Contacts of the strand formed by residues 2 - 10 (chain D) in PDB entry 3BRW
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 ARG 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 1.3 74.6 - - - +
3D GLU* 1.3 70.6 + - - +
4D TYR* 3.3 32.1 + - + +
49D GLN* 5.2 10.2 - - + +
50D GLN 4.0 5.4 + - - +
51D CYS* 4.6 0.6 - - - +
52D MET* 3.1 27.5 + - - +
76D GLN* 5.3 2.8 - - - +
165D ILE* 3.5 30.1 + - - +
166D ASN* 2.9 32.8 + - - +
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Residues in contact with GLU 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 5.3 1.8 - - + +
2D ARG* 1.3 84.5 + - - +
4D TYR* 1.3 63.7 + - - +
5D LYS* 5.1 10.4 - - + +
41D ARG* 4.4 22.0 + - - +
52D MET* 3.5 18.9 - - + +
54D GLU* 5.6 4.2 - - - +
76D GLN* 3.7 16.5 + - - +
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Residues in contact with TYR 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 3.3 37.8 + - + +
3D GLU* 1.3 75.3 - - - +
5D LYS* 1.3 63.0 + - - +
6D LEU* 3.5 5.6 + - + +
49D GLN* 5.4 4.5 - - - +
51D CYS* 3.5 37.0 - - + -
52D MET 3.4 5.5 + - - -
53D LEU* 3.7 18.6 - - + -
54D GLU* 2.9 29.2 + - - +
76D GLN* 4.0 3.8 - - - +
162D VAL* 3.5 23.4 - - + +
165D ILE* 3.5 44.6 - - + -
166D ASN* 2.4 33.7 + - - -
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Residues in contact with LYS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU* 5.1 11.4 - - + +
4D TYR* 1.3 71.9 - - - +
6D LEU* 1.3 61.2 + - - +
7D VAL* 5.0 1.1 - - + -
54D GLU* 3.7 29.6 - - + +
74D ASN* 3.9 38.7 - - + +
75D GLY* 3.9 3.2 - - - -
76D GLN* 2.9 52.8 + - - +
77D GLY 3.4 5.0 + - - -
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 4.3 10.8 - - + +
5D LYS* 1.3 75.3 - - - +
7D VAL* 1.3 65.0 + - - +
8D VAL 4.2 0.2 - - - -
53D LEU* 4.2 11.0 - - + -
54D GLU 2.8 16.3 + - - +
55D ILE* 4.0 16.8 - - + -
56D LEU* 2.8 26.5 + - - +
77D GLY* 3.5 8.5 - - - +
158D PHE* 4.0 36.1 - - + +
161D LEU* 3.8 35.9 - - + -
162D VAL* 4.7 1.6 - - + +
165D ILE* 3.8 29.4 - - + -
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LYS* 4.7 1.3 - - + +
6D LEU* 1.3 81.2 - - - +
8D VAL* 1.3 61.0 + - - +
9D LEU* 3.8 18.9 + - + -
55D ILE* 5.6 0.2 - - - -
56D LEU* 3.8 21.1 - - + -
58D THR* 3.6 26.9 - - + -
71D TYR* 4.1 10.5 - - + +
75D GLY* 4.0 17.9 - - - -
77D GLY 2.9 8.9 + - - -
78D PHE* 3.3 30.7 - - + +
79D ALA* 2.9 25.8 + - - +
161D LEU* 5.9 0.4 - - - -
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU 4.2 0.6 - - - -
7D VAL* 1.3 71.2 - - - +
9D LEU* 1.3 62.5 + - - +
16D LYS* 3.8 20.9 - - + +
19D LEU* 5.6 4.0 - - + -
20D THR* 3.5 23.8 - - - +
55D ILE* 4.1 12.3 - - + +
56D LEU 3.0 15.6 + - - +
57D ASP* 3.9 10.1 - - - +
58D THR* 3.1 23.5 + - - +
79D ALA* 3.5 14.4 - - + +
81D VAL* 3.7 27.1 - - + -
157D ILE* 6.3 0.4 - - + -
158D PHE* 5.0 7.9 - - + -
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 3.8 23.8 - - + +
8D VAL* 1.3 73.0 - - - +
10D GLY* 1.3 58.1 + - - +
16D LYS* 3.4 8.7 - - - +
58D THR* 3.3 20.6 - - + +
68D ARG* 5.6 9.0 - - - +
71D TYR* 5.4 3.6 - - + -
72D MET* 4.1 28.3 - - + -
78D PHE* 4.4 6.3 - - + -
79D ALA 2.9 10.9 + - - +
80D LEU* 3.4 34.9 - - + -
81D VAL* 2.9 24.4 + - - +
96D LEU* 3.7 28.3 - - + -
100D ILE* 4.5 6.1 - - + -
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Residues in contact with GLY 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 1.3 78.0 - - - +
11D SER* 1.3 62.7 + - - -
14D VAL* 4.7 0.4 - - - -
16D LYS* 2.8 22.2 + - - +
58D THR* 4.4 0.2 + - - -
59D ALA 3.9 2.6 - - - +
60D GLY* 3.3 10.6 - - - +
68D ARG* 5.2 3.3 + - - +
81D VAL 3.6 14.8 - - - -
93D LEU* 4.7 3.4 - - - -
96D LEU* 4.0 17.4 - - - +
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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