Contacts of the strand formed by residues 681 - 692 (chain B) in PDB entry 1PO3
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 PHE 681 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B ASP* 4.8 7.9 - - + -
655B PHE* 3.0 21.9 - - - +
656B GLN* 2.9 51.3 + - + -
678B ILE* 6.2 0.9 - - + -
679B PRO 4.6 5.2 - - - -
680B GLY* 1.3 80.4 - - - +
682B MET* 1.3 59.3 + - - +
683B LEU* 3.6 29.6 - - + -
711B GLN* 3.8 19.7 - - - +
713B TYR* 3.4 46.4 - + + -
714B PHE 5.1 4.9 - - - -
715B ILE* 5.5 3.8 - - + -
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Residues in contact with MET 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LEU* 4.8 11.4 - - + -
653B SER* 3.4 18.4 - - - +
654B ASP 3.2 4.7 - - - +
655B PHE* 4.1 28.5 - - + +
681B PHE* 1.3 75.2 - - - +
683B LEU* 1.3 70.1 + - - +
684B TRP* 4.3 22.5 - - + +
711B GLN* 3.8 17.9 - - - +
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Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B SER* 2.9 7.4 + - - -
654B ASP* 2.7 46.7 + - + +
681B PHE* 3.6 25.1 - - + -
682B MET* 1.3 84.5 - - - +
684B TRP* 1.3 65.2 + - - +
707B ASN* 3.5 37.0 - - + +
711B GLN* 3.5 22.9 - - + +
713B TYR* 3.3 35.4 - - + +
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Residues in contact with TRP 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LEU* 3.8 25.1 - - + -
651B LEU* 4.2 30.1 - - + -
652B ASN* 3.0 25.1 - - - -
653B SER* 3.4 19.7 + - - -
654B ASP* 6.0 0.4 - - - -
682B MET* 4.3 23.4 - - + +
683B LEU* 1.3 84.1 - - - +
685B GLY* 1.3 60.9 + - - +
707B ASN* 2.9 26.5 + - - +
708B ILE* 2.9 14.6 + - + +
709B PHE* 3.7 39.0 - + + -
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Residues in contact with GLY 685 (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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651B LEU* 3.2 4.1 - - - +
652B ASN* 2.6 56.1 + - - +
684B TRP* 1.3 76.4 - - - +
686B ALA* 1.3 60.6 + - - +
705B VAL 3.5 8.7 - - - -
706B LYS* 4.6 1.8 - - - -
707B ASN 4.6 1.6 - - - -
708B ILE* 3.4 8.1 - - - -
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Residues in contact with ALA 686 (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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650B ASN* 2.9 11.4 - - - +
651B LEU* 4.3 14.6 - - + -
652B ASN* 4.8 0.2 - - - -
685B GLY* 1.3 75.0 - - - +
687B ARG* 1.3 62.4 + - - +
704B GLY* 3.5 0.5 - - - -
705B VAL* 3.0 31.8 + - + +
708B ILE* 3.5 13.6 - - + +
734B TYR* 4.3 1.0 + - - -
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Residues in contact with ARG 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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113B ALA* 3.2 29.8 + - - +
114B LYS* 3.6 10.8 + - - +
643B LYS* 5.0 2.0 - - - +
648B THR* 3.6 21.7 - - - +
649B PHE* 3.5 4.7 - - - +
650B ASN* 2.5 75.9 + - + +
686B ALA* 1.3 78.0 - - - +
688B VAL* 1.3 67.5 + - - +
689B ALA* 4.3 11.6 - - - +
702B ALA* 4.0 8.8 - - + +
703B PHE 3.5 17.3 - - - +
704B GLY* 3.9 2.0 - - - +
734B TYR* 3.6 20.4 - - - +
736B GLN* 2.9 29.0 + - - -
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Residues in contact with VAL 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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647B TRP* 4.1 23.6 - - + -
648B THR 3.4 4.3 - - - +
649B PHE* 4.0 28.0 - - + +
687B ARG* 1.3 78.2 - - - +
689B ALA* 1.3 65.5 + - - +
702B ALA* 3.2 1.9 - - - +
703B PHE* 3.0 41.0 + - + +
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Residues in contact with ALA 689 (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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647B TRP* 3.5 19.2 - - - -
648B THR* 3.1 35.1 + - - +
687B ARG* 4.3 13.0 - - - +
688B VAL* 1.3 76.1 - - - +
690B TYR* 1.3 65.3 + - - +
700B ASN* 4.7 9.4 - - - +
701B LEU 3.0 15.5 - - - +
702B ALA* 3.4 14.8 - - + -
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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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646B ASN* 3.2 47.3 + - + +
647B TRP* 3.4 48.2 - + + -
648B THR* 5.1 1.1 - - - -
689B ALA* 1.3 78.5 - - - +
691B ASP* 1.3 66.8 + - - +
692B PHE* 3.2 66.3 - + + -
693B GLY 4.8 1.6 + - - -
700B ASN* 3.3 7.8 + - - +
701B LEU 2.9 27.1 + - - +
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Residues in contact with ASP 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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646B ASN* 3.1 35.0 + - - +
648B THR* 5.6 0.9 + - - +
690B TYR* 1.3 75.9 - - - +
692B PHE* 1.3 63.0 + - - +
693B GLY 3.1 16.3 + - - +
694B PRO* 4.0 21.8 - - - +
698B ASP* 4.2 10.4 - - - +
699B LEU 4.3 5.2 + - - -
700B ASN* 2.9 27.5 - - - +
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Residues in contact with PHE 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B TYR* 3.2 51.6 - + + -
691B ASP* 1.3 67.2 - - - +
693B GLY* 1.3 72.4 + - - +
695B GLN 3.5 2.6 - - - +
697B ALA 5.1 1.7 + - - -
698B ASP 4.8 0.2 + - - -
699B LEU* 3.1 43.4 + - + +
701B LEU* 3.7 31.4 - - + -
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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