Contacts of the strand formed by residues 646 - 656 (chain A) in PDB entry 1WXR
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 ARG 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A TYR* 3.4 56.7 + - - +
563A HIS 5.0 0.8 + - - -
587A ASP 2.9 21.1 + - - +
588A GLY 3.1 25.8 + - - +
589A ALA* 4.8 0.2 - - - -
606A GLN 3.7 10.8 - - - +
607A GLY* 3.7 10.5 - - - -
608A HIS* 3.5 33.7 + - - +
644A GLU* 3.6 27.2 + - - +
645A ASN* 1.3 82.5 + - - +
647A SER* 1.3 60.0 + - - +
648A PHE* 3.6 13.6 - - + -
665A ASN 2.9 6.6 + - - +
666A ALA* 3.0 7.6 - - - +
667A THR* 2.9 24.3 + - - -
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Residues in contact with SER 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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589A ALA* 3.4 12.8 - - - +
590A ALA 3.1 24.0 + - - +
646A ARG* 1.3 75.3 - - - +
648A PHE* 1.3 62.7 + - - +
649A THR* 4.1 11.8 + - - -
667A THR* 3.6 10.7 + - - +
669A ASN* 4.1 9.0 + - - -
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Residues in contact with PHE 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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586A MET* 3.4 42.4 - - + -
588A GLY 3.3 17.7 - - - -
589A ALA* 3.8 15.3 - - - -
590A ALA* 3.4 21.1 - - + -
605A LEU* 3.9 35.2 - - + -
606A GLN 3.7 17.7 - - - -
646A ARG* 3.6 23.8 - - + -
647A SER* 1.3 75.3 + - - +
649A THR* 1.3 61.1 + - - +
650A PHE* 4.2 5.4 - + + -
662A LEU* 5.0 0.4 - - + -
666A ALA* 4.1 6.7 - - + -
667A THR 2.7 18.7 + - - +
668A LEU* 3.4 10.4 - - + +
669A ASN 2.9 25.7 + - - -
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Residues in contact with THR 649 (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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590A ALA* 2.7 13.1 + - - +
591A ASP* 3.3 27.8 + - - +
592A ILE 2.9 26.3 + - - +
647A SER* 4.1 6.2 + - - -
648A PHE* 1.3 70.8 - - - +
650A PHE* 1.3 76.3 + - - +
669A ASN* 3.2 37.8 + - + +
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Residues in contact with PHE 650 (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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566A LEU* 5.5 0.2 - - + -
586A MET* 5.4 1.3 - - + -
590A ALA* 3.5 27.1 - - + -
592A ILE* 3.6 27.1 - - + -
594A GLY 3.9 5.2 - - - +
596A PHE* 3.8 31.0 - + + +
603A LEU* 6.4 0.2 - - + -
605A LEU* 3.8 23.6 - - + -
648A PHE* 4.2 6.5 - + + -
649A THR* 1.3 83.8 - - - +
651A ASP* 1.3 58.2 + - - +
652A ARG 3.4 17.0 - - - +
653A LEU* 4.2 20.6 - - + -
668A LEU* 3.5 28.9 - - + -
669A ASN 3.3 7.4 + - - +
670A THR* 2.5 36.2 + - - +
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Residues in contact with ASP 651 (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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592A ILE 3.6 6.1 + - - -
593A SER* 3.2 25.0 - - - +
594A GLY* 3.0 14.3 + - - +
595A THR* 5.0 4.2 - - - +
650A PHE* 1.3 73.1 - - - +
652A ARG* 1.3 89.7 + - + +
670A THR* 3.4 3.1 + - - -
671A THR* 3.5 18.9 + - - -
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Residues in contact with ARG 652 (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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594A GLY 3.6 1.4 + - - -
595A THR* 3.5 25.7 - - + +
596A PHE 2.9 24.9 + - - -
650A PHE* 3.1 7.6 - - - +
651A ASP* 1.3 106.2 + - - +
653A LEU* 1.3 62.4 + - - +
654A SER* 3.9 3.6 - - - +
670A THR* 3.4 5.2 - - - -
671A THR* 3.2 43.7 + - - +
673A GLN* 3.9 34.8 + - + +
721A ASN* 4.9 0.6 - - - +
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Residues in contact with LEU 653 (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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596A PHE* 3.3 38.4 - - + +
603A LEU* 4.0 13.9 - - + -
605A LEU* 5.5 0.2 - - + -
650A PHE* 4.2 13.5 - - + -
652A ARG* 1.3 74.3 - - - +
654A SER* 1.3 59.8 + - - +
655A LEU* 3.6 18.8 + - + -
660A PHE* 3.5 42.4 - - + -
668A LEU* 4.3 11.0 - - + -
670A THR* 3.5 16.1 + - + -
671A THR 2.9 8.3 + - - +
672A ILE* 3.5 9.2 - - + +
673A GLN 2.8 26.1 + - - -
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Residues in contact with SER 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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595A THR* 4.5 5.8 + - - -
596A PHE 2.7 10.0 + - - +
597A THR* 3.5 26.5 - - - +
598A GLN 2.8 30.1 + - - +
652A ARG* 3.9 5.4 - - - +
653A LEU* 1.3 72.3 - - - +
655A LEU* 1.3 65.8 + - - +
656A LYS* 5.5 2.1 - - - +
673A GLN* 3.5 17.8 + - - +
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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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598A GLN* 3.5 13.5 - - + -
603A LEU* 4.4 3.6 - - + -
653A LEU* 3.9 27.4 - - + +
654A SER* 1.3 83.2 + - - +
656A LYS* 1.3 61.6 + - - +
658A THR* 3.4 20.4 - - + +
660A PHE* 3.6 35.9 - - + -
672A ILE* 3.9 23.1 - - + -
673A GLN 2.8 13.1 + - - +
674A ALA* 4.1 2.9 - - + -
675A ASP* 2.8 25.1 + - - +
677A SER* 3.4 11.4 - - - +
679A VAL* 4.0 13.9 - - + -
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Residues in contact with LYS 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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598A GLN 3.1 10.9 + - - +
599A GLU* 3.2 32.8 + - + +
600A ASN 2.8 30.7 + - - -
654A SER* 5.5 2.5 - - - +
655A LEU* 1.3 76.7 - - - +
657A ASN* 1.3 78.4 + - - +
658A THR* 3.2 3.1 + - - +
675A ASP* 3.2 26.5 - - + +
677A SER* 3.3 0.4 + - - -
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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