Contacts of the strand formed by residues 732 - 740 (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 THR 732 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B GLN* 4.0 19.5 - - + +
233B LEU 3.3 15.5 - - - +
234B SER* 3.0 17.3 + - - +
704B GLY 3.9 0.2 - - - +
705B VAL* 3.0 7.4 - - - +
706B LYS* 2.6 52.8 + - + +
729B GLN* 3.3 23.8 + - - +
730B PRO 2.6 19.5 + - - -
731B ARG* 1.3 72.9 - - - +
733B LEU* 1.3 74.0 + - - +
734B TYR* 4.3 1.5 - - + -
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Residues in contact with LEU 733 (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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232B GLN* 3.3 3.5 - - - -
233B LEU* 2.8 41.4 + - + +
235B PRO* 4.3 20.6 - - + -
704B GLY 3.4 5.4 - - - +
705B VAL* 3.6 28.3 - - + -
731B ARG* 4.3 15.7 - - + -
732B THR* 1.3 78.5 - - - +
734B TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 734 (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* 3.5 17.2 - - - -
116B GLY* 3.5 18.0 + - - -
230B GLU* 3.5 20.2 - - - +
231B GLY 2.9 20.2 - - - +
232B GLN* 3.8 6.7 - - + -
686B ALA 4.3 1.7 + - - -
687B ARG* 3.6 24.4 - - - +
703B PHE* 3.3 4.3 - - - +
704B GLY* 2.6 77.2 + - - +
705B VAL* 3.5 7.1 + - - -
706B LYS* 3.8 36.8 - - + -
732B THR* 4.3 2.7 - - + -
733B LEU* 1.3 78.6 - - - +
735B MET* 1.3 59.3 - - - +
736B GLN* 4.0 19.7 - - + -
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Residues in contact with MET 735 (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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229B VAL* 3.7 16.6 - - + +
230B GLU* 3.2 3.3 - - - -
231B GLY* 3.1 29.0 + - - +
701B LEU* 4.6 9.0 - - + -
702B ALA 3.1 14.8 - - - +
703B PHE* 4.1 28.9 - - + -
734B TYR* 1.3 76.8 - - - +
736B GLN* 1.3 95.6 + - - +
737B GLY* 3.1 11.0 - - - +
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Residues in contact with GLN 736 (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 27.1 - - + +
116B GLY* 3.3 16.4 - - - -
117B ALA 4.6 1.0 + - - -
229B VAL 3.4 5.8 - - - +
230B GLU* 3.0 33.3 + - + +
687B ARG* 2.9 33.4 + - - -
700B ASN 3.9 0.7 - - - +
701B LEU* 3.4 5.5 - - - +
702B ALA* 2.9 37.2 + - + +
734B TYR* 4.0 13.2 - - + -
735B MET* 1.3 82.9 - - - +
737B GLY* 1.3 58.7 + - - +
738B SER 4.3 0.2 - - - -
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Residues in contact with GLY 737 (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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227B ALA 4.0 0.2 - - - +
228B GLY* 3.0 3.5 - - - -
229B VAL* 2.8 44.9 + - - +
699B LEU* 5.7 1.6 - - - -
700B ASN 3.5 7.6 - - - -
701B LEU* 4.8 4.5 - - - -
735B MET* 3.1 10.8 - - - +
736B GLN* 1.3 76.2 - - - +
738B SER* 1.3 61.3 + - - -
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Residues in contact with SER 738 (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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227B ALA 3.3 9.2 - - - -
228B GLY* 3.8 5.2 - - - -
698B ASP 4.0 5.1 + - - -
699B LEU* 3.3 20.4 - - - +
700B ASN* 3.2 29.1 + - - +
737B GLY* 1.3 74.6 - - - -
739B LEU* 1.3 80.1 + - - +
740B LYS* 4.6 6.8 - - - +
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Residues in contact with LEU 739 (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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226B GLU* 3.2 4.3 - - - +
227B ALA* 2.9 37.8 + - + +
697B ALA* 3.0 47.8 - - + +
698B ASP 3.0 9.2 - - - -
699B LEU* 4.4 10.8 - - + -
738B SER* 1.3 83.0 + - - +
740B LYS* 1.3 70.7 + - - +
741B PHE* 3.4 32.5 - - + -
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Residues in contact with LYS 740 (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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225B ILE 3.1 8.1 - - - +
226B GLU* 3.3 30.7 + - + +
696B MET 5.1 0.3 - - - +
697B ALA* 4.0 2.1 - - - -
698B ASP* 3.2 51.6 + - + +
738B SER* 4.6 7.0 - - - +
739B LEU* 1.3 83.1 - - - +
741B PHE* 1.3 71.0 + - - +
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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