by residues 2 - 12 (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 ILE 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A SER* 3.5 5.3 - - - -
1A LEU* 1.3 85.7 - - + +
3A ARG* 1.3 73.7 + - - +
90A TYR* 5.3 0.2 - - - -
154A LEU* 3.8 25.4 - - + -
155A LEU 3.3 12.3 - - - +
156A ILE* 4.7 4.3 - - + -
2B ILE* 3.4 17.9 - - + -
93B GLY 5.6 1.4 - - - -
94B ASN* 4.2 1.0 - - - +
154B LEU* 3.6 19.0 - - + +
156B ILE* 4.7 16.1 - - + +
2C ILE* 3.3 41.1 - - + -
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Residues in contact with ARG 3 (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* 3.4 31.3 + - - +
2A ILE* 1.3 77.2 - - - +
4A ILE* 1.3 58.7 + - - +
51A GLY 5.0 0.4 + - - -
52A ALA* 2.6 38.0 + - + +
53A ALA* 3.8 3.5 - - - +
54A ALA* 3.4 18.6 - - - +
90A TYR* 3.3 31.7 + - + +
153A ALA 3.6 0.5 - - - +
154A LEU* 3.2 9.1 - - - +
155A LEU* 2.6 43.7 + - + +
94B ASN* 3.5 24.0 - - - +
126B GLU* 2.9 48.9 + - - -
127B GLN* 3.9 13.9 - - - +
154B LEU* 4.4 0.7 - - - -
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Residues in contact with ILE 4 (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* 1.3 72.4 - - - +
5A GLY* 1.3 64.2 + - - +
52A ALA* 3.2 8.4 - - - -
153A ALA 3.3 2.2 - - - -
154A LEU* 4.0 7.9 - - + -
4B ILE* 3.3 29.6 - - + -
94B ASN* 3.0 38.2 + - - +
95B VAL* 5.3 0.2 - - - -
96B ASP* 4.1 4.9 - - - +
152B VAL* 4.0 28.0 - - + +
153B ALA 4.3 2.5 - - - +
154B LEU* 3.7 27.3 - - + +
4C ILE* 3.2 36.3 - - + -
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Residues in contact with GLY 5 (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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4A ILE* 1.3 76.9 - - - +
6A HIS* 1.3 61.8 + - - +
48A ALA* 3.1 24.2 - - - -
52A ALA* 3.3 4.8 - - - +
152A VAL* 3.2 7.3 - - - +
153A ALA 2.8 32.7 + - - -
96B ASP* 3.3 9.2 - - - -
152B VAL* 4.2 3.7 - - - +
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Residues in contact with HIS 6 (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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5A GLY* 1.3 74.8 - - - +
7A GLY* 1.3 74.3 + - - +
8A PHE* 3.9 8.5 - - + -
48A ALA* 3.6 7.8 - - - +
150A GLU* 3.0 34.5 + - + +
151A ALA 3.3 12.6 - - - -
152A VAL* 4.5 7.0 - - + -
6B HIS* 5.4 2.0 - + - -
96B ASP* 2.8 15.1 + - - +
98B THR* 3.1 21.5 + - - +
131B LYS* 2.7 32.2 + - - -
150B GLU* 3.4 33.3 + - + +
152B VAL* 3.7 32.8 - - + -
6C HIS* 5.4 0.9 - + - -
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Residues in contact with GLY 7 (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* 1.3 80.3 - - - +
8A PHE* 1.3 61.2 + - - +
44A ALA* 3.3 26.0 - - - -
47A ASP* 3.9 7.2 - - - -
48A ALA* 3.7 4.1 - - - +
150A GLU* 3.3 7.1 - - - +
151A ALA 2.7 38.9 + - - +
98B THR* 4.8 1.1 - - - -
131B LYS* 5.2 0.2 - - - -
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Residues in contact with PHE 8 (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* 3.9 15.0 - - + -
7A GLY* 1.3 73.7 - - - +
9A ASP* 1.3 64.3 + - - +
10A VAL* 3.7 29.6 - - + -
44A ALA* 4.0 3.2 - - - +
47A ASP* 4.1 9.7 - - - +
100A ILE* 4.8 7.4 - - + -
140A PHE* 5.2 3.6 - + - -
148A ALA* 4.0 16.2 - - + -
149A CYS 3.2 20.9 - - - -
150A GLU* 4.4 17.9 - - + -
170A ACY 5.7 5.2 - - + -
98B THR* 4.4 12.0 - - + +
100B ILE* 3.6 39.7 - - + -
131B LYS* 5.8 0.4 - - - +
133B THR* 3.7 25.1 + - + +
134B THR 5.5 0.9 - - - -
135B THR* 4.3 5.4 - - + -
150B GLU* 4.6 2.7 - - - -
171B ACY 5.2 6.7 - - + -
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Residues in contact with ASP 9 (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* 1.3 79.4 - - - +
10A VAL* 1.3 70.3 + - - +
11A HIS* 5.3 0.3 - - - +
38A GLY 5.1 0.5 - - - +
40A VAL* 3.2 26.2 - - + +
43A HIS* 3.3 43.8 - - + +
44A ALA 4.0 8.7 - - - +
47A ASP* 5.4 3.0 - - - +
148A ALA* 3.1 4.7 - - - +
149A CYS 2.9 32.8 + - - -
169A MN 2.4 32.0 + - - -
133B THR* 4.3 5.7 + - - -
134B THR 5.4 0.4 - - - -
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Residues in contact with VAL 10 (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* 3.7 27.8 - - + -
9A ASP* 1.3 90.8 + - - +
11A HIS* 1.3 72.0 + - - +
12A ALA 4.4 0.2 - - - +
40A VAL* 3.7 3.8 - - - -
140A PHE* 3.8 24.2 - - + -
147A ILE 3.3 10.5 - - - +
148A ALA* 3.7 9.2 - - + -
169A MN 3.8 5.7 + - - -
134B THR 4.2 3.5 + - - +
135B THR* 3.5 38.1 - - + +
136B GLU* 3.0 20.3 - - - +
138B LEU* 4.0 3.6 - - + -
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Residues in contact with HIS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 5.3 0.7 - - - +
10A VAL* 1.3 78.7 - - - +
12A ALA* 1.3 78.1 + - - +
13A PHE* 4.0 22.3 - + - -
14A GLY 5.0 3.7 + - - -
32A PHE 6.2 0.2 - - - -
34A ALA* 4.6 19.0 - - + +
37A ASP 5.3 2.0 + - - -
38A GLY* 3.6 43.0 - - - +
40A VAL* 3.8 3.1 - - + +
146A GLY* 3.1 4.3 - - - -
147A ILE* 2.9 44.8 + - + -
136B GLU* 3.4 7.9 + - - -
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Residues in contact with ALA 12 (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 4.1 0.2 - - - -
11A HIS* 1.3 91.4 - - - +
13A PHE* 1.3 67.3 + - - +
14A GLY* 3.5 1.0 + - - -
32A PHE* 3.8 20.6 - - + +
145A GLU 4.3 0.2 - - - +
136B GLU* 2.7 36.8 + - + +
138B LEU* 3.6 29.6 - - + +
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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