Contacts of the strand formed by residues 640 - 649 (chain F) in PDB entry 2W3S
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 640 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357E PHE* 3.0 22.5 - - - -
457E VAL* 3.8 6.5 - - - +
632F VAL 3.2 14.8 - - - +
633F ILE* 3.5 13.7 - - + -
638F GLY 2.8 23.0 + - - -
639F GLU* 1.3 78.9 - - - +
641F ARG* 1.3 63.3 + - - +
642F ILE* 6.2 0.5 - - - +
676F THR* 5.2 6.4 - - - +
677F THR* 6.0 1.7 - - - +
743F LEU* 4.0 21.0 - - + +
761F ALA 4.7 3.3 + - - +
762F THR 4.6 0.8 - - - -
763F PRO* 4.0 15.2 - - - +
766F VAL* 3.9 12.5 - - - +
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Residues in contact with ARG 641 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E PHE* 3.9 16.4 - - + -
457E VAL* 3.5 36.8 + - + -
458E LEU* 3.5 35.5 + - + +
460E VAL 4.0 11.3 + - - -
631F VAL* 3.2 4.9 - - - -
632F VAL* 2.9 35.2 + - + +
640F ASN* 1.3 80.1 + - - +
642F ILE* 1.3 66.3 + - - +
643F LEU* 3.4 6.2 + - + +
702F SER* 4.6 10.2 + - - -
703F ASP* 6.1 2.7 - - - +
704F ARG 5.9 0.2 - - - -
706F ARG* 3.3 57.9 - - - +
743F LEU* 5.5 0.2 - - - +
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Residues in contact with ILE 642 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629F THR* 3.6 12.1 - - + -
630F GLU 3.5 5.4 - - - +
631F VAL* 3.7 17.3 - - + -
640F ASN* 6.2 0.4 - - - +
641F ARG* 1.3 72.0 - - - +
643F LEU* 1.3 61.8 + - - +
644F ARG 4.2 1.8 - - - +
645F THR* 3.6 24.0 - - - +
668F TYR* 3.9 7.0 - - + +
672F ALA* 4.0 14.8 - - + -
676F THR* 5.3 8.1 - - + +
703F ASP 4.9 13.1 + - - +
704F ARG 4.5 1.6 - - - +
705F PRO* 3.4 16.9 - - + +
706F ARG* 3.3 19.1 + - - +
739F ALA* 3.7 24.9 - - + -
743F LEU* 6.2 2.2 - - + -
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Residues in contact with LEU 643 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460E VAL* 3.9 13.7 - - + +
461E MET 3.3 30.1 - - - +
462E PRO* 3.7 15.1 - - + +
446F ARG* 3.7 17.5 - - - +
630F GLU* 2.7 34.8 + - - +
631F VAL 4.0 1.6 - - - -
632F VAL* 3.6 39.9 - - + +
641F ARG* 3.4 6.5 + - - +
642F ILE* 1.3 71.3 - - - +
644F ARG* 1.3 60.3 + - + +
706F ARG* 3.0 20.6 + - + +
707F ILE 2.9 22.2 + - - -
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Residues in contact with ARG 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E PRO 5.1 4.7 - - - -
424F SER 4.5 3.4 + - - -
425F ALA* 3.5 19.6 + - - +
426F ASN* 5.3 2.4 - - - +
430F ARG* 3.3 38.3 + - - +
628F ILE 3.7 1.0 - - - +
629F THR* 3.3 2.4 - - - +
630F GLU* 2.8 41.1 + - + +
642F ILE* 3.5 2.3 - - - -
643F LEU* 1.3 82.5 - - + +
645F THR* 1.3 67.4 + - - +
646F ASP* 2.7 40.7 + - - +
705F PRO* 4.7 0.7 - - - -
707F ILE* 3.3 41.7 - - + +
709F ASN* 4.0 8.6 - - - +
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Residues in contact with THR 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627F ALA* 4.5 1.6 - - + -
628F ILE 3.3 9.0 - - - +
629F THR* 3.8 2.8 - - - +
642F ILE* 3.6 3.8 - - - +
644F ARG* 1.3 76.7 + - - +
646F ASP* 1.3 60.8 + - - +
647F ILE* 3.7 24.5 - - + -
668F TYR* 2.9 46.0 + - + +
705F PRO* 3.3 23.1 - - - +
707F ILE 2.8 11.7 + - - +
708F PHE* 4.0 3.5 - - + -
709F ASN* 2.7 32.4 + - - +
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Residues in contact with ASP 646 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F LEU* 3.6 13.0 - - + +
424F SER 5.2 0.3 - - - +
425F ALA* 3.8 21.8 - - + +
430F ARG* 2.9 18.2 + - - -
627F ALA* 3.3 2.8 - - - -
628F ILE* 2.8 35.8 + - + +
644F ARG* 2.7 45.2 + - - +
645F THR* 1.3 71.4 - - - +
647F ILE* 1.3 60.8 + - - +
709F ASN* 2.9 28.1 + - + +
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Residues in contact with ILE 647 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F LEU* 4.2 2.9 - - - -
626F ALA 3.5 7.2 - - - +
627F ALA* 3.7 16.6 - - + -
645F THR* 3.7 18.6 - - + -
646F ASP* 1.3 77.5 - - - +
648F LEU* 1.3 67.3 + - - +
649F HIS* 4.0 2.7 - - + +
664F ILE* 4.0 14.6 - - + -
668F TYR* 3.9 22.4 - - + -
708F PHE* 3.9 13.7 - - + -
709F ASN 2.5 19.6 + - - +
710F VAL* 4.1 11.9 - - + -
711F ALA* 2.7 33.4 + - - +
735F LEU* 3.2 37.2 - - + -
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Residues in contact with LEU 648 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F LEU* 3.4 47.5 - - + +
420F ARG* 4.0 21.8 - - + -
421F LEU* 4.0 19.7 - - + +
424F SER* 5.9 0.2 - - - +
625F GLY* 3.4 2.9 - - - -
626F ALA 3.1 28.0 + - - -
647F ILE* 1.3 74.3 - - - +
649F HIS* 1.3 58.4 + - - +
711F ALA* 3.2 18.4 - - + +
712F LEU 3.7 31.6 - - - +
713F TRP* 3.8 18.4 - - + +
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Residues in contact with HIS 649 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F LEU* 4.9 0.2 - - - -
453F VAL* 5.0 2.0 - - + -
623F ALA* 4.9 1.0 - - - +
624F TYR 3.4 20.1 + - - -
625F GLY* 3.7 9.5 - - - -
647F ILE* 4.1 10.5 - - + -
648F LEU* 1.3 74.5 - - - +
650F ASP* 1.3 80.0 + - - +
651F ALA 3.7 2.0 + - - -
664F ILE* 3.7 37.9 - - + -
711F ALA 2.8 7.5 + - - +
712F LEU* 3.1 8.7 - - - +
713F TRP* 2.6 31.8 + - - -
728F VAL* 4.5 10.6 - - + +
731F PRO* 3.9 16.2 - - + +
732F PRO* 3.8 36.9 - - + +
735F LEU* 4.2 9.2 - - + +
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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