Contacts of the strand formed by residues 640 - 650 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LYS 5.7 0.4 + - - -
357A PHE* 3.0 25.8 - - - -
457A VAL* 3.9 3.6 - - - -
632B VAL 3.1 18.4 - - - +
633B ILE* 4.0 11.2 - - + -
638B GLY 2.9 19.3 + - - +
639B GLU* 1.3 78.0 - - - +
641B ARG* 1.3 60.7 + - - +
676B THR* 5.2 6.1 - - - +
677B THR* 6.3 0.4 - - - +
743B LEU* 3.6 30.2 - - + +
761B ALA 4.7 5.7 + - - +
763B PRO* 4.2 17.8 - - - +
766B VAL* 4.7 1.9 - - - +
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Residues in contact with ARG 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PHE* 4.7 10.3 - - + -
457A VAL* 3.7 13.5 + - + +
458A LEU* 3.2 36.7 + - + +
460A VAL 3.1 25.9 + - - -
462A PRO* 4.9 2.4 - - - +
631B VAL* 3.1 7.7 - - - +
632B VAL* 3.0 38.7 + - + +
640B ASN* 1.3 79.6 - - - +
642B ILE* 1.3 78.3 + - - +
643B LEU* 3.7 12.5 + - - +
702B SER 4.9 6.7 + - - +
703B ASP* 6.1 2.0 - - - +
704B ARG 6.1 0.4 - - - +
706B ARG* 2.6 46.4 - - - +
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Residues in contact with ILE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B THR* 3.3 25.6 - - + -
630B GLU 3.5 5.6 - - - +
631B VAL* 3.7 13.9 - - + -
641B ARG* 1.3 89.5 - - - +
643B LEU* 1.3 63.0 + - - +
644B ARG 3.8 2.7 - - - +
645B THR* 3.5 16.2 - - - +
668B TYR* 4.2 15.9 - - + +
672B ALA* 4.3 19.1 - - + -
676B THR* 5.6 6.7 - - + -
703B ASP 4.7 15.4 + - - +
704B ARG 4.5 2.1 - - - +
705B PRO* 3.9 16.3 - - + +
706B ARG* 3.9 10.7 + - - +
739B ALA* 4.4 6.5 - - + -
743B LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 643 (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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460A VAL* 4.0 25.8 - - + +
461A MET 5.1 0.7 - - - +
462A PRO* 3.6 26.6 - - + +
446B ARG* 3.7 20.6 - - - +
630B GLU* 2.6 38.3 + - - +
631B VAL 3.9 7.0 - - - +
632B VAL* 3.7 32.5 - - + -
641B ARG* 3.9 19.3 - - - +
642B ILE* 1.3 73.3 - - - +
644B ARG* 1.3 59.8 + - + +
706B ARG* 3.1 16.3 - - - +
707B ILE 2.9 21.1 + - - -
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Residues in contact with ARG 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A PRO* 5.5 2.2 - - + -
424B SER 4.4 3.8 + - - -
425B ALA* 3.3 22.8 + - - +
426B ASN* 5.1 3.2 - - - +
430B ARG* 3.5 42.8 - - - +
628B ILE 3.7 1.2 - - - +
629B THR* 3.5 0.3 - - - -
630B GLU* 2.7 38.2 + - + +
642B ILE* 3.7 2.0 - - - +
643B LEU* 1.3 83.3 - - + +
645B THR* 1.3 68.6 + - - +
646B ASP* 2.6 36.1 + - - +
705B PRO* 4.4 0.4 - - - -
707B ILE* 3.3 38.2 - - + +
709B ASN* 3.9 10.5 - - - +
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Residues in contact with THR 645 (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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627B ALA* 4.7 2.0 - - + -
628B ILE 3.4 5.2 - - - +
629B THR* 3.9 4.3 - - - +
642B ILE* 3.5 2.3 - - - +
644B ARG* 1.3 76.8 + - - +
646B ASP* 1.3 71.9 + - - +
647B ILE* 3.9 20.2 - - + -
668B TYR* 2.9 47.1 + - + +
705B PRO* 3.2 24.5 - - - +
707B ILE 2.8 10.6 + - - +
708B PHE* 4.4 6.7 - - + -
709B ASN* 2.9 25.9 + - - +
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Residues in contact with ASP 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 3.3 15.3 - - + +
424B SER* 4.6 2.6 + - - +
425B ALA* 3.7 28.0 - - + +
430B ARG* 3.3 7.8 + - - -
627B ALA* 3.3 3.5 - - - -
628B ILE* 3.1 32.2 + - + +
644B ARG* 2.6 46.1 + - - +
645B THR* 1.3 80.9 - - - +
647B ILE* 1.3 61.7 + - - +
709B ASN* 3.3 20.1 + - + +
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Residues in contact with ILE 647 (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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421B LEU* 3.8 4.2 - - - +
626B ALA 3.5 6.1 - - - +
627B ALA* 3.9 9.6 - - + -
645B THR* 3.9 10.8 - - + -
646B ASP* 1.3 75.3 - - - +
648B LEU* 1.3 71.6 + - - +
649B HIS* 4.1 4.0 - - + +
664B ILE* 3.8 26.9 - - + -
668B TYR* 3.8 29.6 - - + -
708B PHE* 3.8 22.7 - - + -
709B ASN 2.6 14.2 + - - +
710B VAL* 3.5 9.2 - - + -
711B ALA* 2.8 28.1 + - - +
735B LEU* 3.3 24.0 - - + -
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Residues in contact with LEU 648 (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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417B LEU* 3.2 47.0 - - + +
420B ARG* 3.8 33.0 - - + +
421B LEU* 3.6 18.4 - - + +
626B ALA 2.8 35.1 + - - +
647B ILE* 1.3 73.0 - - - +
649B HIS* 1.3 61.9 + - - +
711B ALA* 3.0 41.3 - - + +
712B LEU 3.7 3.4 - - - +
713B TRP* 3.5 21.1 - - + +
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Residues in contact with HIS 649 (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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453B VAL* 4.6 3.4 - - + -
623B ALA* 4.9 1.2 - - - +
624B TYR 3.2 23.1 + - - -
625B GLY* 3.4 10.8 - - - -
647B ILE* 4.1 11.0 - - + -
648B LEU* 1.3 75.1 - - - +
650B ASP* 1.3 77.8 + - - +
651B ALA 3.7 1.7 + - - -
664B ILE* 4.0 24.7 - - + -
710B VAL* 5.9 0.2 - - + -
711B ALA 3.0 7.8 + - - +
712B LEU* 3.2 11.2 - - - +
713B TRP* 2.5 30.1 + - - +
728B VAL* 4.1 21.6 - - + +
731B PRO* 3.6 34.3 - - + +
732B PRO* 3.8 17.1 - - + +
735B LEU* 4.1 11.2 - - + +
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Residues in contact with ASP 650 (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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413B VAL* 4.9 3.4 - - + -
417B LEU* 4.4 4.0 - - + +
623B ALA* 4.7 2.9 - - - +
624B TYR* 3.1 38.6 + - + +
649B HIS* 1.3 82.5 + - - +
651B ALA* 1.3 57.3 + - - +
652B GLY* 3.0 22.7 + - - -
713B TRP* 3.5 34.6 - - + +
715B GLN* 4.0 3.1 - - - +
726B LYS* 2.7 44.5 + - - +
727B ALA 4.9 1.7 - - - +
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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