Contacts of the strand formed by residues 681 - 691 (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 PHE 681 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A ASP* 5.3 3.6 - - + -
655A PHE* 2.8 9.0 - - - +
656A GLN* 2.6 82.6 + - + +
678A ILE* 6.4 0.4 - - + -
679A PRO 4.3 5.4 - - - -
680A GLY* 1.3 88.0 - - - +
682A MET* 1.3 63.3 + - - +
683A LEU* 3.9 29.4 - - + -
711A GLN* 4.6 13.9 - - - +
712A ASP 5.3 0.2 - - - +
713A TYR* 3.4 47.6 - + + -
714A PHE 5.3 4.5 - - - -
715A ILE* 5.5 3.8 - - + -
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Residues in contact with MET 682 (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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638A LEU* 4.5 13.9 - - + -
653A SER* 3.3 19.1 - - - +
654A ASP 2.9 8.3 - - - +
655A PHE* 3.8 27.8 - - + +
681A PHE* 1.3 75.7 - - - +
683A LEU* 1.3 67.3 + - - +
684A TRP* 3.9 27.3 - - + +
711A GLN* 4.5 13.7 - - - +
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Residues in contact with LEU 683 (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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653A SER* 2.5 26.4 + - - -
654A ASP* 2.7 41.6 + - + +
681A PHE* 3.9 20.6 - - + -
682A MET* 1.3 80.4 - - - +
684A TRP* 1.3 59.3 + - - +
707A ASN* 3.0 37.7 - - + +
711A GLN* 4.2 14.1 - - + +
713A TYR* 3.5 46.2 - - + +
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Residues in contact with TRP 684 (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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638A LEU* 3.7 21.1 - - + -
639A GLY* 5.9 0.9 - - - -
651A LEU* 4.3 30.3 - - + -
652A ASN* 3.4 21.8 - - - -
653A SER* 3.2 28.3 + - - -
654A ASP* 5.9 0.7 - - - -
682A MET* 3.9 26.8 - - + -
683A LEU* 1.3 77.7 - - - +
685A GLY* 1.3 55.0 + - - +
707A ASN* 3.1 10.4 + - - +
708A ILE* 2.8 40.4 + - + -
709A PHE* 3.5 43.7 - + + +
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Residues in contact with GLY 685 (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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651A LEU* 3.5 4.6 - - - +
652A ASN* 2.6 55.6 + - - +
654A ASP* 5.7 0.4 + - - -
683A LEU 4.3 0.2 - - - -
684A TRP* 1.3 75.3 - - - +
686A ALA* 1.3 61.4 + - - +
705A VAL 3.7 11.4 - - - -
706A LYS* 4.8 1.6 - - - -
707A ASN 4.3 3.4 - - - -
708A ILE* 3.9 3.1 - - - -
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Residues in contact with ALA 686 (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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114A LYS 5.8 0.2 - - - -
650A ASN* 2.8 13.7 - - - +
651A LEU* 4.2 13.2 - - + -
652A ASN* 4.4 1.1 - - - -
685A GLY* 1.3 75.0 - - - +
687A ARG* 1.3 69.0 + - - +
704A GLY* 3.6 0.3 - - - -
705A VAL* 3.1 29.2 + - + +
708A ILE* 3.9 14.3 - - + +
734A TYR* 3.8 3.1 + - - -
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Residues in contact with ARG 687 (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* 3.0 33.2 + - - +
114A LYS* 3.6 14.5 + - - +
648A THR* 3.6 16.6 - - - +
649A PHE* 3.5 4.9 - - - +
650A ASN* 2.6 65.0 + - + +
686A ALA* 1.3 81.6 - - - +
688A VAL* 1.3 68.2 + - - +
689A ALA* 4.4 12.2 - - - +
702A ALA* 4.4 7.3 - - + +
703A PHE 3.4 17.3 - - - +
704A GLY* 3.8 3.1 - - - -
734A TYR* 3.4 21.8 - - + +
736A GLN* 2.7 38.9 + - - -
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Residues in contact with VAL 688 (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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647A TRP* 4.1 18.8 - - + -
648A THR 3.3 2.9 - - - +
649A PHE* 3.4 31.9 - - + -
687A ARG* 1.3 76.9 - - - +
689A ALA* 1.3 63.1 + - - +
702A ALA* 3.2 4.2 - - - -
703A PHE* 3.0 42.9 + - + +
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Residues in contact with ALA 689 (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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647A TRP* 3.4 6.3 - - - +
648A THR* 2.6 55.0 + - - +
687A ARG* 4.3 15.4 - - - +
688A VAL* 1.3 75.2 - - - +
690A TYR* 1.3 61.3 + - - +
700A ASN* 5.2 6.5 - - + +
701A LEU 3.4 5.6 - - - +
702A ALA* 3.2 22.2 - - + -
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Residues in contact with TYR 690 (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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646A ASN* 3.2 35.2 + - + +
647A TRP* 3.1 61.6 - + + -
689A ALA* 1.3 75.0 - - - +
691A ASP* 1.3 74.2 + - - +
692A PHE* 3.4 54.9 + + + -
693A GLY 4.6 1.8 - - - -
700A ASN* 3.2 15.4 + - - -
701A LEU* 3.2 22.8 + - + +
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Residues in contact with ASP 691 (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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646A ASN* 3.1 23.9 + - + +
690A TYR* 1.3 77.1 - - - +
692A PHE* 1.3 52.8 + - - +
693A GLY 2.8 17.7 + - - -
694A PRO* 3.2 41.4 - - - +
698A ASP* 4.0 10.9 - - - +
699A LEU 4.0 2.6 - - - +
700A ASN* 2.6 34.8 - - - +
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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