Contacts of the strand formed by residues 680 - 684 (chain B) in PDB entry 1B0P
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 ASN 680 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1216A ARG 3.2 1.8 + - - -
1217A ALA* 2.8 38.3 + - - +
1222A GLN 5.9 0.2 - - - -
1223A GLN* 4.6 4.4 - - - +
1226A LEU* 3.2 32.4 - - - +
678B ALA* 3.8 0.3 - - - +
679B ILE* 1.3 97.9 - - - +
681B VAL* 1.3 65.4 + - - +
747B GLY* 3.1 27.7 - - - -
764B MET* 4.3 12.3 - - + +
765B GLN 3.0 14.6 - - - +
766B PRO* 3.5 14.0 - - - +
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Residues in contact with VAL 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678B ALA* 3.6 21.5 - - + -
680B ASN* 1.3 79.3 - - - +
682B PRO* 1.3 79.0 - - + +
683B GLN 3.7 0.2 + - - -
740B ILE* 4.9 0.2 - - + -
742B THR* 3.8 22.2 - - + +
745B CYS* 3.9 9.6 - - + -
764B MET* 4.1 2.2 - - - -
765B GLN* 2.7 29.3 + - - +
767B LEU* 3.7 25.1 - - + -
770B GLN* 3.5 34.5 - - + -
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Residues in contact with PRO 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681B VAL* 1.3 97.9 - - + +
683B GLN* 1.3 58.5 + - - +
684B TRP 4.3 0.4 - - - -
740B ILE* 3.6 34.5 - - + +
742B THR* 5.0 0.7 - - - +
745B CYS* 3.7 16.8 - - - -
751B CYS* 3.7 20.0 - - - -
762B LEU* 4.0 17.0 - - + -
763B VAL 3.4 7.2 - - - +
764B MET* 3.3 26.9 - - + -
770B GLN* 4.3 2.6 - - - +
774B GLN* 6.1 0.3 - - - +
1234B SF4 3.9 9.9 - - - -
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Residues in contact with GLN 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682B PRO* 1.3 73.6 - - - +
684B TRP* 1.3 72.4 + - - +
685B VAL* 3.7 15.8 + - - +
740B ILE* 4.8 1.6 - - - -
762B LEU* 3.5 4.4 - - - -
763B VAL* 2.8 37.2 + - - +
765B GLN* 3.6 25.5 + - + +
770B GLN* 3.4 32.2 + - - +
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Residues in contact with TRP 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B GLN* 1.3 85.6 - - - +
685B VAL* 1.3 58.9 + - - +
686B PRO* 3.4 34.1 - - + +
689B CYS* 3.2 32.6 - - + +
722B THR 3.4 23.3 - - - -
724B LEU* 3.6 31.9 - - + -
736B PHE* 3.6 25.4 - + - -
737B ARG* 3.6 17.5 - - + +
738B ILE* 3.6 46.4 - - + +
740B ILE* 4.6 6.7 - - + +
761B ALA* 3.2 19.7 - - + -
762B LEU* 3.8 8.0 - - + +
1233B SF4 3.5 14.1 - - - -
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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