Contacts of the strand formed by residues 523 - 532 (chain A) in PDB entry 2XWB
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 GLU 523 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A THR* 3.6 11.6 - - - +
427A VAL* 3.6 31.2 + - + +
430A SER* 2.6 31.3 + - - -
432A ASN* 3.2 30.5 + - - +
513A TYR 4.1 0.7 - - - +
514A THR* 3.3 26.9 + - - -
515A LEU* 3.2 21.1 + - + +
517A GLY* 5.3 6.5 - - - +
518A ALA* 5.2 6.6 + - + +
521A GLN* 2.9 10.0 + - + +
522A ARG* 1.3 74.1 - - - +
524A VAL* 1.3 68.5 + - - +
525A VAL* 3.6 7.5 - - + +
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Residues in contact with VAL 524 (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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3A MET* 4.4 13.2 - - + -
424A TYR* 4.1 1.2 + - - -
427A VAL* 4.0 12.3 - - - +
512A TYR* 4.4 19.3 - - + -
513A TYR 4.1 2.2 - - - -
514A THR* 4.5 5.6 - - - +
522A ARG* 4.2 1.3 + - + +
523A GLU* 1.3 79.8 - - - +
525A VAL* 1.3 73.4 + - - +
613A TYR* 3.2 44.7 - - + +
617A PHE* 4.7 9.2 - - + -
624A PHE* 4.3 24.7 - - + -
630A GLN* 4.4 19.5 - - + +
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Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 3.8 14.1 - - + +
426A THR* 5.4 0.7 - - + -
427A VAL 6.0 0.4 - - - +
432A ASN* 3.3 28.3 - - + +
433A TYR* 3.7 13.0 - - - -
434A LEU* 3.9 4.7 - - + +
512A TYR* 3.1 5.1 - - - +
513A TYR* 3.0 73.0 + - + +
515A LEU* 5.9 0.4 - - + -
523A GLU* 3.6 20.4 - - + +
524A VAL* 1.3 82.1 - - - +
526A ALA* 1.3 66.5 + - - +
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Residues in contact with ALA 526 (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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343A LYS* 5.6 1.6 - - - -
424A TYR* 3.5 20.3 + - - -
434A LEU* 4.5 5.6 + - - +
510A VAL* 6.1 1.3 - - + -
511A ALA 3.2 8.3 - - - +
512A TYR* 3.5 18.2 - - + -
524A VAL* 5.2 0.2 - - + -
525A VAL* 1.3 81.4 - - - +
527A ASP* 1.3 65.8 + - - +
613A TYR* 4.6 4.7 - - + +
616A VAL* 3.9 20.8 - - + +
617A PHE* 3.9 22.7 - - + -
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Residues in contact with ASP 527 (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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343A LYS* 3.2 22.8 + - - -
434A LEU* 3.3 25.2 - - + +
435A HIS* 3.5 2.8 + - - -
436A LEU* 3.2 40.4 + - + +
510A VAL* 3.2 4.5 - - - +
511A ALA 3.0 30.3 + - - +
526A ALA* 1.3 80.9 - - - +
528A SER* 1.3 75.8 + - - +
529A VAL* 5.7 0.3 - - - +
609A SER* 3.6 11.3 + - - -
616A VAL* 3.5 9.8 - - - +
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Residues in contact with SER 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO* 5.6 1.7 - - - +
508A ARG* 5.8 4.3 - - - -
509A LEU 3.3 5.8 - - - -
510A VAL* 3.5 22.9 - - - -
527A ASP* 1.3 88.2 + - - +
529A VAL* 1.3 65.1 + - - +
606A THR 5.4 0.3 + - - -
608A GLY* 3.4 10.9 - - - -
609A SER* 2.7 36.4 + - - +
616A VAL* 3.5 14.9 + - - +
619A ASP* 5.8 0.7 - - - +
620A ALA* 4.2 10.3 + - - +
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Residues in contact with VAL 529 (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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339A PRO* 6.3 0.9 - - - -
436A LEU* 3.8 39.3 - - + +
438A VAL* 4.7 16.2 - - + +
451A VAL* 5.8 0.2 - - + -
507A PHE 4.1 0.3 - - - +
508A ARG* 3.7 3.1 - - - -
509A LEU* 3.1 43.9 + - + +
528A SER* 1.3 78.5 - - - +
530A TRP* 1.3 72.7 + - - +
531A VAL* 3.9 13.9 + - + +
607A PRO 4.4 3.4 - - - -
608A GLY* 4.7 0.2 - - - -
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Residues in contact with TRP 530 (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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337A LYS* 3.7 59.7 - - + -
351A MET* 5.7 8.2 - - + +
506A SER* 3.2 29.9 + - - -
507A PHE 4.0 7.6 - - - -
508A ARG* 3.9 40.9 - - + +
529A VAL* 1.3 78.2 - - - +
531A VAL* 1.3 73.7 + - - +
532A ASP* 4.0 28.0 - - + -
599A GLU* 4.6 16.7 + - + -
602A ASP* 5.4 0.4 + - - -
607A PRO* 3.4 28.9 + - + +
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Residues in contact with VAL 531 (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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438A VAL* 4.8 19.1 - - + -
440A ARG* 4.6 8.7 - - - +
443A LEU* 3.5 32.5 - - + -
449A LEU* 4.6 3.8 - - + -
506A SER* 3.6 1.9 - - - -
507A PHE* 3.1 57.5 + - + +
509A LEU* 6.0 0.7 - - + -
529A VAL* 4.1 20.2 - - + +
530A TRP* 1.3 86.4 - - - +
532A ASP* 1.3 65.5 + - - +
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Residues in contact with ASP 532 (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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440A ARG* 3.7 25.4 + - - +
443A LEU* 4.1 7.8 + - - +
505A PRO* 3.8 4.9 - - - +
506A SER* 4.5 6.4 - - - -
530A TRP* 4.0 27.3 - - + -
531A VAL* 1.3 84.6 - - - +
533A VAL* 1.3 82.4 + - - +
534A LYS* 4.9 0.3 - - - -
535A ASP* 3.2 23.5 - - - +
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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