Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 1BWN
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 ILE 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 5.0 4.9 - - + -
56A ILE* 3.6 25.6 - - + -
57A ASP 3.9 1.1 - - - +
58A VAL* 3.2 30.9 + - + +
59A GLU 3.4 0.5 - - - +
60A LYS* 1.3 79.5 - - - +
62A THR* 1.3 63.5 + - - +
63A CYS 3.6 9.0 - - - +
64A VAL* 3.9 22.0 - - + -
104A VAL* 3.7 20.4 - - + -
105A VAL 3.4 11.9 - - - +
106A TYR* 3.8 0.7 - - - -
128A LEU* 4.5 14.8 - - + -
132A ILE* 3.9 20.0 - - + -
135A ASN* 3.0 20.4 + - - +
137A ASP 5.0 0.7 - - - -
138A LEU* 3.7 7.8 + - - +
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Residues in contact with THR 62 (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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60A LYS 3.5 12.1 - - - +
61A ILE* 1.3 78.7 - - - +
63A CYS* 1.3 62.7 + - - +
105A VAL* 2.7 25.5 + - - +
106A TYR* 4.3 6.0 - - - -
107A ASP* 4.5 7.2 - - + +
137A ASP* 3.3 34.5 - - + +
138A LEU* 3.4 13.8 - - - +
139A VAL* 3.1 33.8 + - + +
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Residues in contact with CYS 63 (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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61A ILE* 3.5 4.1 - - - +
62A THR* 1.3 84.6 + - - +
64A VAL* 1.3 68.6 + - - +
65A GLU* 3.7 28.7 - - - -
103A GLN* 5.8 0.2 - - - -
105A VAL* 2.5 50.8 + - + +
132A ILE* 4.6 4.0 - - - -
139A VAL* 3.7 20.9 - - + +
141A LYS 5.7 0.2 - - - -
142A TYR* 3.8 23.3 - - + -
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Residues in contact with VAL 64 (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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61A ILE* 3.9 18.4 - - + -
63A CYS* 1.3 80.5 - - - +
65A GLU* 1.3 66.6 + - - +
102A PHE* 4.7 3.4 - - + -
103A GLN 3.4 11.7 - - - +
104A VAL* 4.2 12.8 - - + -
125A ILE* 3.9 28.2 - - + +
128A LEU* 4.0 38.1 - - + -
129A LYS* 3.0 32.6 + - + +
132A ILE* 4.2 12.4 - - + +
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Residues in contact with GLU 65 (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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63A CYS* 3.7 15.2 - - - -
64A VAL* 1.3 82.4 + - - +
66A THR* 1.3 63.9 + - - +
102A PHE* 3.2 4.0 - - - +
103A GLN* 2.9 33.3 + - - +
125A ILE* 4.0 11.8 - - - +
129A LYS* 2.9 22.2 + - - +
142A TYR* 3.4 41.6 + - + -
168A LEU* 4.2 24.1 - - - +
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Residues in contact with THR 66 (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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65A GLU* 1.3 84.7 + - - +
67A VAL* 1.3 64.3 + - - +
101A PRO 3.7 5.8 - - - -
102A PHE* 4.1 1.3 - - - +
103A GLN* 3.0 15.4 - - - +
121A ARG* 3.8 31.4 - - - +
125A ILE* 3.6 20.6 - - + +
142A TYR* 3.8 10.2 + - - -
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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