Contacts of the strand formed by residues 643 - 648 (chain A) in PDB entry 3WOO
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 PRO 643 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A PHE* 3.7 14.6 - - + -
601A THR 3.4 7.4 - - - +
634A LEU 4.0 10.5 - - - +
636A ASP* 4.5 2.7 - - + -
639A ILE* 3.7 19.7 - - + -
641A SER 3.8 7.2 - - - +
642A VAL* 1.3 96.2 - - + +
644A VAL* 1.3 62.5 + - - +
697A ASP* 3.5 18.1 - - + +
699A ARG* 3.3 36.1 - - + +
700A TYR* 3.4 18.4 + - - +
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Residues in contact with VAL 644 (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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221A HIS* 3.9 24.5 - - - +
601A THR* 2.9 16.6 + - - +
602A THR 3.2 34.1 - - - +
603A LEU* 3.4 9.9 - - + +
606A VAL* 3.9 7.9 - - + -
642A VAL 4.0 1.1 - - - +
643A PRO* 1.3 77.3 - - - +
645A ASN* 1.3 72.6 + - - +
696A VAL* 3.7 1.0 - - - +
697A ASP* 2.9 25.7 + - - +
700A TYR* 3.7 42.7 - - + +
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Residues in contact with ASN 645 (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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218A TRP* 3.8 11.4 - - + -
220A ARG* 3.1 39.9 - - - +
222A THR 2.8 34.1 - - - +
600A PHE* 3.4 6.1 - - - -
601A THR* 2.9 24.9 + - - +
644A VAL* 1.3 89.9 - - - +
646A TYR* 1.3 67.3 + - - +
673A PHE* 3.3 19.8 - - - -
694A ILE* 4.3 2.2 - - + -
695A ALA 3.1 11.7 - - - +
696A VAL* 3.5 8.1 - - - -
697A ASP 4.4 0.7 - - - +
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Residues in contact with TYR 646 (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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218A TRP* 3.7 8.1 - - - -
261A LEU* 3.5 18.9 - - + +
267A VAL* 4.6 1.6 - - + -
586A VAL* 4.2 14.4 - - + -
599A PRO 3.0 15.0 - - - +
600A PHE* 3.7 20.0 - + + -
645A ASN* 1.3 77.2 - - - +
647A LEU* 1.3 71.1 + - - +
648A SER* 4.9 2.0 - - - -
661A VAL* 3.5 23.7 - - + +
669A VAL* 2.9 33.6 + - - +
670A GLY* 3.7 2.8 - - - -
693A MET* 3.5 6.0 - - + +
694A ILE* 3.5 5.0 - - - -
695A ALA* 2.9 50.2 + - + -
696A VAL 4.4 0.2 - - - -
697A ASP* 3.5 35.4 - - + -
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Residues in contact with LEU 647 (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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218A TRP* 3.3 59.5 - - + +
586A VAL* 3.5 12.3 - - - +
587A MET 3.0 33.9 + - - +
588A GLY* 4.0 12.3 - - - -
589A TYR* 4.0 15.3 - - + -
597A TYR* 4.1 2.2 - - + -
598A THR 3.6 10.5 - - - +
599A PRO 2.9 8.1 + - - +
646A TYR* 1.3 73.1 - - - +
648A SER* 1.3 62.9 + - - +
676A ASN* 4.9 1.1 - - + -
692A ARG* 3.9 17.5 - - + -
693A MET 3.3 5.8 - - - +
694A ILE* 3.9 18.2 - - + -
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Residues in contact with SER 648 (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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267A VAL* 3.9 14.4 - - - -
585A ASN 3.2 22.7 - - - -
586A VAL* 3.9 3.4 - - - -
587A MET 3.8 2.7 - - - -
646A TYR* 4.9 3.0 - - - -
647A LEU* 1.3 76.2 - - - +
649A ASP* 1.3 59.9 + - - +
650A LEU* 3.1 9.3 + - - +
692A ARG* 3.2 11.2 - - - -
693A MET* 2.9 61.2 + - - +
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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