Contacts of the strand formed by residues 609 - 614 (chain O) in PDB entry 2O93
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 VAL 609 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598O LEU* 4.4 9.6 - - + -
608O LYS* 1.3 75.5 - - - +
610O VAL* 1.3 75.3 + - - +
611O PHE* 4.2 15.7 - - + -
625O GLU* 3.4 6.6 - - - +
626O ALA* 3.3 19.2 + - + -
628O VAL* 3.3 27.2 - - + +
638O LEU* 4.5 11.2 - - + -
640O VAL* 3.8 26.7 - - + -
658O PHE* 3.8 26.2 - - + -
659O TYR 3.3 9.4 - - - +
660O VAL* 4.5 5.8 - - + -
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Residues in contact with VAL 610 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608O LYS* 5.1 2.0 - - + -
609O VAL* 1.3 84.5 - - - +
611O PHE* 1.3 67.8 + - - +
612O THR* 3.3 23.8 - - + -
623O GLU* 3.8 14.8 - - + -
624O MET 3.7 5.8 - - - +
625O GLU* 4.3 14.6 - - + -
626O ALA 4.6 0.2 - - - +
658O PHE* 2.9 4.4 - - - -
659O TYR* 2.8 66.7 + - + +
661O ILE* 4.5 9.6 - - + -
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Residues in contact with PHE 611 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596O MET* 4.2 17.0 - - + -
609O VAL* 4.2 8.3 - - + -
610O VAL* 1.3 72.7 - - - +
612O THR* 1.3 65.7 + - - +
622O TRP* 3.9 17.7 - - + -
624O MET 2.7 40.4 + - - +
626O ALA* 4.1 13.2 - - + -
640O VAL* 4.6 1.3 - - + -
642O ILE* 4.4 7.9 - - + -
643O PRO* 3.6 28.0 - - + -
656O VAL* 4.2 16.8 - - + -
657O ASN 3.3 3.8 - - - -
658O PHE* 3.6 32.1 - + + -
673O PHE* 3.7 34.1 - + + -
675O TYR* 4.0 15.0 - + - -
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Residues in contact with THR 612 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610O VAL* 3.3 21.1 - - + +
611O PHE* 1.3 82.5 - - - +
613O GLU* 1.3 59.6 + - - +
614O LYS* 3.5 17.7 - - - -
620O GLN* 4.0 15.3 + - - +
622O TRP* 2.9 23.8 - - - +
623O GLU* 3.9 9.6 - - + -
656O VAL* 3.6 2.3 - - - +
657O ASN* 2.6 43.1 + - - +
659O TYR* 3.8 18.8 - - + +
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Residues in contact with GLU 613 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612O THR* 1.3 76.9 - - - +
614O LYS* 1.3 74.3 + - - +
620O GLN* 3.6 2.4 - - - -
621O ILE* 2.9 29.5 + - + +
622O TRP* 2.9 21.8 + - + +
645O TYR* 2.5 26.5 + - - -
646O ARG* 3.3 19.1 + - - -
654O VAL* 2.9 25.3 - - - +
655O LYS 3.7 10.9 - - - +
656O VAL* 3.5 19.5 - - + +
657O ASN 4.7 0.9 - - - +
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Residues in contact with LYS 614 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612O THR* 3.5 23.6 - - - +
613O GLU* 1.3 84.6 - - - +
615O THR* 1.3 68.8 + - - +
616O THR 3.9 0.5 + - - -
618O GLY* 4.1 11.3 + - - -
619O GLN 3.0 21.1 - - - +
620O GLN* 3.4 26.6 + - - +
621O ILE* 4.5 2.7 - - - -
657O ASN* 4.0 23.1 - - - +
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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