Contacts of the helix formed by residues 6 - 20 (chain A) in PDB entry 2VBJ
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 ASN 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS 3.8 1.6 + - - -
5A TYR* 1.3 75.4 - - - +
7A LYS* 1.3 63.3 + - - +
8A GLU* 3.2 13.2 + - - +
9A PHE* 3.1 34.6 + - - +
10A LEU* 3.1 20.5 + - - +
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Residues in contact with LYS 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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5A TYR 3.7 1.8 + - - -
6A ASN* 1.3 75.7 - - - +
8A GLU* 1.3 62.3 - - + +
10A LEU* 3.3 9.7 + - - +
11A LEU* 2.9 39.6 + - + +
94A PHE* 3.5 27.6 - - + -
8B GLU* 3.5 33.9 - - + -
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Residues in contact with GLU 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 ASN* 3.2 8.8 + - - +
7A LYS* 1.3 84.8 - - + +
9A PHE* 1.3 63.2 + - - +
11A LEU* 3.6 2.0 + - - +
12A TYR* 3.2 24.6 + - - +
7B LYS* 2.8 39.6 + - - -
11B LEU* 3.7 35.1 - - + +
94B PHE* 5.3 2.6 - - - -
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Residues in contact with PHE 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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5A TYR* 3.9 36.1 - + + -
6A ASN* 3.1 29.8 + - - +
7A LYS 3.2 0.2 - - - -
8A GLU* 1.3 78.9 - - - +
10A LEU* 1.3 66.2 + - + +
12A TYR* 3.9 6.0 - + - +
13A LEU* 2.8 65.1 + - + +
58A LEU* 4.4 5.4 - - + -
61A GLU* 3.5 50.3 - - + -
62A ILE* 4.1 13.7 - - + -
87A PHE* 4.8 1.1 - + - -
96B LYS* 6.4 2.0 - - - -
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Residues in contact with LEU 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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4A LYS* 6.0 1.3 - - - +
5A TYR* 3.7 48.7 - - + +
6A ASN 3.1 10.8 + - - +
7A LYS* 3.3 7.4 + - - +
9A PHE* 1.3 85.5 - - + +
11A LEU* 1.3 60.1 + - - +
13A LEU* 4.4 2.7 - - + -
14A ALA* 2.8 32.1 + - - +
87A PHE* 4.7 4.0 - - + -
90A GLN* 3.8 26.0 - - + +
91A LEU* 3.7 26.2 - - + +
94A PHE* 3.9 24.6 - - + +
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Residues in contact with LEU 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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7A LYS* 2.9 37.9 + - + +
8A GLU 3.9 1.8 - - - +
9A PHE 3.4 0.2 - - - -
10A LEU* 1.3 73.9 - - - +
12A TYR* 1.3 62.5 + - - +
14A ALA* 3.3 2.8 + - - +
15A GLY 3.2 16.5 + - - -
94A PHE* 3.4 32.3 - - + +
8B GLU* 3.6 48.9 - - + +
11B LEU* 3.7 30.3 - - + -
12B TYR* 3.4 23.2 - - + +
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Residues in contact with TYR 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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8A GLU 3.2 15.5 + - - +
9A PHE* 3.9 6.3 - + - +
11A LEU* 1.3 79.1 - - - +
13A LEU* 1.3 69.9 + - + +
15A GLY 3.2 2.6 + - - -
16A PHE* 3.0 25.9 + + + -
54A PHE* 3.6 25.0 - + - -
11B LEU* 3.4 23.4 + - + +
14B ALA* 3.8 1.1 - - + -
15B GLY* 3.3 29.2 - - - -
18B ASP* 2.5 38.3 + - - +
94B PHE* 3.6 24.7 - - + -
96B LYS* 3.5 40.0 - - + +
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Residues in contact with LEU 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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9A PHE* 2.8 52.6 + - + +
10A LEU* 4.0 4.0 - - + +
12A TYR* 1.3 81.3 - - + +
14A ALA* 1.3 57.7 + - - +
16A PHE* 3.2 11.5 + - + -
17A VAL* 2.8 52.2 + - + +
43A PHE* 5.2 1.3 - - + -
54A PHE* 6.0 1.6 - - + -
58A LEU* 3.8 27.6 - - + -
62A ILE* 4.2 6.7 - - + -
87A PHE* 3.5 31.6 - - + -
91A LEU* 4.4 5.8 - - + -
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Residues in contact with ALA 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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10A LEU 2.8 20.0 + - - +
11A LEU 3.8 3.1 - - - +
12A TYR 3.3 0.2 - - - -
13A LEU* 1.3 78.2 - - - +
15A GLY* 1.3 56.9 + - - +
17A VAL* 4.4 0.2 - - - -
18A ASP* 2.9 34.1 + - - -
91A LEU* 3.8 13.6 - - + +
94A PHE* 3.5 39.3 - - + +
95A LEU* 3.6 11.0 - - + +
12B TYR* 3.8 2.5 - - + -
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Residues in contact with GLY 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 LEU 3.2 5.5 + - - -
12A TYR 3.2 4.8 + - - -
14A ALA* 1.3 79.9 - - - +
16A PHE* 1.3 61.3 + - - +
18A ASP 3.4 0.5 + - - -
19A GLY* 3.0 17.2 + - - -
12B TYR* 3.4 41.0 - - - -
16B PHE* 3.3 21.4 - - - -
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Residues in contact with PHE 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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12A TYR* 3.0 32.5 + - + +
13A LEU* 3.2 14.3 + - + +
15A GLY* 1.3 77.2 - - - +
17A VAL* 1.3 53.1 + - - +
19A GLY* 3.2 0.9 + - - -
20A ASP* 2.7 54.7 + - + -
21A GLY 3.7 0.3 + - - -
45A VAL* 3.7 29.2 - - + -
47A GLN* 3.5 13.2 - - - -
54A PHE* 3.5 32.1 - + - -
15B GLY* 3.4 22.9 - - - +
18B ASP* 3.8 14.4 - - + -
19B ALA* 3.7 3.7 - - + +
97B LEU* 3.6 24.9 - - + -
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Residues in contact with VAL 17 (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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13A LEU* 2.8 41.3 + - + +
14A ALA 3.8 3.1 - - - +
16A PHE* 1.3 71.7 - - + +
18A ASP* 1.3 66.9 + - - +
19A GLY 3.0 1.3 - - - -
21A GLY* 2.9 29.8 + - - +
22A SER 5.0 0.4 - - - +
23A ILE* 5.0 6.1 - - + -
43A PHE* 3.5 44.2 - - + -
45A VAL* 4.2 6.7 - - + -
91A LEU* 4.3 5.4 - - + -
95A LEU* 3.9 18.4 - - + -
98A LYS* 3.4 16.7 - - + -
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Residues in contact with ASP 18 (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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14A ALA 2.9 16.4 + - - +
15A GLY 3.8 3.4 - - - +
17A VAL* 1.3 76.2 - - - +
19A GLY* 1.3 60.4 + - - +
95A LEU* 3.3 12.4 - - - +
96A LYS 2.7 21.6 + - - -
97A LEU* 3.1 28.6 + - + +
98A LYS* 3.0 45.5 + - - +
1155A CA 4.3 2.9 - - - -
12B TYR* 2.5 33.7 + - - +
16B PHE* 3.8 8.9 - - + -
20B ASP* 4.4 0.2 - - - +
47B GLN* 4.9 0.7 - - - +
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Residues in contact with GLY 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 GLY 3.0 10.6 + - - -
16A PHE 3.5 2.5 - - - -
17A VAL 3.0 1.6 - - - -
18A ASP* 1.3 79.6 - - - +
20A ASP* 1.3 61.5 + - - +
21A GLY 3.5 1.0 - - - +
98A LYS* 5.0 0.7 - - - -
1155A CA 2.4 26.9 - - - -
16B PHE* 3.7 7.6 - - - -
19B ALA* 3.7 11.9 - - - -
20B ASP* 3.3 17.9 - - - -
15C A 3.1 8.1 + - - +
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Residues in contact with ASP 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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16A PHE* 2.7 26.8 + - + -
19A GLY* 1.3 70.9 - - - -
21A GLY* 1.3 59.1 + - - +
45A VAL* 4.7 1.8 - - + -
46A THR* 3.3 34.5 + - - +
47A GLN* 2.9 17.1 + - - -
1154A CA 2.5 30.4 - - - -
19B ALA* 3.3 18.8 - - - +
20B ASP* 3.7 4.3 - - - +
14C A 3.4 16.7 - - - +
15C A 3.6 13.8 - - - +
15E A 3.2 9.7 + - - -
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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