Contacts of the strand formed by residues 602 - 611 (chain A) in PDB entry 2OK5
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 ASP 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A GLN* 1.3 81.4 + - - +
603A ILE* 1.3 61.8 + - - +
604A LYS 3.8 2.1 + - - -
621A TYR* 4.4 14.2 - - + -
622A ILE 3.3 4.5 - - - +
623A LYS* 3.4 25.5 - - - +
624A ASN 4.5 0.5 + - - -
625A GLY* 5.0 1.6 + - - -
626A ASP* 5.3 1.6 - - - +
627A LYS* 2.7 36.9 + - - +
663A PRO* 3.6 27.5 - - + +
664A TYR* 6.1 0.2 - - + -
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Residues in contact with ILE 603 (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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597A LEU 3.5 18.2 - - - +
598A LEU* 3.6 29.8 - - + -
599A PRO* 3.5 33.0 - - + +
601A GLN* 3.7 10.1 - - + +
602A ASP* 1.3 72.5 - - - +
604A LYS* 1.3 76.2 + - - +
605A ALA 3.4 0.9 + - - -
621A TYR* 3.2 5.8 - - - -
622A ILE* 2.8 46.9 + - + +
624A ASN* 3.6 18.8 - - + -
680A VAL* 4.3 13.2 - - + -
682A LYS* 6.1 2.2 - - - +
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Residues in contact with LYS 604 (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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431A LYS* 4.4 17.6 - - - +
602A ASP 3.8 1.8 + - - -
603A ILE* 1.3 81.5 - - - +
605A ALA* 1.3 63.9 + - - +
619A GLU* 3.6 28.0 + - + +
620A VAL 3.7 3.8 - - - -
621A TYR* 3.7 32.8 - - + +
680A VAL* 4.0 14.0 - - - +
681A HIS* 5.0 4.8 + - + +
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Residues in contact with ALA 605 (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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603A ILE 3.4 0.2 + - - -
604A LYS* 1.3 78.0 - - - +
606A LEU* 1.3 65.5 + - - +
619A GLU* 3.4 7.3 - - - +
620A VAL* 2.9 30.8 + - + +
622A ILE* 3.8 33.7 - - + -
678A LEU* 4.1 11.2 - - + -
679A ILE 3.2 18.2 - - - +
680A VAL* 4.2 3.1 - - + +
681A HIS 5.5 0.9 - - - +
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Residues in contact with LEU 606 (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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470A TRP* 5.2 1.3 - - + -
605A ALA* 1.3 77.2 - - - +
607A PHE* 1.3 77.6 + - - +
608A VAL* 4.4 3.6 - - + -
617A ARG* 4.2 28.3 - - + +
618A LYS 3.3 17.5 - - - +
619A GLU* 4.3 2.9 - - + -
620A VAL* 4.4 1.6 - - - -
678A LEU* 3.7 5.3 - - - +
679A ILE* 2.8 60.2 + - + +
681A HIS* 4.1 28.3 - - + +
686A PHE* 4.2 16.8 - - + -
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Residues in contact with PHE 607 (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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606A LEU* 1.3 79.6 - - - +
608A VAL* 1.3 74.8 + - - +
609A SER* 4.0 11.2 - - - -
617A ARG* 3.6 3.3 - - - -
618A LYS* 2.9 51.0 + - + -
620A VAL* 3.5 34.1 - - + -
658A THR* 6.0 0.2 - - - -
667A PRO 4.3 5.2 - - - -
668A ASN 3.7 21.1 - - - -
669A THR* 3.6 28.9 - - + -
673A ASP* 3.8 16.8 - - - -
677A PRO 3.6 17.5 - - - +
678A LEU* 4.7 5.6 - - + -
679A ILE* 5.2 0.2 - - - -
692A ILE* 3.7 17.0 - - + -
715A ASP* 5.5 0.4 - - - -
717A HIS* 5.5 2.7 - + - -
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Residues in contact with VAL 608 (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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468A GLN* 3.6 30.7 - - + -
470A TRP* 4.2 12.1 - - + +
471A GLN* 3.8 34.9 + - - +
487A MET* 4.3 2.3 - - - +
606A LEU* 4.4 9.4 - - + -
607A PHE* 1.3 86.3 - - - +
609A SER* 1.3 62.2 + - - +
615A LEU* 3.8 38.8 - - + -
616A THR 3.7 6.7 - - - +
617A ARG* 4.6 3.1 - - + -
673A ASP* 3.9 11.3 - - - +
676A GLY* 5.9 0.9 - - - -
677A PRO* 4.5 4.6 + - + +
679A ILE* 4.7 3.1 - - + -
692A ILE* 5.1 2.5 - - - +
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Residues in contact with SER 609 (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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607A PHE* 4.0 12.3 + - - -
608A VAL* 1.3 75.4 - - - +
610A GLU* 1.3 66.2 + - - +
611A GLU* 4.0 2.1 + - - +
614A LYS 3.5 0.9 - - - +
615A LEU* 3.4 4.4 - - - -
616A THR* 3.0 40.2 + - - +
618A LYS* 4.1 13.8 - - - -
668A ASN 5.6 0.2 + - - -
670A CYS* 4.3 10.9 - - - -
673A ASP* 2.7 24.3 + - - -
700A CYS* 5.2 0.7 - - - -
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Residues in contact with GLU 610 (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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465A TYR* 5.5 0.5 + - - -
473A LYS* 3.6 24.8 + - - +
487A MET* 3.9 18.2 - - + +
609A SER* 1.3 77.9 + - - +
611A GLU* 1.3 63.2 + - - +
612A GLU* 4.1 2.5 + - - -
613A LYS* 3.2 58.4 + - - +
614A LYS 3.3 10.1 - - - +
615A LEU* 4.0 11.4 - - + +
670A CYS* 5.3 5.2 - - - +
672A GLY 6.3 0.4 - - - -
673A ASP* 3.2 10.0 + - - +
701A LYS* 5.2 4.7 - - - -
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Residues in contact with GLU 611 (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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609A SER* 4.0 2.6 + - - +
610A GLU* 1.3 74.0 - - - +
612A GLU* 1.3 93.9 + - + +
613A LYS 3.5 0.2 - - - -
614A LYS* 3.0 27.6 + - + +
616A THR* 5.7 7.6 - - + +
701A LYS* 4.0 36.8 + - - +
704A LYS* 4.2 22.6 - - - +
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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