Contacts of the strand formed by residues 617 - 621 (chain B) in PDB entry 2OX8
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 LYS 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ZN 4.1 0.4 - - - -
3B ZN 4.1 1.8 - - - -
8B CL 3.7 17.1 - - - +
612B LYS 3.5 2.1 - - - +
613B ASN* 3.0 20.5 + - - -
614B PHE 3.1 16.1 + - - +
615B THR* 3.5 8.0 - - + -
616B ASP* 1.3 92.4 + - - +
618B CYS* 1.3 64.1 + - - +
619B TYR* 3.1 27.3 - - + +
650B GLU* 4.3 2.2 - - - -
731B GLU* 3.0 30.3 + - + +
732B LYS 3.3 9.6 - - - +
733B ASP* 3.3 31.8 + - - +
734B ARG* 4.8 0.2 - - - -
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Residues in contact with CYS 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B SER 4.5 0.2 - - - -
607B CYS* 2.0 52.9 - - + -
608B PRO* 4.2 6.1 - - + -
611B TRP* 3.7 20.3 - - + -
612B LYS 3.2 4.5 - - - -
617B LYS* 1.3 72.1 - - - +
619B TYR* 1.3 63.1 + - - +
731B GLU* 3.3 5.0 - - - -
732B LYS* 3.0 39.9 + - + -
734B ARG* 3.6 23.8 - - - -
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Residues in contact with TYR 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B HIS 4.4 0.2 - - - +
611B TRP* 3.3 5.1 - - - -
612B LYS* 2.7 45.3 + - - +
614B PHE* 3.9 16.8 - - + -
617B LYS* 3.1 33.9 - - + +
618B CYS* 1.3 78.8 - - - +
620B TYR* 1.3 61.8 + - - +
621B PHE* 3.7 20.6 + + + -
643B VAL* 3.6 33.4 - - + -
650B GLU* 2.7 31.3 + - + +
653B TRP* 3.5 31.6 - + + -
654B ILE* 4.1 10.3 - - + -
729B ILE* 4.3 7.9 - - + -
730B CYS 3.1 5.2 - - - +
731B GLU* 3.6 11.7 - - + -
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Residues in contact with TYR 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B HIS* 3.7 27.6 - - + -
611B TRP* 3.6 41.3 - + + -
619B TYR* 1.3 75.2 - - - +
621B PHE* 1.3 65.6 + - - +
622B SER* 3.3 30.6 + - - -
623B VAL* 4.0 14.0 + - + +
634B PHE* 3.7 37.3 - + - -
728B PHE* 4.6 0.2 - + - -
729B ILE* 3.3 6.6 - - - -
730B CYS* 2.7 42.1 + - + -
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Residues in contact with PHE 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B HIS 4.9 2.6 + - - -
612B LYS* 3.9 36.3 - - + +
619B TYR* 3.7 26.0 - - + -
620B TYR* 1.3 83.6 - - - +
622B SER* 1.3 68.7 + - - +
623B VAL* 4.6 4.9 - - - +
653B TRP* 4.6 4.7 - + - -
654B ILE* 4.1 17.0 - - + -
657B GLN* 3.6 34.1 - - + -
658B MET* 4.2 11.7 - - + -
664B HIS* 4.4 13.5 - + + -
728B PHE 3.9 3.8 - - - -
729B ILE* 3.4 34.8 - - + -
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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