Contacts of the helix formed by residues 10 - 22 (chain A) in PDB entry 2VRB
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY 2.9 9.1 + - - -
9A THR* 1.3 82.2 - - - +
11A GLN* 1.3 66.8 + - - +
12A LEU 3.5 2.0 - - - -
14A GLY* 3.0 19.2 + - - -
1286A NAP 2.8 37.2 + - - -
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Residues in contact with GLN 11 (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 GLY* 1.3 74.2 - - - +
12A LEU* 1.3 64.2 + - - +
14A GLY* 4.0 0.5 - - - -
15A LEU* 3.3 26.0 + - + +
175A ARG* 3.4 51.1 + - - +
1286A NAP 3.0 27.0 + - - +
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Residues in contact with LEU 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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11A GLN* 1.3 73.6 - - - +
13A GLY* 1.3 58.2 + - - +
15A LEU* 3.1 7.9 + - - +
16A VAL* 2.9 34.6 + - + +
73A ILE* 4.3 13.5 - - + -
105A THR* 3.9 28.5 - - + -
140A ASN* 4.0 7.2 - - - +
143A TYR* 3.7 23.1 - - + +
175A ARG* 3.5 35.1 - - + +
178A LEU* 4.2 10.5 - - + +
179A ALA* 3.8 15.3 - - - +
182A ALA* 6.2 1.1 - - + -
1286A NAP 2.6 29.2 + - - +
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Residues in contact with GLY 13 (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 VAL* 4.2 6.2 - - - +
7A GLY 3.6 13.8 + - - -
8A ALA* 3.7 7.4 - - - -
10A GLY 3.8 2.6 + - - -
11A GLN 3.5 0.2 - - - -
12A LEU* 1.3 77.5 - - - +
14A GLY* 1.3 62.1 + - - +
16A VAL* 3.3 4.2 + - - +
17A ILE* 3.1 28.6 + - - +
73A ILE* 3.4 26.0 - - - +
1286A NAP 4.3 0.6 + - - -
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Residues in contact with GLY 14 (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 ALA 3.3 14.7 + - - -
9A THR 5.4 0.4 - - - -
10A GLY 3.0 18.3 + - - -
11A GLN 4.0 0.9 - - - -
13A GLY* 1.3 74.4 - - - +
15A LEU* 1.3 59.7 + - - +
17A ILE* 3.4 6.0 + - - +
18A GLN* 3.1 28.9 + - - +
42A LEU* 5.5 4.6 - - - +
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Residues in contact with LEU 15 (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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11A GLN* 3.3 16.2 + - + +
12A LEU* 3.1 7.4 + - - +
14A GLY* 1.3 72.0 - - - +
16A VAL* 1.3 66.3 + - - +
18A GLN* 3.3 10.9 + - + +
19A HIS* 2.9 30.4 + - - +
175A ARG* 3.9 31.4 - - + +
176A ASN* 3.7 32.3 - - + +
179A ALA* 3.5 13.0 - - + -
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Residues in contact with VAL 16 (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 VAL* 4.2 6.1 - - + -
12A LEU* 2.9 27.3 + - + +
13A GLY* 3.3 10.7 + - - +
15A LEU* 1.3 76.3 - - - +
17A ILE* 1.3 51.7 + - - +
19A HIS* 3.1 4.9 + - - +
20A LEU* 2.7 53.2 + - + +
71A LEU* 3.8 31.4 - - + -
73A ILE* 4.7 0.2 - - + -
179A ALA* 3.7 33.0 - - - +
182A ALA* 4.1 5.6 - - + -
183A ALA 4.6 3.8 - - - +
186A LEU* 4.5 5.2 - - + -
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Residues in contact with ILE 17 (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 VAL* 4.3 20.2 - - + -
8A ALA* 3.6 35.2 - - + +
13A GLY 3.1 14.5 + - - +
14A GLY* 3.7 5.4 - - - +
15A LEU 3.3 0.2 - - - -
16A VAL* 1.3 74.4 - - - +
18A GLN* 1.3 59.3 + - - +
20A LEU* 3.2 7.9 + - - +
21A LEU* 2.8 48.5 + - + +
29A ILE* 4.4 11.9 - - + -
31A ALA* 4.0 15.7 - - + -
42A LEU* 4.1 22.2 - - + -
47A VAL* 4.1 12.8 - - + -
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Residues in contact with GLN 18 (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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14A GLY 3.1 18.2 + - - +
15A LEU* 3.8 13.9 - - + +
16A VAL 3.3 0.4 - - - -
17A ILE* 1.3 80.2 - - - +
19A HIS* 1.3 61.4 + - + +
21A LEU* 3.5 20.7 + - - +
22A LYS* 3.5 22.3 + - - +
42A LEU* 4.6 3.6 - - - +
45A GLN* 2.9 35.3 + - - +
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Residues in contact with HIS 19 (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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15A LEU* 2.9 25.8 + - + +
16A VAL 3.5 6.7 - - - +
18A GLN* 1.3 75.9 - - + +
20A LEU* 1.3 63.2 + - - +
22A LYS* 3.2 38.3 + - - +
23A LYS* 3.7 13.7 + - - +
176A ASN* 2.7 39.6 + - - -
179A ALA* 3.9 5.2 - - + +
180A LEU* 3.7 47.8 - - + +
183A ALA* 3.6 18.4 - - + -
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Residues in contact with LEU 20 (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 ILE* 4.0 19.5 - - + -
5A VAL* 3.9 27.4 - - + -
16A VAL* 2.7 29.5 + - + +
17A ILE* 3.6 5.6 - - - +
19A HIS* 1.3 72.7 - - - +
21A LEU* 1.3 54.8 + - - +
23A LYS* 3.0 5.8 + - - +
24A VAL* 2.8 37.4 + - + +
29A ILE* 3.8 26.7 - - + -
183A ALA* 3.9 19.1 - - + +
186A LEU* 4.3 9.9 - - + -
187A THR* 3.6 29.2 - - + -
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Residues in contact with LEU 21 (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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17A ILE* 2.8 36.7 + - + +
18A GLN* 3.6 16.4 - - - +
19A HIS 3.2 0.2 - - - -
20A LEU* 1.3 77.7 - - - +
22A LYS* 1.3 60.1 + - + +
23A LYS 3.5 0.3 + - - -
24A VAL 3.6 9.5 + - - +
26A ALA* 3.6 30.5 - - + +
29A ILE* 3.4 22.0 - - + -
45A GLN* 3.4 29.6 - - + +
47A VAL* 4.1 9.2 - - + -
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Residues in contact with LYS 22 (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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18A GLN* 3.6 15.7 + - - +
19A HIS* 3.2 35.6 + - - +
20A LEU 3.1 0.8 - - - -
21A LEU* 1.3 78.4 - - + +
23A LYS* 1.3 62.7 + - + +
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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