Contacts of the strand formed by residues 699 - 706 (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 LEU 699 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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691B ASP* 4.3 1.0 + - - -
692B PHE* 3.1 45.0 + - + +
697B ALA* 2.3 23.3 + - + +
698B ASP* 1.3 69.3 - - - +
700B ASN* 1.3 63.0 + - - +
701B LEU* 3.7 35.7 - - + -
737B GLY* 5.7 1.6 - - - -
738B SER 3.3 17.0 - - - +
739B LEU* 4.4 14.1 - - + -
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Residues in contact with ASN 700 (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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648B THR* 5.3 3.6 + - - -
689B ALA* 4.7 7.7 - - - +
690B TYR 3.3 23.7 + - - +
691B ASP* 2.9 35.5 - - - +
698B ASP* 3.8 3.5 + - - +
699B LEU* 1.3 77.1 + - - +
701B LEU* 1.3 63.1 + - - +
736B GLN 4.4 0.9 - - - -
737B GLY* 3.5 5.0 - - - -
738B SER* 3.2 42.1 + - - +
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Residues in contact with LEU 701 (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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689B ALA* 3.0 4.1 - - - +
690B TYR* 2.9 30.7 + - - +
692B PHE* 3.7 27.8 - - + -
699B LEU* 3.7 25.5 + - + -
700B ASN* 1.3 74.5 - - - +
702B ALA* 1.3 63.3 + - - +
703B PHE* 4.1 26.2 - - + -
735B MET* 4.6 11.4 - - + -
736B GLN 3.4 11.7 - - - +
737B GLY* 4.8 2.7 - - - -
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Residues in contact with ALA 702 (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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687B ARG* 4.0 10.5 - - - +
688B VAL 3.2 7.0 - - - +
689B ALA* 3.4 19.1 - - + -
701B LEU* 1.3 77.5 - - - +
703B PHE* 1.3 71.7 + - - +
735B MET* 3.1 7.8 - - - +
736B GLN* 2.9 55.8 + - + +
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Residues in contact with PHE 703 (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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687B ARG* 3.5 2.6 - - - +
688B VAL* 3.0 41.5 + - + +
701B LEU* 4.1 24.9 - - + -
702B ALA* 1.3 83.4 - - - +
704B GLY* 1.3 60.0 + - - +
734B TYR 3.3 7.2 - - - +
735B MET* 4.1 25.8 - - + -
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Residues in contact with GLY 704 (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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686B ALA 3.5 9.0 - - - -
687B ARG* 3.9 2.2 - - - -
703B PHE* 1.3 76.7 - - - +
705B VAL* 1.3 64.3 + - - +
733B LEU* 3.4 3.3 - - - +
734B TYR* 2.6 67.9 + - - +
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Residues in contact with VAL 705 (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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685B GLY* 3.5 3.1 - - - -
686B ALA* 3.0 19.9 + - + +
704B GLY* 1.3 77.7 - - - +
706B LYS* 1.3 75.3 + - - +
708B ILE* 3.2 39.9 - - + +
731B ARG* 3.9 18.6 - - + -
732B THR 3.0 10.5 - - - +
733B LEU* 3.6 20.0 - - + -
734B TYR* 3.8 3.9 + - - -
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Residues in contact with LYS 706 (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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115B THR 3.3 24.7 - - - +
116B GLY 3.4 15.9 + - - -
122B GLU* 2.6 29.9 + - - -
230B GLU* 4.5 0.2 + - - -
232B GLN* 3.4 21.7 + - - +
684B TRP 4.4 0.4 - - - -
685B GLY* 4.6 2.5 - - - -
705B VAL* 1.3 77.5 - - - +
707B ASN* 1.3 69.6 + - + +
708B ILE* 3.3 2.2 + - - -
729B GLN* 3.3 32.1 - - - +
731B ARG* 3.0 0.9 - - - -
732B THR* 2.6 47.5 + - - -
734B TYR* 3.8 18.4 - - + -
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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