Contacts of the strand formed by residues 677 - 682 (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 PRO 677 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A TRP* 3.8 20.9 - - + +
471A GLN* 3.7 17.7 - - - +
488A GLY 3.9 13.5 - - - +
489A ALA* 3.7 14.4 - - + -
570A ILE* 4.5 0.9 - - + -
607A PHE* 3.6 23.4 - - - +
608A VAL* 4.5 3.1 + - + +
676A GLY* 1.3 84.6 - - - +
678A LEU* 1.3 58.8 + - - +
679A ILE* 3.8 16.1 - - + +
688A GLN* 3.3 37.9 - - + +
692A ILE* 4.5 1.1 - - - -
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Residues in contact with LEU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ALA* 4.1 7.9 - - + -
606A LEU 3.7 14.6 - - - +
607A PHE* 4.7 4.3 - - + -
620A VAL* 3.8 26.2 - - + -
622A ILE* 3.8 25.6 - - + -
656A LEU* 4.1 13.2 - - + -
658A THR* 4.4 4.7 - - + -
676A GLY 3.7 0.8 + - - -
677A PRO* 1.3 71.9 - - - +
679A ILE* 1.3 59.1 + - - +
688A GLN* 3.6 2.3 - - - -
689A VAL* 2.9 31.8 + - + +
690A GLY* 2.7 23.3 + - - +
692A ILE* 4.9 1.6 - - + -
717A HIS* 3.7 46.2 - - + +
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Residues in contact with ILE 679 (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* 3.6 39.7 - - + +
570A ILE* 3.7 15.0 - - + -
605A ALA* 3.2 5.2 - - - -
606A LEU* 2.8 60.0 + - + +
608A VAL* 4.7 4.5 - - + -
677A PRO* 3.8 20.6 - - + +
678A LEU* 1.3 78.7 - - - +
680A VAL* 1.3 77.3 + - - +
681A HIS 4.1 0.2 + - - -
686A PHE* 3.9 28.7 - - + -
687A ILE 3.4 12.6 - - - +
688A GLN* 4.5 0.4 - - - -
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Residues in contact with VAL 680 (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* 4.3 26.7 - - + +
598A LEU* 5.1 0.2 - - + -
603A ILE* 4.3 8.3 - - + -
604A LYS 4.0 21.3 - - - +
605A ALA* 4.2 5.8 - - + -
622A ILE* 4.8 1.1 - - + -
679A ILE* 1.3 79.1 - - - +
681A HIS* 1.3 69.8 + - - +
682A LYS* 3.7 24.9 + - + -
685A ARG 3.6 2.4 - - - +
687A ILE* 2.8 39.0 + - - +
689A VAL* 3.8 30.0 - - + +
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Residues in contact with HIS 681 (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* 4.1 21.5 + - - -
604A LYS* 5.0 5.9 + - + +
605A ALA* 5.5 0.6 - - - +
606A LEU* 4.1 20.1 - - + +
617A ARG* 4.9 6.6 + - - -
679A ILE 4.1 1.4 + - - -
680A VAL* 1.3 76.1 - - - +
682A LYS* 1.3 60.1 + - - +
684A SER* 3.9 16.6 - - - -
685A ARG 3.3 21.3 - - - -
686A PHE* 3.5 38.7 - + + -
1354A GOL 5.9 3.8 - - - -
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Residues in contact with LYS 682 (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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434A GLU* 5.1 5.6 - - - +
581A ALA 4.2 1.9 - - - +
582A LEU* 3.8 28.4 - - + +
596A GLU* 2.8 38.7 + - + +
597A LEU* 4.5 5.6 + - + +
599A PRO* 5.5 3.2 - - - +
603A ILE* 6.1 2.2 - - - +
680A VAL* 3.7 21.4 + - + -
681A HIS* 1.3 75.2 - - - +
683A ARG* 1.3 82.4 + - + +
684A SER 3.2 1.6 - - - -
685A ARG* 3.0 24.1 + - - +
687A ILE* 4.3 8.0 - - + +
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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