Contacts of the helix formed by residues 8 - 18 (chain A) in PDB entry 5BNG
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 VAL 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LYS* 1.3 99.3 - - + +
9A ALA* 1.3 64.7 + - - +
10A THR 3.1 2.9 - - - -
11A ASN* 3.1 30.0 + - + +
12A ILE* 3.3 20.9 + - + +
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Residues in contact with ALA 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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6A PRO* 3.6 34.7 - - + +
7A LYS 3.2 2.0 - - - +
8A VAL* 1.3 80.6 - - - +
10A THR* 1.3 62.2 + - - +
12A ILE* 3.1 12.6 + - - +
13A MET* 3.0 29.2 + - + +
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Residues in contact with THR 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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6A PRO 4.8 4.5 + - - -
7A LYS 3.9 10.9 + - - -
8A VAL* 3.1 0.6 - - - -
9A ALA* 1.3 78.5 - - - +
11A ASN* 1.3 60.8 + - - +
13A MET* 3.1 7.8 + - - +
14A ARG* 2.8 64.8 + - - +
48A TRP* 4.1 15.6 + - + +
5D G 4.9 8.2 + - - +
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Residues in contact with ASN 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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8A VAL* 3.1 23.2 + - + +
10A THR* 1.3 83.1 - - - +
12A ILE* 1.3 60.3 + - + +
14A ARG* 3.9 12.1 - - - +
15A ALA* 2.8 30.9 + - - +
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Residues in contact with ILE 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 VAL* 3.4 21.5 - - + +
9A ALA* 3.1 14.0 + - - +
11A ASN* 1.3 79.2 - - + +
13A MET* 1.3 63.7 + - + +
15A ALA* 3.3 16.3 + - + +
16A TRP* 3.3 12.6 + - - +
34A LEU* 4.3 23.5 - - + +
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Residues in contact with MET 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 ALA* 3.0 18.9 + - + +
10A THR 3.6 5.6 - - - +
12A ILE* 1.3 77.9 - - + +
14A ARG* 1.3 57.1 + - - +
16A TRP* 3.4 8.4 + - - +
17A LEU* 3.1 23.9 + - - +
34A LEU* 4.3 32.8 - - - +
45A VAL* 4.2 15.3 - - + -
48A TRP* 3.6 54.7 - - + +
49A PHE* 3.4 35.6 - - + -
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Residues in contact with ARG 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 THR* 2.8 42.9 + - - +
11A ASN* 3.9 12.6 - - - +
13A MET* 1.3 73.4 - - - +
15A ALA* 1.3 66.0 + - - +
17A LEU* 3.0 16.3 + - - -
18A PHE* 3.1 43.0 + - + +
48A TRP* 3.6 15.8 - - + -
56A ILE* 3.1 34.6 - - + +
4D T 2.7 32.5 + - - -
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Residues in contact with ALA 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 ASN 2.8 19.2 + - - +
12A ILE* 3.3 10.7 + - + +
14A ARG* 1.3 77.5 - - - +
16A TRP* 1.3 56.6 + - - +
18A PHE* 4.9 1.7 - - - +
19A GLN* 3.2 27.6 + - - +
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Residues in contact with TRP 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 ILE 3.3 8.7 + - - +
13A MET 3.7 8.3 - - - +
14A ARG 3.1 0.4 - - - -
15A ALA* 1.3 77.3 - - - +
17A LEU* 1.3 68.4 - - - +
19A GLN* 3.3 9.5 + - - -
20A HIS* 2.9 64.7 + + + -
23A HIS 5.0 0.4 - - - -
24A PRO* 4.7 4.0 - - + -
25A TYR 3.9 9.9 - - - -
26A PRO* 3.4 43.7 - - + -
30A GLN* 3.3 39.9 - - + +
33A GLN* 6.0 6.1 - - - +
34A LEU* 4.1 30.9 - - + +
49A PHE* 3.6 20.0 - + - -
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Residues in contact with LEU 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 MET 3.1 13.8 + - - +
14A ARG* 3.0 10.4 + - - +
16A TRP* 1.3 78.2 - - + +
18A PHE* 1.3 67.1 + - + +
19A GLN 3.0 3.8 - - - -
20A HIS 2.8 31.9 + - - +
21A LEU* 3.6 8.9 + - + +
24A PRO* 4.4 19.7 - - + -
48A TRP* 4.4 5.4 - - + -
49A PHE* 4.0 23.1 - - + -
52A ALA* 4.2 14.4 - - + +
53A ARG* 5.7 2.5 - - + -
56A ILE* 3.8 44.4 - - + -
57A VAL* 4.6 11.7 - - + -
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Residues in contact with PHE 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 ARG* 3.1 49.1 + - + +
15A ALA* 5.0 2.0 - - - +
17A LEU* 1.3 87.9 - - + +
19A GLN* 1.3 58.8 + - - +
20A HIS 3.2 0.6 + - - -
21A LEU* 3.5 37.5 + - + +
56A ILE* 3.7 26.7 - - + -
60A MET* 4.7 5.6 - - + -
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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