Contacts of the strand formed by residues 685 - 695 (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 ARG 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A GLN* 5.5 0.2 - - - -
445A ASP* 3.1 31.1 + - - -
452A LEU* 3.4 32.2 - - - +
453A CYS* 2.8 41.8 + - - +
454A GLY 3.3 8.9 + - - +
455A MET* 3.7 13.4 - - - +
571A CYS* 5.2 0.2 - - - -
577A GLY* 4.3 3.2 + - - -
580A ARG* 4.5 3.0 + - - +
581A ALA* 3.6 44.1 - - + +
583A ARG* 3.4 22.3 - - - +
680A VAL 3.6 1.0 - - - +
681A HIS* 3.3 5.2 - - - -
682A LYS 3.0 31.9 + - - +
683A ARG 3.8 0.2 - - - +
684A SER* 1.3 83.0 - - - +
686A PHE* 1.3 65.9 + - - +
687A ILE* 4.0 3.3 + - + +
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Residues in contact with PHE 686 (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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203A GLN* 6.3 2.9 - - + -
454A GLY* 2.9 29.6 + - - +
456A VAL* 3.7 26.9 - - + -
470A TRP* 3.8 33.0 - + + -
570A ILE* 3.4 17.9 - - + +
571A CYS* 3.4 12.7 + - - +
606A LEU* 4.2 10.3 - - + -
617A ARG* 3.6 36.1 - - - -
679A ILE* 3.9 20.0 - - + -
680A VAL 3.7 1.6 - - - -
681A HIS* 3.5 42.8 - + + -
684A SER 4.7 4.7 - - - -
685A ARG* 1.3 74.8 - - - +
687A ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 687 (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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571A CYS* 3.6 24.5 - - + +
572A LEU 4.5 3.8 - - - -
573A PRO* 4.5 1.1 - - + -
578A THR* 4.0 21.3 - - + +
581A ALA* 4.5 9.0 - - + -
582A LEU* 4.2 16.2 - - + -
597A LEU* 3.9 41.7 - - + -
679A ILE* 3.4 4.5 - - - +
680A VAL 2.8 42.8 + - - +
682A LYS* 4.3 8.7 - - + +
685A ARG 4.0 16.2 - - - +
686A PHE* 1.3 76.7 - - - +
688A GLN* 1.3 70.9 + - - +
689A VAL* 3.5 4.5 + - + +
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Residues in contact with GLN 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ALA* 3.4 23.7 - - - +
491A VAL* 4.3 0.3 - - - +
497A LEU* 3.9 16.4 + - - +
570A ILE* 3.4 22.7 - - + +
571A CYS 2.9 16.8 + - - +
572A LEU* 4.1 3.6 - - + +
573A PRO* 3.0 31.0 - - - +
676A GLY 4.6 0.8 + - - -
677A PRO* 3.3 25.5 - - + +
678A LEU 3.6 4.7 - - - +
679A ILE* 4.4 0.7 - - - +
687A ILE* 1.3 70.0 - - - +
689A VAL* 1.3 58.0 + - - +
690A GLY 3.0 27.4 + - - +
691A VAL* 3.7 18.2 - - - +
720A LEU* 3.7 13.7 - - + +
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Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A PRO* 4.3 5.2 - - - -
597A LEU* 4.5 23.3 - - + -
598A LEU* 4.1 20.6 - - + -
622A ILE* 4.1 20.2 - - + -
656A LEU* 3.9 3.5 - - + +
678A LEU* 2.9 22.8 + - + +
680A VAL* 3.8 34.3 - - + +
687A ILE* 3.5 6.5 + - + +
688A GLN* 1.3 77.0 - - - +
690A GLY* 1.3 58.1 + - - +
719A ASN* 3.7 9.2 - - - +
720A LEU* 3.0 25.8 + - - +
721A PHE* 4.6 6.3 + - + -
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Residues in contact with GLY 690 (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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656A LEU* 4.7 1.3 - - - -
678A LEU* 2.7 43.6 + - - -
688A GLN* 3.0 16.9 + - - +
689A VAL* 1.3 81.3 - - - +
691A VAL* 1.3 62.5 + - - -
717A HIS* 4.8 0.7 - - - -
718A ILE 3.0 12.3 - - - -
719A ASN* 4.7 0.2 - - - -
720A LEU* 4.1 2.9 - - - +
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Residues in contact with VAL 691 (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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497A LEU* 4.1 13.0 - - + -
498A THR 3.7 19.7 - - - +
499A ALA* 3.8 9.0 - - + +
551A ASP 4.3 4.5 - - - +
552A VAL* 3.9 24.5 - - + -
675A GLY 3.6 19.1 - - - +
676A GLY 3.6 2.7 - - - -
688A GLN* 3.7 16.2 - - - +
690A GLY* 1.3 75.1 - - - -
692A ILE* 1.3 72.7 + - - +
693A SER* 3.3 1.7 + - - -
717A HIS* 3.1 5.2 - - - -
718A ILE* 2.8 36.0 + - + +
720A LEU* 3.9 12.1 - - + -
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Residues in contact with ILE 692 (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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499A ALA* 4.0 2.4 - - - +
607A PHE* 3.7 32.3 - - + -
608A VAL 5.1 2.0 - - - +
669A THR* 3.9 31.2 - - + +
673A ASP* 3.5 16.4 - - + +
674A SER* 3.9 19.3 + - - +
675A GLY* 2.8 32.2 + - - +
676A GLY* 2.9 27.3 + - - +
677A PRO 4.1 4.5 - - - +
678A LEU* 4.7 1.1 - - + +
690A GLY 4.3 0.2 - - - -
691A VAL* 1.3 71.4 - - - +
693A SER* 1.3 63.6 + - - +
694A TRP 5.3 0.9 - - - +
715A ASP* 6.0 0.9 - - + -
717A HIS* 3.5 25.8 - - + +
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Residues in contact with SER 693 (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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499A ALA* 5.2 0.2 - - - -
501A HIS* 3.0 23.8 + - - -
548A TYR* 3.9 3.5 - - - +
551A ASP* 2.7 32.7 + - - +
655A PHE* 3.8 11.6 - - - -
674A SER* 3.8 4.3 + - - -
691A VAL 3.3 7.8 + - - -
692A ILE* 1.3 77.5 - - - +
694A TRP* 1.3 76.7 + - - +
716A PHE 3.1 18.1 + - - -
717A HIS* 4.2 0.9 - - - -
718A ILE* 4.3 6.1 - - - -
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Residues in contact with TRP 694 (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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548A TYR* 3.4 43.3 - + + +
635A ALA* 3.8 14.1 - - + -
638A ALA* 4.0 14.8 - - + -
641A TYR* 3.5 32.8 - + - -
650A VAL 4.1 17.7 + - - -
651A VAL* 4.1 7.0 - - + -
655A PHE* 3.2 26.6 - + - -
669A THR* 5.9 0.9 - - - -
692A ILE* 5.3 1.3 - - - +
693A SER* 1.3 96.0 - - - +
695A GLY* 1.3 73.5 + - - +
696A VAL* 4.8 0.2 - - + -
715A ASP* 3.6 3.9 - - - +
716A PHE* 2.7 76.7 + + + +
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Residues in contact with GLY 695 (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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638A ALA* 4.6 2.9 - - - +
639A PRO* 4.9 3.6 - - - +
694A TRP* 1.3 88.7 - - - +
696A VAL* 1.3 66.9 + - - +
697A VAL 3.4 5.6 + - - -
714A ARG 3.5 9.6 - - - -
715A ASP* 3.8 11.4 - - - -
716A PHE* 4.8 0.4 - - - -
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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