Contacts of the strand formed by residues 580 - 589 (chain A) in PDB entry 2WKP
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 PHE 580 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LEU* 4.0 30.3 - - + -
423A PRO* 3.7 37.7 - - + -
426A PRO* 6.0 1.8 - - + -
447A GLY* 4.8 7.6 - - - +
578A THR* 3.9 3.4 - - - +
579A VAL* 1.3 94.7 + - + +
581A ASP* 1.3 66.5 + - - +
582A ASN* 5.3 0.2 - - - +
599A TRP* 5.7 1.6 - + - -
600A ASP 3.5 13.9 - - - +
601A THR* 4.1 10.5 - - + -
602A ALA 5.5 0.2 - - - -
607A TYR* 6.1 0.4 - + - -
610A LEU* 3.4 42.6 - - + -
611A ARG* 3.9 9.4 - - - -
613A LEU* 4.4 1.8 - - + -
614A SER* 3.8 23.1 - - - -
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Residues in contact with ASP 581 (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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446A LEU 3.2 7.6 - - - +
447A GLY* 3.4 8.5 - - - -
578A THR* 4.0 8.9 - - + +
580A PHE* 1.3 77.4 - - - +
582A ASN* 1.3 84.1 + - - +
583A TYR* 4.0 18.2 + - + +
600A ASP* 2.8 44.5 + - + +
1727A CA 2.5 30.2 - - - -
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Residues in contact with ASN 582 (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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422A LEU* 3.8 20.4 - - - +
426A PRO* 5.0 1.4 - - - +
427A ILE 4.1 17.6 + - - +
428A ILE* 3.4 29.2 - - + +
443A GLU* 5.6 1.9 - - - +
446A LEU* 3.3 21.0 - - + +
447A GLY* 4.2 6.3 - - - +
580A PHE* 5.3 0.6 - - - +
581A ASP* 1.3 101.4 + - - +
583A TYR* 1.3 73.4 + - - +
597A GLY* 5.8 0.2 - - - -
598A LEU 3.3 7.2 + - - +
599A TRP* 3.1 37.3 - - - -
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Residues in contact with TYR 583 (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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428A ILE 4.7 2.1 - - - +
443A GLU* 4.2 23.8 - - + +
446A LEU* 3.6 5.6 - - - -
560A THR* 3.7 13.9 - - - +
563A LEU* 3.8 27.4 - - + -
564A ILE* 3.5 35.0 - - + +
567A THR* 3.7 31.2 - - + -
581A ASP* 4.0 18.7 + - + +
582A ASN* 1.3 84.8 - - - +
584A SER* 1.3 66.2 + - - +
597A GLY* 3.7 1.7 - - - -
598A LEU* 2.9 45.4 + - + +
600A ASP* 3.9 23.4 + - + -
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Residues in contact with SER 584 (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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428A ILE 3.3 23.4 + - - -
429A PHE* 3.9 25.4 - - - -
442A ARG* 4.4 20.1 - - - +
443A GLU* 5.6 1.5 + - - +
446A LEU* 3.4 14.0 - - - +
546A LEU* 6.4 0.2 - - - -
567A THR* 3.6 16.9 - - - +
583A TYR* 1.3 74.7 + - - +
585A ALA* 1.3 63.4 + - - +
586A ASN* 5.7 0.9 - - - -
596A LEU 3.4 8.7 + - - -
597A GLY* 5.0 1.2 - - - -
598A LEU* 5.0 1.1 - - - -
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Residues in contact with ALA 585 (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 TYR* 3.8 31.6 - - + +
567A THR* 4.6 4.0 - - + -
584A SER* 1.3 76.6 - - - +
586A ASN* 1.3 67.1 + - - +
587A VAL* 3.9 11.2 - - + -
594A VAL 3.6 0.9 - - - +
596A LEU* 2.8 40.5 + - + +
598A LEU* 4.8 3.6 - - + -
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Residues in contact with ASN 586 (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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409A GLU* 3.7 30.8 - - + +
429A PHE* 4.5 12.2 - - - -
442A ARG* 6.3 1.0 - - - -
584A SER* 5.7 0.9 - - - -
585A ALA* 1.3 76.9 + - - +
587A VAL* 1.3 60.1 + - - +
588A MET* 4.2 1.6 + - - +
593A PRO* 6.0 2.7 - - + -
594A VAL 3.3 7.9 - - - +
595A ASN* 2.7 30.1 + - - +
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Residues in contact with VAL 587 (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 TYR* 3.1 29.2 - - + +
585A ALA* 4.0 17.5 - - + +
586A ASN* 1.3 76.2 - - - +
588A MET* 1.3 68.6 + - - +
589A VAL* 3.4 14.1 + - + -
593A PRO* 4.5 1.3 - - - -
594A VAL* 2.8 39.4 + - - +
596A LEU* 4.6 4.3 - - + -
712A PHE* 5.3 0.4 - - + -
713A ASP* 4.5 13.0 - - + +
716A ILE* 3.6 31.4 - - + -
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Residues in contact with MET 588 (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 ASN 4.2 1.9 + - - +
587A VAL* 1.3 76.0 - - - +
589A VAL* 1.3 64.7 + - - +
590A ASP 4.1 1.1 + - - -
591A GLY* 3.0 44.0 - - - +
592A LYS 3.5 1.1 - - - -
593A PRO* 3.8 29.2 - - + -
713A ASP* 4.1 5.9 - - - +
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Residues in contact with VAL 589 (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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587A VAL* 3.9 21.8 - - + +
588A MET* 1.3 78.4 - - - +
590A ASP* 1.3 75.3 + - + +
592A LYS* 2.8 27.7 + - - +
594A VAL* 4.2 10.0 - - + +
713A ASP* 3.9 10.3 - - - +
716A ILE* 3.8 30.3 - - + -
717A ARG* 3.9 36.1 - - + +
720A LEU* 5.1 5.8 - - + -
721A CYS* 5.5 4.3 - - - -
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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