Contacts of the strand formed by residues 682 - 688 (chain A) in PDB entry 4APT
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 VAL 682 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A SER* 3.5 34.3 - - - +
614A SER 3.8 2.7 - - - +
615A THR* 3.7 21.8 - - + +
653A VAL* 3.4 6.1 - - - +
654A PHE* 2.6 56.1 + - + +
680A GLY 3.4 11.6 + - - +
681A ASP* 1.3 71.3 - - - +
683A CYS* 1.3 57.2 + - - +
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Residues in contact with CYS 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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612A ASP 3.6 1.0 - - - +
613A SER* 3.4 2.8 - - - -
614A SER* 2.8 46.8 + - - +
616A VAL* 3.9 22.9 - - - -
632A PHE* 4.0 7.0 - - - -
651A PHE* 3.8 28.0 - - + -
652A PHE 3.4 8.1 - - - +
653A VAL* 4.2 4.9 - - - +
677A LEU* 4.2 10.5 - - - -
681A ASP 4.3 0.9 - - - -
682A VAL* 1.3 72.8 - - - +
684A ILE* 1.3 63.7 + - - +
685A SER* 4.0 2.8 + - - -
568B PRO* 4.2 17.7 - - + -
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Residues in contact with ILE 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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596A THR* 3.7 24.5 - - + +
599A PHE* 3.6 31.2 - - + -
611A ILE* 3.9 16.8 - - + -
612A ASP 3.5 3.1 - - - -
613A SER* 3.8 18.4 - - - +
652A PHE* 3.0 50.2 + - + +
654A PHE* 3.8 30.3 - - + +
682A VAL 3.6 0.4 + - - +
683A CYS* 1.3 71.9 - - - +
685A SER* 1.3 67.6 + - - +
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Residues in contact with SER 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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599A PHE* 4.9 4.9 - - - -
611A ILE* 3.3 8.7 - - - +
612A ASP* 2.9 35.6 + - - +
683A CYS 4.3 1.7 + - - -
684A ILE* 1.3 79.5 + - - +
686A LEU* 1.3 63.2 + - - +
687A THR* 4.6 0.7 - - - -
568B PRO* 3.7 28.6 + - - +
571B LEU* 3.8 26.5 - - - -
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Residues in contact with LEU 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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599A PHE* 4.0 27.9 - - + +
602A SER* 4.9 5.2 - - - -
603A ALA* 4.1 19.7 - - + +
609A LEU* 4.1 23.8 - - + -
610A LYS 3.8 4.0 - - - +
611A ILE* 4.5 7.0 - - + -
685A SER* 1.3 76.8 - - - +
687A THR* 1.3 65.8 + - - +
571B LEU* 4.7 2.6 - - - +
572B PRO 4.2 3.8 - - - +
574B TYR* 3.1 31.8 - - + +
575B PHE* 3.6 53.4 - - + +
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Residues in contact with THR 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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609A LEU* 3.3 10.8 - - - -
610A LYS* 2.7 59.9 + - - +
612A ASP* 3.4 33.0 - - + +
685A SER 3.7 1.5 + - - +
686A LEU* 1.3 79.7 - - - +
688A LEU* 1.3 59.7 + - - +
571B LEU* 3.6 36.3 - - + -
574B TYR* 4.1 5.8 - - - -
646B LEU* 6.5 0.4 - - - -
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Residues in contact with LEU 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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608A ASP* 3.8 7.4 - - + +
609A LEU* 4.2 11.2 - - + -
610A LYS* 3.6 15.2 - - - +
687A THR* 1.3 80.5 + - - +
689A LYS* 1.3 64.6 - - + +
574B TYR* 3.5 12.3 - - - +
646B LEU* 4.2 16.0 - - + +
648B GLU* 3.2 21.3 - - - +
665B ARG* 3.3 24.2 - - - +
669B LEU* 3.8 33.9 - - + -
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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