Contacts of the helix formed by residues 3 - 11 (chain A) in PDB entry 1BRW
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 MET 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG* 1.3 70.5 - - - +
4A VAL* 1.3 65.3 + - - +
6A LEU* 3.0 8.9 + - - +
7A ILE* 2.9 25.9 + - + +
23A TRP* 3.8 20.5 - - + -
24A ILE* 4.1 25.6 - - + -
33A ILE* 3.8 28.5 - - + -
37A GLN* 3.7 55.6 - - + +
38A MET* 4.2 8.7 - - - -
41A LEU* 4.0 26.9 - - + -
1366B ALA* 5.8 1.4 + - - +
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Residues in contact with VAL 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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2A ARG* 3.8 30.1 - - + +
3A MET* 1.3 77.4 - - - +
5A ASP* 1.3 70.1 + - - +
7A ILE* 3.3 11.6 + - - +
8A ALA* 3.0 28.8 + - - +
37A GLN* 3.3 13.2 - - - +
1169B ASP 5.1 3.4 - - - +
1170B VAL* 3.0 41.3 - - + +
1171B THR 4.9 0.7 - - - +
1172B ALA* 4.0 8.0 - - + +
1365B ARG 5.2 1.3 - - - +
1366B ALA* 3.5 13.7 - - - +
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Residues in contact with ASP 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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2A ARG* 2.8 49.2 + - - +
4A VAL* 1.3 83.8 - - - +
6A LEU* 1.3 62.0 + - + +
8A ALA* 3.5 8.2 - - - +
9A LYS* 3.1 30.2 + - + +
1356B THR* 4.1 8.0 - - - +
1360B TRP* 2.8 35.9 + - + -
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Residues in contact with LEU 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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1A MET* 4.1 17.7 - - + -
2A ARG 3.5 10.5 - - - +
3A MET* 3.0 9.0 + - - +
5A ASP* 1.3 79.5 - - + +
7A ILE* 1.3 64.2 + - - +
8A ALA 3.2 0.2 - - - -
9A LYS* 3.2 15.6 + - + +
10A LYS* 3.2 19.9 + - - +
16A LEU* 3.8 12.9 - - + +
20A GLU* 3.6 39.5 - - + +
23A TRP* 3.9 22.0 - - + -
24A ILE* 3.7 36.3 - - + -
41A LEU* 4.7 2.7 - - - +
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Residues in contact with ILE 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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3A MET* 2.9 35.4 + - + +
4A VAL* 3.5 13.2 - - - +
6A LEU* 1.3 74.5 - - - +
8A ALA* 1.3 58.4 + - - +
10A LYS* 3.2 4.9 + - - +
11A ARG* 2.9 26.7 + - - +
37A GLN* 3.6 35.9 - - + +
40A ALA* 4.4 1.6 - - + +
41A LEU* 4.2 30.5 - - + +
44A ALA* 4.6 1.9 - - + +
1043B MET* 3.8 16.6 - - + -
1171B THR* 3.6 29.6 - - - +
1172B ALA* 3.8 5.8 - - + -
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Residues in contact with ALA 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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4A VAL 3.0 13.5 + - - +
5A ASP* 3.5 13.0 - - - +
7A ILE* 1.3 77.9 - - - +
9A LYS* 1.3 62.2 + - - +
11A ARG* 3.3 21.7 + - - +
12A ASP* 3.0 31.9 + - - +
1172B ALA* 3.9 13.9 - - + +
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Residues in contact with LYS 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 ASP 3.1 19.5 + - - +
6A LEU* 3.2 16.1 + - + +
8A ALA* 1.3 76.2 - - - +
10A LYS* 1.3 61.1 + - - +
12A ASP 3.4 1.6 + - - -
13A GLY 3.4 2.6 + - - -
14A LYS* 2.8 67.7 + - + +
15A ALA 3.3 22.2 + - - -
16A LEU* 4.0 10.3 - - + -
17A THR* 4.6 6.5 - - - +
20A GLU* 2.9 39.7 + - - +
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Residues in contact with LYS 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 LEU 3.2 8.9 + - - +
7A ILE 3.6 7.0 - - - +
9A LYS* 1.3 77.9 - - - +
11A ARG* 1.3 59.7 + - - +
13A GLY* 2.9 18.6 + - - -
14A LYS 3.2 16.4 + - - -
16A LEU* 4.3 15.2 - - + +
41A LEU* 4.0 12.8 - - + -
44A ALA* 3.9 20.0 - - + +
45A ILE* 4.0 17.9 - - + -
48A ARG* 3.1 26.2 + - + +
49A GLY 3.0 28.3 + - - +
50A MET* 4.2 8.0 - - - +
54A GLU* 3.1 31.3 + - - -
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Residues in contact with ARG 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 ILE 2.9 16.7 + - - +
8A ALA* 3.5 17.1 - - - +
10A LYS* 1.3 74.5 - - - +
12A ASP* 1.3 89.9 + - - +
44A ALA* 4.3 5.6 - - + +
48A ARG* 3.0 26.2 + - - +
1043B MET* 4.3 11.4 - - + -
1046B TYR* 3.6 39.7 + - + -
1047B PHE* 3.7 15.9 - - + -
1172B ALA* 3.0 42.9 + - - +
1174B VAL* 5.0 4.8 - - - +
1175B ASN* 3.5 27.8 + - - +
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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