Contacts of the strand formed by residues 589 - 599 (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 ALA 589 (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* 3.6 25.1 - - + +
564A GLY 3.2 6.2 + - - +
565A GLN* 3.1 31.8 - - + +
566A LEU* 3.1 3.8 + - - +
586A MET* 4.8 2.6 - - - +
588A GLY* 1.3 75.3 - - - +
590A ALA* 1.3 62.6 + - - +
646A ARG* 4.8 0.4 - - - -
647A SER* 3.4 22.4 - - - +
648A PHE* 3.8 9.7 - - - -
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Residues in contact with ALA 590 (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* 3.4 19.1 - - + +
567A LYS* 6.1 0.4 - - - -
586A MET* 4.5 5.8 - - + -
589A ALA* 1.3 77.7 - - - +
591A ASP* 1.3 60.5 + - - +
592A ILE* 5.0 1.6 - - + -
647A SER* 3.1 12.1 + - - +
648A PHE* 3.7 12.1 - - + -
649A THR* 2.7 27.6 + - - +
650A PHE* 3.5 32.5 - - + -
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Residues in contact with ASP 591 (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 2.9 9.2 + - - +
567A LYS* 3.5 13.6 - - + +
568A GLY* 3.0 22.7 + - - -
590A ALA* 1.3 77.1 - - - +
592A ILE* 1.3 62.0 + - - +
649A THR* 3.3 29.1 - - - +
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Residues in contact with ILE 592 (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* 3.8 31.4 - - + +
567A LYS 4.2 1.3 - - - +
568A GLY 3.2 11.7 - - - +
570A LEU* 3.5 31.9 - - + +
572A VAL* 4.0 20.4 - - + -
590A ALA* 5.0 1.1 - - + -
591A ASP* 1.3 82.8 + - - +
593A SER* 1.3 61.7 + - - +
594A GLY 3.9 13.9 - - - +
595A THR 4.3 8.3 - - - -
596A PHE* 4.4 1.6 - - + +
649A THR* 2.9 9.9 + - - +
650A PHE* 3.6 45.2 - - + -
651A ASP 3.6 2.4 + - - -
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Residues in contact with SER 593 (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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473A ARG* 3.5 12.7 + - - -
568A GLY 2.9 11.2 + - - -
569A ASN* 3.0 32.9 + - - -
592A ILE* 1.3 73.5 - - - +
594A GLY* 1.3 59.3 + - - +
651A ASP* 3.2 19.8 - - - +
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Residues in contact with GLY 594 (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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473A ARG* 3.4 21.1 - - - -
570A LEU 3.1 20.1 + - - -
592A ILE* 3.9 7.5 - - - +
593A SER* 1.3 81.5 + - - +
595A THR* 1.3 64.4 + - - -
650A PHE* 3.9 0.7 - - - +
651A ASP* 3.0 28.5 + - - +
652A ARG 3.6 0.5 + - - -
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Residues in contact with THR 595 (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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473A ARG* 5.4 2.0 - - - +
571A ASN* 2.9 22.2 + - - +
572A VAL 2.8 32.2 + - - +
573A ASP* 4.9 0.2 - - - +
592A ILE* 4.3 2.9 - - - -
594A GLY* 1.3 75.4 - - - -
596A PHE* 1.3 55.9 + - - +
597A THR* 3.3 18.5 + - - -
651A ASP* 5.0 4.7 - - - +
652A ARG* 3.4 36.9 + - + +
654A SER* 4.5 5.7 - - - -
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Residues in contact with PHE 596 (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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478A LEU* 5.7 0.4 - - + -
566A LEU* 4.1 7.2 - - + -
572A VAL* 3.3 37.0 - - + +
574A ASN* 4.6 3.8 - - + -
584A LEU* 3.7 26.0 - - + -
586A MET* 4.0 17.9 - - - -
592A ILE* 4.4 1.7 - - + +
594A GLY 4.1 0.4 + - - -
595A THR* 1.3 72.3 - - - +
597A THR* 1.3 64.7 + - - +
598A GLN* 3.8 24.2 - - + -
603A LEU* 3.9 12.6 - - + -
605A LEU* 6.0 0.4 - - + -
650A PHE* 3.8 38.3 - + + +
652A ARG 2.9 7.2 + - - +
653A LEU* 3.3 23.5 - - + +
654A SER 2.7 32.6 + - - +
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Residues in contact with THR 597 (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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572A VAL 2.8 8.3 + - - +
573A ASP* 3.7 18.5 + - - -
574A ASN* 2.7 34.8 + - - +
575A ARG* 3.8 35.0 + - + +
595A THR* 3.3 18.5 + - - -
596A PHE* 1.3 73.6 - - - +
598A GLN* 1.3 66.4 + - - +
599A GLU* 5.6 1.3 - - + +
654A SER* 3.5 19.7 - - - +
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Residues in contact with GLN 598 (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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574A ASN* 2.7 34.4 + - - +
576A LEU* 4.0 4.3 - - - +
584A LEU* 3.7 4.0 - - - +
596A PHE* 3.8 12.5 + - + -
597A THR* 1.3 77.8 - - - +
599A GLU* 1.3 71.1 + - - +
600A ASN 3.0 27.7 + - - -
602A ARG 3.4 16.7 + - - +
603A LEU* 3.5 32.7 - - + +
654A SER* 2.8 14.4 + - - +
655A LEU* 3.5 14.8 - - + -
656A LYS* 3.1 23.8 + - - +
658A THR* 4.0 6.8 + - + +
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Residues in contact with GLU 599 (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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574A ASN 3.1 6.1 + - - -
575A ARG* 3.4 42.5 + - + +
576A LEU* 3.0 26.7 + - - +
597A THR* 5.6 1.9 - - + +
598A GLN* 1.3 78.2 + - - +
600A ASN* 1.3 86.2 + - - +
656A LYS* 3.2 46.9 + - + +
657A ASN* 4.6 2.9 + - - +
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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