Contacts of the strand formed by residues 653 - 658 (chain A) in PDB entry 2WKP
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 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A PHE* 3.4 9.0 - - + +
623A ILE* 3.7 34.5 - - + -
641A TYR* 4.2 16.8 - - + -
644A VAL* 4.1 17.0 - - + -
645A ARG* 3.4 37.2 - - - +
651A THR 3.5 3.3 + - - +
652A PRO* 1.3 78.7 - - - +
654A ILE* 1.3 77.7 + - - +
655A LEU 4.2 1.8 - - - +
692A ILE* 4.3 10.1 - - + +
693A GLY 5.3 0.4 + - - -
694A ALA* 3.3 15.4 - - + +
695A VAL* 2.9 30.9 + - - +
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Residues in contact with ILE 654 (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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620A VAL* 4.3 8.5 - - + -
621A PHE 2.8 7.3 + - - -
622A LEU* 3.4 15.5 - - + -
623A ILE 2.9 24.9 + - - +
653A ILE* 1.3 80.3 - - - +
655A LEU* 1.3 65.6 + - - +
656A VAL* 3.7 18.6 + - + -
695A VAL* 3.9 14.4 - - + -
696A LYS* 3.6 16.6 - - + +
698A LEU* 4.2 16.4 - - + -
711A VAL 4.3 2.0 - - - +
714A GLU* 3.5 16.4 - - + +
715A ALA* 3.4 42.8 - - + +
718A ALA* 4.5 2.7 - - + -
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Residues in contact with LEU 655 (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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623A ILE* 3.4 20.0 - - + +
625A PHE* 3.9 21.8 - - + -
636A VAL* 3.8 25.8 - - + -
653A ILE* 4.8 1.1 - - - -
654A ILE* 1.3 72.1 - - - +
656A VAL* 1.3 61.6 + - - +
685A GLY 3.6 12.6 - - - +
688A MET* 3.7 16.4 - - + -
689A ALA* 3.5 28.7 - - + +
692A ILE* 4.4 5.8 - - + -
694A ALA* 4.0 14.1 - - + +
696A LYS 3.0 12.7 + - - +
697A TYR* 3.4 14.9 - - + -
698A LEU 2.9 25.5 + - - -
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Residues in contact with VAL 656 (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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562A LEU* 4.7 3.8 - - + -
622A LEU* 4.2 14.8 - - + -
623A ILE 2.8 13.3 + - - +
624A CYS* 3.2 11.7 - - - +
625A PHE* 3.0 30.5 + - - +
654A ILE* 3.9 23.8 - - + +
655A LEU* 1.3 79.6 - - - +
657A GLY* 1.3 61.9 + - - +
658A THR* 3.8 9.5 + - + -
698A LEU* 3.3 8.3 - - + +
700A CYS* 3.9 27.1 - - - -
711A VAL* 4.1 25.8 - - + -
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Residues in contact with GLY 657 (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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625A PHE* 3.4 23.2 - - - -
627A LEU* 3.8 18.4 - - - +
656A VAL* 1.3 74.0 - - - +
658A THR* 1.3 60.4 + - - -
697A TYR* 4.1 4.0 - - - -
698A LEU 2.8 13.2 + - - -
699A GLU* 3.3 3.4 - - - -
700A CYS 2.9 27.5 + - - +
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Residues in contact with THR 658 (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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557A VAL 2.6 29.3 + - - +
558A GLY* 5.0 2.7 - - - -
562A LEU* 3.8 30.7 - - + -
624A CYS* 4.1 18.6 - - + -
625A PHE 2.9 21.5 + - - +
626A SER* 3.3 5.5 - - - -
627A LEU* 3.0 25.6 + - - +
656A VAL* 4.1 5.8 - - + -
657A GLY* 1.3 74.9 - - - -
659A LYS* 1.3 68.4 + - - +
660A LEU 3.2 3.3 + - - -
700A CYS* 3.5 7.0 - - - -
1724A GTP 5.8 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