Contacts of the strand formed by residues 2 - 12 (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 ILE 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ILE* 3.4 30.1 - - + -
0B SER* 3.6 6.3 - - - -
1B LEU* 1.3 97.6 - - + +
3B ARG* 1.3 70.2 + - - +
154B LEU* 3.5 22.0 - - + -
155B LEU 3.3 7.4 - - - +
156B ILE* 5.0 4.3 - - + -
2C ILE* 3.3 30.5 - - + -
93C GLY 5.5 1.0 - - - -
94C ASN* 5.5 0.2 - - - +
154C LEU* 3.4 18.8 - - + +
156C ILE* 4.5 17.1 - - + +
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Residues in contact with ARG 3 (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* 2.8 24.2 + - - +
2B ILE* 1.3 77.6 - - - +
4B ILE* 1.3 58.5 + - - +
52B ALA* 3.0 37.0 + - + +
53B ALA* 4.0 10.1 - - - +
54B ALA* 4.1 2.6 - - - +
90B TYR* 3.3 28.4 + - + +
153B ALA 3.7 0.5 - - - +
154B LEU* 3.2 10.5 - - - +
155B LEU* 2.7 47.6 + - + -
93C GLY 4.4 0.6 + - - -
94C ASN* 3.2 34.7 - - - +
126C GLU* 2.6 59.4 + - - -
127C GLN* 3.7 8.7 - - - +
154C LEU* 4.3 0.7 - - - -
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Residues in contact with ILE 4 (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* 3.3 35.7 - - + -
152A VAL* 6.4 0.2 - - + -
3B ARG* 1.3 74.3 - - - +
5B GLY* 1.3 63.4 - - - +
52B ALA* 3.1 10.5 - - - -
153B ALA 3.3 2.2 - - - -
154B LEU* 4.5 2.9 - - + -
4C ILE* 3.4 26.0 - - + -
94C ASN* 2.8 47.7 + - - +
95C VAL* 5.3 0.2 - - - -
96C ASP* 4.2 3.3 - - - +
152C VAL* 4.0 31.4 - - + +
153C ALA 4.3 4.0 - - - +
154C LEU* 3.6 27.1 - - + +
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Residues in contact with GLY 5 (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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4B ILE* 1.3 79.3 - - - +
6B HIS* 1.3 61.1 + - - +
48B ALA* 3.3 22.7 - - - -
52B ALA* 3.5 2.9 - - - +
152B VAL* 3.2 7.3 - - - +
153B ALA 2.8 31.7 + - - -
96C ASP* 3.4 11.0 - - - -
152C VAL* 4.3 3.3 - - - +
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Residues in contact with HIS 6 (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* 5.4 1.8 - + - -
150A GLU* 5.0 1.1 - - - -
5B GLY* 1.3 75.5 - - - +
7B GLY* 1.3 75.5 + - - +
8B PHE* 4.0 5.4 - - + -
48B ALA* 3.6 8.5 - - - +
150B GLU* 3.1 27.1 + - + +
151B ALA 3.3 12.3 - - - +
152B VAL* 4.5 6.5 - - + -
6C HIS* 5.5 1.6 - + - -
96C ASP* 2.8 14.3 + - + +
98C THR* 2.9 29.3 + - - +
131C LYS* 2.7 34.4 + - - +
150C GLU* 3.0 39.7 + - + +
152C VAL* 3.8 31.4 - - + -
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Residues in contact with GLY 7 (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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6B HIS* 1.3 85.5 + - - +
8B PHE* 1.3 60.0 + - - -
44B ALA* 3.4 24.2 - - - -
47B ASP* 4.0 9.4 - - - -
48B ALA* 3.6 1.2 - - - +
150B GLU* 3.2 3.8 - - - -
151B ALA 2.8 39.1 + - - +
98C THR* 4.7 1.3 - - - -
131C LYS* 5.2 0.2 - - - -
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Residues in contact with PHE 8 (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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6B HIS* 4.0 14.3 - - + +
7B GLY* 1.3 75.7 - - - +
9B ASP* 1.3 63.4 + - - +
10B VAL* 3.7 28.3 - - + -
44B ALA* 4.0 2.1 - - - +
47B ASP* 4.2 10.8 + - - +
100B ILE* 5.2 6.1 - - + -
140B PHE* 5.0 5.4 - + - -
148B ALA* 4.1 19.5 - - + -
149B CYS 3.1 18.4 - - - -
150B GLU* 4.2 17.5 - - - +
171B ACY 5.5 5.4 - - + -
98C THR* 4.5 11.5 - - + +
100C ILE* 3.8 34.5 - - + -
133C THR* 3.7 25.1 + - + +
134C THR 5.2 0.4 - - - -
135C THR* 4.1 16.4 - - + -
150C GLU* 5.0 1.8 - - - -
170C ACY 5.1 6.3 - - + -
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Residues in contact with ASP 9 (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* 1.3 79.4 - - - +
10B VAL* 1.3 76.6 + - - +
11B HIS* 5.4 1.0 - - - +
40B VAL* 2.9 44.3 - - + +
43B HIS* 3.1 38.3 + - - +
44B ALA* 3.9 8.3 - - - +
47B ASP* 5.0 3.4 - - - +
58B ILE* 6.0 1.9 - - - +
148B ALA* 3.2 3.6 - - - +
149B CYS 3.0 19.0 + - - +
169B MN 3.2 20.8 + - - -
133C THR* 4.4 6.6 + - - -
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Residues in contact with VAL 10 (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* 3.7 29.6 - - + -
9B ASP* 1.3 89.9 + - - +
11B HIS* 1.3 72.8 + - - +
12B ALA 4.4 0.4 - - - +
40B VAL* 4.1 0.7 - - - -
140B PHE* 4.0 20.2 - - + -
147B ILE 3.4 10.3 - - - +
148B ALA* 4.0 8.5 - - + -
169B MN 3.2 12.5 + - - -
134C THR 4.2 3.1 + - - +
135C THR* 3.5 39.7 - - + +
136C GLU* 3.1 17.5 - - - +
138C LEU* 4.3 4.3 - - + -
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Residues in contact with HIS 11 (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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9B ASP* 5.4 0.9 - - - +
10B VAL* 1.3 77.4 - - - +
12B ALA* 1.3 76.7 + - - +
13B PHE* 4.1 23.6 - + - -
14B GLY 5.3 1.1 + - - -
34B ALA* 4.5 20.5 - - + +
37B ASP 5.3 2.3 + - - -
38B GLY* 3.7 42.4 - - - +
40B VAL* 4.6 2.8 - - + +
146B GLY* 3.2 4.0 - - - -
147B ILE* 3.0 43.5 + - + -
136C GLU* 3.2 8.8 + - - -
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Residues in contact with ALA 12 (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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11B HIS* 1.3 90.5 - - - +
13B PHE* 1.3 66.6 + - - +
14B GLY* 3.6 0.7 + - - -
32B PHE* 4.1 18.7 - - + +
145B GLU 3.8 0.9 - - - +
136C GLU* 2.7 32.0 + - + +
138C LEU* 3.5 35.9 - - + -
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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