Contacts of the strand formed by residues 683 - 692 (chain B) in PDB entry 3UO8
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 683 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B ASP 3.3 12.5 - - - +
636B PRO* 3.3 18.3 - - + +
681B HIS* 2.9 22.1 + - + +
682B LEU* 1.3 74.4 - - - +
684B PHE* 1.3 63.7 + - - +
704B GLU* 3.6 37.2 - - + +
705B VAL 3.2 13.7 - - - +
706B ASN* 3.7 29.6 - - + +
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Residues in contact with PHE 684 (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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602B LEU* 3.8 33.2 - - + -
604B PHE* 4.1 7.2 - + - -
614B ILE* 3.9 23.1 - - + -
632B VAL* 4.1 20.0 - - + -
633B THR 3.5 6.3 - - - +
634B ASP 3.6 7.4 - - - +
635B PHE* 3.4 39.5 - + + -
682B LEU* 4.1 22.9 - - + -
683B VAL* 1.3 78.4 - - - +
685B THR* 1.3 66.7 + - - +
686B VAL* 4.5 3.4 - - + -
704B GLU* 3.6 4.1 - - - +
705B VAL* 2.8 39.7 + - + +
707B VAL* 4.3 15.5 - - + -
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Residues in contact with THR 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B TYR 3.6 0.5 - - - +
632B VAL* 3.2 7.1 - - - +
633B THR* 2.9 42.5 + - - +
634B ASP* 3.5 19.8 + - - +
684B PHE* 1.3 77.0 + - - +
686B VAL* 1.3 64.1 + - - +
687B CYS* 3.6 24.0 + - - -
702B LYS* 3.8 30.4 - - + +
703B GLN 3.5 9.0 - - - +
704B GLU* 4.3 11.8 - - - +
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Residues in contact with VAL 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B LEU* 3.4 31.6 - - + -
594B PHE* 3.4 23.9 - - + -
600B ILE* 4.2 24.7 - - + -
602B LEU* 4.2 12.6 - - + -
616B THR* 5.1 2.9 - - + -
630B ALA* 4.7 3.4 - - + -
631B TYR 3.4 9.9 - - - +
632B VAL* 4.5 6.7 - - + -
684B PHE* 4.5 7.6 - - + -
685B THR* 1.3 75.4 - - - +
687B CYS* 1.3 61.3 + - - +
702B LYS* 3.6 0.2 - - - -
703B GLN 3.0 27.3 + - - +
705B VAL* 3.8 13.5 - - + -
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Residues in contact with CYS 687 (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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629B ASP 4.4 0.2 - - - -
630B ALA* 3.0 8.8 - - - +
631B TYR* 2.8 71.3 + - + +
633B THR* 3.5 24.5 - - - -
685B THR* 3.6 15.5 - - - -
686B VAL* 1.3 73.1 - - - +
688B LEU* 1.3 61.2 + - - +
701B ASP 3.7 5.8 - - - +
702B LYS* 4.2 17.9 - - + +
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Residues in contact with LEU 688 (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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594B PHE* 3.7 38.1 - - + -
596B CYS* 3.5 20.2 - - - -
598B VAL* 3.8 19.3 - - + -
600B ILE* 3.7 20.4 - - + -
618B ILE* 4.6 0.4 - - + -
628B CYS* 4.2 13.5 - - + -
629B ASP 3.3 15.3 - - - +
630B ALA* 4.3 0.4 - - + -
686B VAL 4.0 0.2 + - - -
687B CYS* 1.3 76.1 - - - +
689B SER* 1.3 62.8 + - - +
690B TYR* 3.4 27.8 - - + -
699B VAL 3.9 0.5 - - - +
700B GLU* 3.5 4.3 - - - +
701B ASP* 2.9 35.2 + - + +
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Residues in contact with SER 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B CYS* 2.8 27.3 - - - +
629B ASP* 2.8 23.6 + - - -
631B TYR* 4.7 12.9 + - - -
687B CYS 4.3 0.2 - - - -
688B LEU* 1.3 75.2 + - - +
690B TYR* 1.3 62.1 + - - +
698B THR* 4.4 12.3 - - - +
699B VAL 3.4 7.0 - - - -
700B GLU* 3.8 18.2 + - - +
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Residues in contact with TYR 690 (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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595B ASP* 5.7 1.7 - - - +
596B CYS* 3.6 34.6 + - + +
598B VAL* 5.0 0.2 - - + -
625B ILE* 3.8 23.8 - - + -
627B MET 3.0 14.4 - - - +
628B CYS* 3.6 9.9 - - + -
688B LEU* 3.4 28.0 - - + -
689B SER* 1.3 73.7 - - - +
691B GLN* 1.3 65.1 + - - +
692B TYR* 3.8 20.0 + + - -
698B THR* 3.7 5.4 - - - +
699B VAL* 2.9 71.0 + - + +
701B ASP* 4.1 20.7 + - + +
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Residues in contact with GLN 691 (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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625B ILE* 3.3 6.2 - - - -
626B ILE* 2.9 54.3 + - + +
627B MET* 3.1 11.2 + - + +
690B TYR* 1.3 80.1 - - - +
692B TYR* 1.3 67.5 + - - +
695B LEU* 3.0 24.4 + - + +
696B GLU* 3.5 19.8 + - - +
697B ASP 3.6 19.3 - - - +
698B THR* 4.6 9.5 + - - +
699B VAL* 5.4 0.4 - - - -
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Residues in contact with TYR 692 (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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596B CYS* 3.7 22.4 - - + +
624B GLU* 3.2 25.8 - - + +
625B ILE* 3.9 17.5 - - + -
626B ILE* 4.0 3.4 - - - +
690B TYR* 3.8 22.8 + + - -
691B GLN* 1.3 79.5 - - - +
693B SER* 1.3 71.4 + - - +
694B GLY 3.3 0.3 + - - -
695B LEU* 3.1 50.4 + - + +
697B ASP 5.0 0.8 + - - -
699B VAL* 4.5 13.5 - - + -
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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