Contacts of the strand formed by residues 9 - 15 (chain A) in PDB entry 4BC4
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 CYS 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 1.3 75.9 - - - +
10A CYS* 1.3 65.3 + - - +
11A LEU* 4.8 0.2 - - - -
24A ALA* 4.4 3.8 - - - -
25A VAL 3.1 15.9 - - - +
32A PHE* 3.7 30.1 - - + -
84A PHE* 4.1 12.3 - - - -
88A GLN* 2.9 23.3 + - - -
89A VAL* 3.4 23.6 - - - -
90A LEU* 2.8 32.5 + - - +
478A PHE* 4.1 5.2 - - - -
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Residues in contact with CYS 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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9A CYS* 1.3 77.8 - - - +
11A LEU* 1.3 63.8 + - - +
12A GLY 4.1 0.3 + - - -
23A VAL 3.9 0.3 - - - +
24A ALA* 3.5 2.4 - - - -
25A VAL* 2.9 33.3 + - - +
89A VAL* 4.8 0.2 - - - -
91A ALA* 3.2 22.4 - - - +
474A ALA* 4.1 4.6 - - - +
477A ALA* 3.8 17.5 - - + -
478A PHE* 3.6 32.2 - - + -
481A LEU* 3.4 32.5 - - - -
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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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9A CYS* 4.8 0.4 - - - -
10A CYS* 1.3 74.9 - - - +
12A GLY* 1.3 57.5 + - - +
13A TRP* 3.7 34.5 - - + +
22A VAL* 4.1 4.3 - - + -
23A VAL 3.4 5.6 - - - +
24A ALA* 3.8 15.3 - - + -
79A MSE 4.1 16.8 - - + -
84A PHE* 3.7 28.5 - - + -
86A PHE* 4.7 0.4 - - + -
89A VAL* 3.9 16.4 - - + +
91A ALA 3.2 5.7 + - - -
92A LEU* 3.3 7.7 - - + -
93A SER 3.1 26.2 + - - -
268A PHE* 3.9 31.0 - - + -
474A ALA* 4.1 7.4 - - - -
477A ALA* 4.4 0.5 - - - +
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Residues in contact with GLY 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 LEU* 1.3 73.2 - - - +
13A TRP* 1.3 61.5 + - - -
22A VAL* 3.3 3.3 - - - -
23A VAL 2.9 35.5 + - - -
93A SER 3.5 4.3 - - - -
470A CYS* 3.2 32.6 - - - +
473A SER* 3.8 0.7 - - - -
474A ALA* 3.6 12.2 - - - +
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Residues in contact with TRP 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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11A LEU* 3.7 31.1 - - + +
12A GLY* 1.3 76.0 - - - -
14A ASP* 1.3 62.6 + - - +
15A PHE* 4.1 17.0 - + + -
20A VAL* 4.1 11.0 - - + -
21A LYS 3.4 11.0 - - - -
22A VAL* 3.6 28.9 - - + -
72A LEU* 3.7 17.0 - - + -
75A ILE* 3.6 28.5 - - + -
76A LEU* 3.9 18.8 - - + -
79A MSE 4.0 9.9 - - - -
92A LEU* 4.1 13.9 - - + +
93A SER 3.0 23.7 + - - +
94A GLY* 3.2 6.4 - - - -
95A ALA* 2.8 23.5 + - - +
204A PHE* 3.4 34.7 - + - -
268A PHE* 5.2 0.2 - + - -
277A PHE* 4.3 2.2 - + + -
470A CYS* 4.1 2.3 - - - -
473A SER* 3.5 6.2 + - - -
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Residues in contact with ASP 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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13A TRP* 1.3 76.4 - - - +
15A PHE* 1.3 64.2 + - - +
16A SER* 3.3 27.9 + - - -
19A GLN 3.7 0.5 - - - +
20A VAL* 3.4 2.3 - - - -
21A LYS* 2.8 44.7 + - + +
95A ALA* 3.4 14.2 - - - +
96A GLY 4.7 0.2 + - - -
280A ASP* 4.2 9.2 - - - +
469A ALA* 3.6 21.8 - - + +
470A CYS* 3.5 23.9 - - - +
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Residues in contact with PHE 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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13A TRP* 4.1 22.0 - + + -
14A ASP* 1.3 71.9 - - - +
16A SER* 1.3 61.4 + - - +
19A GLN 4.2 2.2 - - - -
20A VAL* 3.9 36.6 - - + -
39A PHE* 6.0 0.2 - - - -
68A TRP* 4.2 21.5 - + + -
72A LEU* 4.2 29.6 - - + -
95A ALA 2.8 16.5 + - - +
96A GLY* 3.5 0.4 - - - -
97A GLN* 2.9 32.5 + - - +
196A VAL* 3.8 18.2 - - + -
199A PHE* 4.6 16.6 - + - -
200A ALA* 3.6 33.2 - - + -
203A LEU* 4.9 2.0 - - + -
204A PHE* 4.4 6.1 - + - -
277A PHE* 4.6 0.7 - + - -
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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