Contacts of the strand formed by residues 513 - 519 (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 THR 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A ASN* 3.8 2.1 - - - -
508A ASN* 2.8 27.3 + - - +
511A THR* 2.8 37.8 + - - +
512A ASN* 1.3 78.7 - - - +
514A THR* 1.3 62.8 + - - +
515A ASP* 2.7 24.6 + - - -
531A GLN* 3.4 3.9 + - - +
542A HIS* 3.8 17.7 - - + +
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Residues in contact with THR 514 (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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505A LYS* 3.8 28.7 - - + +
506A TYR 3.5 5.4 - - - +
507A ASN* 3.4 14.6 + - - +
513A THR* 1.3 74.4 - - - +
515A ASP* 1.3 57.4 + - - +
516A TYR* 3.7 26.5 - - + +
542A HIS* 2.7 42.5 + - - +
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Residues in contact with ASP 515 (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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504A TYR 3.8 0.3 - - - +
505A LYS* 3.7 2.1 - - - -
506A TYR* 2.7 48.8 + - + +
508A ASN* 2.7 34.3 + - - +
513A THR* 2.7 22.8 + - - -
514A THR* 1.3 72.3 - - - +
516A TYR* 1.3 63.7 + - - +
517A PHE* 3.6 24.1 - - + -
531A GLN* 3.0 11.1 + - - +
539A PHE* 3.8 11.9 - - + -
541A GLY 3.9 3.6 - - - -
542A HIS* 3.1 16.1 + - - -
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Residues in contact with TYR 516 (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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489A LEU* 4.2 11.4 - - + -
503A LEU* 4.1 15.0 - - + -
504A TYR 3.4 13.2 - - - +
505A LYS* 3.7 36.2 + - + +
514A THR* 3.7 20.4 - - + +
515A ASP* 1.3 75.2 - - - +
517A PHE* 1.3 56.4 + - - +
539A PHE* 3.6 6.4 - - - -
540A VAL* 2.7 35.6 + - + -
541A GLY 3.0 20.5 + - - +
542A HIS* 3.5 20.6 - - - -
543A SER 3.9 4.5 - - - -
544A GLN* 3.2 43.4 + - + +
547A ALA* 3.7 21.8 - - + -
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Residues in contact with PHE 517 (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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503A LEU* 3.3 6.6 - - - +
504A TYR* 2.8 39.1 + - - +
506A TYR* 4.1 5.2 - + + -
515A ASP* 3.6 28.3 - - + -
516A TYR* 1.3 75.2 - - - +
518A ILE* 1.3 60.2 + - - +
519A LEU 4.0 0.2 + - - -
527A PHE* 3.5 28.9 - + + -
528A PRO* 3.7 36.3 - - + -
531A GLN* 4.7 3.6 - - - -
532A SER 3.4 22.9 - - - -
537A TRP* 3.5 31.6 - - + -
538A GLU 3.1 6.3 - - - +
539A PHE* 3.5 35.0 - + + -
540A VAL* 4.5 0.2 - - - -
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Residues in contact with ILE 518 (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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501A GLY* 3.7 21.1 - - - +
502A ASN 3.4 4.5 - - - +
503A LEU* 4.2 5.8 - - + -
517A PHE* 1.3 75.6 - - - +
519A LEU* 1.3 75.3 + - - +
520A LYS* 3.6 3.6 + - + +
537A TRP* 3.7 3.8 - - - -
538A GLU* 2.8 45.0 + - + +
540A VAL* 3.7 24.4 - - + +
550A LEU* 4.0 9.0 - - + -
551A VAL* 3.8 29.4 - - + -
554A ARG* 3.6 29.8 - - - +
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A GLY* 3.5 25.4 - - - -
499A THR 3.5 21.1 - - - +
501A GLY 2.7 29.8 + - - -
502A ASN 3.0 15.5 + - - +
504A TYR* 3.9 11.7 - - + +
518A ILE* 1.3 75.8 - - - +
520A LYS* 1.3 64.1 + - - +
521A GLN* 2.9 31.9 - - - +
523A THR 4.3 1.6 - - - +
524A TYR* 3.9 30.7 - - + -
536A THR 3.5 12.8 - - - +
537A TRP* 3.9 20.9 - - + -
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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