Contacts of the strand formed by residues 571 - 580 (chain A) in PDB entry 2VKW
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 571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A ALA* 3.4 4.3 - - - -
540A VAL* 2.8 51.5 + - + +
570A THR* 1.3 76.5 - - - +
572A TYR* 1.3 62.6 + - - +
592A GLU* 3.4 20.6 - - + +
593A PHE 3.3 12.6 - - - +
594A LYS* 3.7 22.2 - - + +
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Residues in contact with TYR 572 (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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537A TRP* 4.2 17.0 - + + -
538A ARG 3.5 5.8 - - - -
539A ALA* 3.4 35.1 - - + +
546A HIS* 5.8 3.4 - + - -
565A GLY 5.0 0.2 + - - -
566A LEU* 3.6 19.1 - - + -
567A LYS* 2.9 36.3 + - - +
570A THR* 3.2 44.6 - - + +
571A THR* 1.3 72.5 - - - +
573A ALA* 1.3 60.6 + - - +
591A SER 3.7 0.2 - - - +
592A GLU* 3.0 15.6 - - - -
593A PHE* 2.7 67.2 + + + -
595A THR* 3.8 16.4 - - + -
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Residues in contact with ALA 573 (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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537A TRP* 3.1 6.5 - - - +
538A ARG* 3.0 47.4 + - - +
545A TRP* 3.8 19.2 - - + -
572A TYR* 1.3 74.2 - - - +
574A VAL* 1.3 61.0 + - - +
590A ALA* 4.5 9.9 - - + -
591A SER 3.2 6.5 - - - +
592A GLU* 3.2 18.6 - - - +
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Residues in contact with VAL 574 (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 ILE* 3.6 19.6 - - + +
508A VAL* 4.2 9.0 - - + -
517A VAL* 4.4 9.0 - - + -
535A ALA* 5.0 2.0 - - + -
536A GLU 3.1 13.9 - - - +
537A TRP* 4.3 1.8 - - + -
545A TRP* 5.0 0.2 - - - -
563A ILE* 3.3 29.4 - - + -
573A ALA* 1.3 75.6 - - - +
575A ARG* 1.3 71.0 + - - +
576A LEU* 5.0 1.8 - - + -
590A ALA* 3.3 4.1 - - - -
591A SER* 2.7 49.7 + - - +
593A PHE* 3.9 24.5 - - + -
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Residues in contact with ARG 575 (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 ILE* 4.2 2.5 - - - -
534A LYS 3.7 0.5 - - - +
535A ALA* 3.4 3.6 - - - -
536A GLU* 2.7 66.2 + - + +
545A TRP* 3.6 53.6 - - + +
574A VAL* 1.3 77.9 - - - +
576A LEU* 1.3 66.8 + - - +
587A ILE* 3.4 33.0 - - + +
588A SER* 3.5 22.9 - - - +
589A ALA 4.0 2.9 - - - +
590A ALA* 4.2 7.2 - - - -
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Residues in contact with LEU 576 (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 PRO* 3.6 17.7 - - + +
505A ILE* 3.8 20.0 - - + -
517A VAL* 3.9 7.4 - - + -
519A PHE* 3.6 47.1 - - + -
533A TYR* 5.2 7.2 - - + -
534A LYS 3.3 5.4 - - - +
535A ALA* 3.6 31.2 - - + +
536A GLU* 5.9 0.2 - - - -
561A VAL* 4.0 17.9 - - + -
574A VAL* 5.0 2.5 - - + -
575A ARG* 1.3 76.7 - - - +
577A ALA* 1.3 60.1 + - - +
587A ILE* 3.5 3.5 - - - -
588A SER* 2.7 43.0 + - - +
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Residues in contact with ALA 577 (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 PRO* 4.0 6.1 - - - -
533A TYR* 3.3 6.8 - - - -
534A LYS* 2.8 35.9 + - + +
536A GLU* 4.9 3.6 - - - +
576A LEU* 1.3 76.2 - - - +
578A ALA* 1.3 60.6 + - - +
584A LEU* 3.8 31.4 - - + -
585A GLY 4.4 1.8 - - - +
586A GLU 3.9 15.0 - - - +
587A ILE* 4.2 12.8 - - + -
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Residues in contact with ALA 578 (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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500A PRO* 3.7 18.1 - - + +
501A SER 4.5 1.1 - - - +
503A PRO* 4.1 3.0 - - - +
522A PRO* 3.8 30.3 - - + -
530A ILE* 3.9 15.3 - - + -
532A LYS 3.6 4.0 - - - -
533A TYR* 4.0 6.7 - - + -
577A ALA* 1.3 74.3 - - - +
579A LEU* 1.3 59.3 + - - +
584A LEU* 3.4 4.0 - - - -
585A GLY* 2.7 32.8 + - - +
586A GLU 4.5 2.0 + - - -
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Residues in contact with LEU 579 (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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500A PRO* 4.5 1.3 - - - -
530A ILE* 3.6 2.4 - - - -
531A LEU* 2.7 42.4 + - + -
532A LYS* 2.9 27.6 + - + +
549A TRP* 3.8 34.1 - - + -
578A ALA* 1.3 74.6 - - - +
580A ASN* 1.3 59.5 + - - +
583A GLY* 3.5 30.7 - - - -
584A LEU* 3.6 11.2 - - + +
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Residues in contact with ASN 580 (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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498A ASP 3.1 16.2 + - - -
500A PRO* 3.5 14.8 - - + +
525A THR 2.9 26.9 + - - -
526A GLY* 4.4 0.6 - - - -
528A VAL* 3.4 20.0 + - - +
529A PRO 3.5 20.6 - - - +
530A ILE* 3.9 2.9 - - - -
531A LEU* 4.2 9.9 - - - +
579A LEU* 1.3 81.4 - - - +
581A GLY* 1.3 67.8 + - - +
582A LYS* 2.8 17.2 + - - +
583A GLY* 2.9 22.3 + - - +
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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