Contacts of the strand formed by residues 732 - 740 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A GLN* 3.9 18.4 - - + +
233A LEU 2.9 29.8 - - - +
234A SER* 3.2 14.1 + - - +
704A GLY 3.8 0.3 - - - +
705A VAL* 3.2 3.3 - - - -
706A LYS* 2.5 56.4 + - + +
729A GLN* 3.3 20.4 + - - +
730A PRO 2.7 18.8 + - - -
731A ARG* 1.3 74.5 - - - +
733A LEU* 1.3 64.2 + - - +
734A TYR* 3.9 2.0 + - + +
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Residues in contact with LEU 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLY 4.6 0.2 - - - -
232A GLN* 3.4 1.2 - - - -
233A LEU* 2.8 36.0 + - + +
235A PRO* 4.1 23.6 - - + -
704A GLY 3.6 4.5 - - - +
705A VAL* 3.7 31.4 - - + -
731A ARG* 4.3 13.5 - - + -
732A THR* 1.3 73.5 - - - +
734A TYR* 1.3 59.0 + - - +
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Residues in contact with TYR 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR 3.7 3.4 - - - -
116A GLY* 3.2 38.6 + - - -
230A GLU* 4.3 5.8 - - - +
231A GLY 2.9 16.8 - - - +
232A GLN* 3.6 16.4 - - + -
686A ALA 3.8 3.3 + - - -
687A ARG* 3.4 32.2 - - - +
702A ALA 5.2 0.2 - - - -
703A PHE* 3.6 6.0 - - - +
704A GLY* 2.7 65.8 + - - -
705A VAL 4.0 3.1 - - - -
706A LYS* 3.7 34.8 - - + -
732A THR* 4.3 4.5 - - + -
733A LEU* 1.3 75.6 - - - +
735A MET* 1.3 64.2 + - - +
736A GLN* 4.0 14.1 - - + -
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Residues in contact with MET 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A VAL* 3.9 20.0 - - + +
230A GLU* 2.8 28.8 - - - +
231A GLY* 2.8 14.8 + - - +
701A LEU* 5.3 8.1 - - + -
702A ALA 3.3 13.2 - - - +
703A PHE* 3.9 32.3 - - + -
734A TYR* 1.3 75.6 - - - +
736A GLN* 1.3 100.7 + - - +
737A GLY* 3.5 6.5 - - - +
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Residues in contact with GLN 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA* 3.6 31.6 + - + +
116A GLY* 3.8 6.1 - - - -
117A ALA 4.4 2.0 + - - -
229A VAL 3.1 7.0 - - - +
230A GLU* 3.1 28.4 + - + +
687A ARG* 2.7 37.0 + - - -
700A ASN 5.3 0.2 - - - -
701A LEU* 3.4 5.4 - - - +
702A ALA* 2.9 35.3 + - + +
734A TYR* 4.0 12.8 - - + -
735A MET* 1.3 90.1 - - - +
737A GLY* 1.3 59.5 + - - +
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Residues in contact with GLY 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ALA 3.7 0.9 - - - +
228A GLY* 2.9 7.1 - - - -
229A VAL* 2.7 42.8 + - - +
699A LEU* 5.5 1.1 - - - -
700A ASN 3.3 9.0 - - - -
701A LEU* 4.6 5.4 - - - -
735A MET* 3.5 7.1 - - - +
736A GLN* 1.3 77.5 - - - +
738A SER* 1.3 60.6 + - - -
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Residues in contact with SER 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLU* 6.1 0.2 - - - +
227A ALA 3.4 5.0 + - - -
228A GLY* 4.3 2.5 - - - -
698A ASP 4.0 7.4 + - - -
699A LEU* 2.9 11.4 - - - +
700A ASN* 2.7 49.9 + - - -
737A GLY* 1.3 74.2 - - - -
739A LEU* 1.3 67.8 + - - +
740A LYS 4.7 0.2 + - - -
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Residues in contact with LEU 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 4.0 3.6 - - + +
226A GLU* 3.2 3.5 - - - +
227A ALA* 2.7 50.9 + - + +
697A ALA* 3.8 26.5 - - + +
699A LEU* 3.6 24.0 - - + -
738A SER* 1.3 79.9 + - - +
740A LYS* 1.3 58.3 + - - +
741A PHE* 3.8 29.4 - - + -
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Residues in contact with LYS 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE 3.3 6.3 - - - -
226A GLU* 4.2 9.4 - - - +
697A ALA* 3.1 27.1 + - - +
698A ASP* 4.4 15.9 + - - +
739A LEU* 1.3 75.4 - - - +
741A PHE* 1.3 77.4 + - - +
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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