Contacts of the strand formed by residues 85 - 92 (chain A) in PDB entry 1BRP
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 LYS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A VAL 5.1 0.6 + - - -
7A SER* 5.7 4.0 + - - +
9A PHE 4.5 6.8 + - - -
11A VAL* 3.8 21.9 - - + +
79A ASP* 4.4 0.2 - - - -
80A THR* 2.6 37.3 + - + +
82A ASP* 2.8 39.2 + - + +
83A PRO 3.2 0.4 - - - -
84A ALA* 1.3 84.3 - - - +
86A PHE* 1.3 68.0 + - - +
104A HIS 3.8 2.5 - - - -
105A TRP* 3.3 58.4 - - + +
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Residues in contact with PHE 86 (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 PHE* 3.6 18.6 - + - -
17A LYS* 3.8 22.2 - - + -
53A MET* 3.4 33.0 - - + -
77A PHE* 3.8 30.1 - + + -
78A THR 3.2 7.4 - - - +
79A ASP* 3.9 21.5 - - - -
80A THR* 3.7 6.5 - - - -
82A ASP 5.7 0.2 - - - -
83A PRO 3.2 28.3 - - - -
84A ALA 3.8 9.0 - - - -
85A LYS* 1.3 79.1 - - - +
87A LYS* 1.3 64.4 + - - +
103A ASP* 3.6 5.9 - - - +
104A HIS* 2.9 38.6 + + - +
105A TRP* 4.5 1.7 - - - -
106A ILE* 4.1 8.1 - - + -
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Residues in contact with LYS 87 (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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77A PHE* 3.4 0.9 - - - -
78A THR* 2.5 57.0 + - + +
79A ASP 5.2 1.1 - - - +
80A THR* 4.2 17.5 - - + -
86A PHE* 1.3 75.3 - - - +
88A MET* 1.3 58.7 + - - +
89A LYS 4.1 0.4 - - - -
101A ASN* 3.6 23.3 - - - +
102A ASP 3.9 1.8 - - - -
103A ASP* 3.2 24.9 + - - +
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Residues in contact with MET 88 (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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75A GLY* 4.3 3.8 - - - -
76A THR 3.7 3.8 - - - +
77A PHE* 3.7 40.2 - - + -
86A PHE 3.9 0.4 - - - -
87A LYS* 1.3 71.5 - - - +
89A LYS* 1.3 70.7 - - - +
90A TYR* 3.7 11.2 + - + -
101A ASN* 3.3 4.1 - - - +
102A ASP* 2.6 56.6 + - + +
104A HIS* 4.0 13.5 - - + +
133A TYR* 3.7 22.7 - - - +
183A RTL 3.5 51.4 - - + -
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Residues in contact with LYS 89 (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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75A GLY* 3.2 1.6 - - - -
76A THR* 2.8 43.0 + - - +
78A THR* 5.2 3.8 + - - +
87A LYS 4.0 1.2 + - - -
88A MET* 1.3 71.2 - - - +
90A TYR* 1.3 63.3 + - - +
91A TRP* 3.5 28.8 - - + -
100A GLY 3.6 9.9 - - - +
101A ASN* 3.8 16.7 + - + +
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Residues in contact with TYR 90 (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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73A MET* 3.5 23.3 - - + -
74A VAL 3.1 11.9 - - - +
75A GLY* 4.0 0.2 - - - -
88A MET* 4.2 18.4 - - + -
89A LYS* 1.3 75.2 - - - +
91A TRP* 1.3 70.7 + - - +
98A GLN* 2.6 53.4 + - + +
99A LYS* 3.5 6.7 + - - +
100A GLY* 2.9 57.1 + - - +
101A ASN 3.8 2.7 - - - -
102A ASP* 3.9 18.3 + - - -
121A ARG* 4.1 7.3 + - - -
183A RTL 3.7 34.8 - - + -
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Residues in contact with TRP 91 (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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73A MET* 3.6 6.3 - - - -
74A VAL* 2.7 64.8 + - + +
76A THR* 3.1 31.2 - - + -
89A LYS* 3.5 46.4 - - + -
90A TYR* 1.3 94.8 - - - +
92A GLY* 1.3 78.7 + - - +
93A VAL* 5.3 0.2 - - - -
98A GLN 3.7 10.3 - - - -
99A LYS* 4.0 20.2 - - + +
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Residues in contact with GLY 92 (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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72A ASP 3.7 12.3 - - - -
73A MET* 3.8 11.9 - - - -
91A TRP* 1.3 94.3 - - - +
93A VAL* 1.3 66.0 + - - -
94A ALA 3.4 9.7 + - - +
97A LEU* 4.0 12.3 + - - -
98A GLN 3.6 8.1 + - - -
99A LYS* 5.0 3.8 + - - +
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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