Contacts of the strand formed by residues 684 - 692 (chain T) in PDB entry 2P8Z
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 684 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565T GLU 3.7 16.4 - - - +
566T THR* 3.8 10.5 - - - +
567T VAL* 4.2 10.1 - - + +
590T ALA* 4.6 5.2 - - + -
591T GLU 4.1 1.3 - - - -
593T ILE* 3.6 2.2 - - - +
643T PRO 3.8 0.8 + - - -
644T ASN* 3.0 20.2 + - + +
645T LEU 3.0 23.9 + - - +
667T PHE* 4.4 2.2 - - + -
681T MET* 4.0 18.2 - - + -
682T ARG 3.6 13.7 - - - +
683T SER* 1.3 78.4 - - - +
685T ARG* 1.3 69.5 + - - +
686T VAL* 4.2 15.9 - - + -
713T THR* 5.9 0.2 - - + -
717T PHE* 3.9 19.5 - - + -
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Residues in contact with ARG 685 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590T ALA* 3.1 6.6 - - - +
591T GLU* 2.8 72.4 + - + +
592T PRO 4.6 2.0 - - - +
593T ILE* 3.5 17.9 - - + +
625T TRP* 3.6 48.6 - - + -
626T ASP 5.9 1.0 - - - +
629T ASP* 2.8 38.4 + - - +
645T LEU* 3.6 7.4 - - + +
647T ILE* 4.1 7.9 - - + +
649T GLN* 3.6 5.1 - - - +
684T VAL* 1.3 73.7 - - - +
686T VAL* 1.3 65.8 + - - +
687T ASN* 2.8 28.4 + - - +
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Residues in contact with VAL 686 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588T LEU* 3.7 37.5 - - + -
589T LYS 3.5 2.9 - - - -
590T ALA* 4.5 9.0 - - + -
645T LEU 2.9 13.4 + - - +
646T VAL* 3.5 3.9 - - + +
647T ILE* 2.9 26.7 + - - +
667T PHE* 3.8 24.2 - - + -
684T VAL* 4.2 13.0 - - + -
685T ARG* 1.3 80.1 - - - +
687T ASN* 1.3 66.7 + - - +
688T ILE* 4.0 2.6 + - + +
709T MET* 4.4 13.0 - - + -
713T THR* 4.3 14.6 - - + +
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Residues in contact with ASN 687 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570T GLU* 5.2 5.9 + - - -
588T LEU* 3.1 6.9 - - - +
589T LYS* 2.8 40.9 + - + +
591T GLU* 2.8 35.0 + - - +
647T ILE* 3.6 12.8 - - - +
649T GLN* 3.3 27.4 + - - +
685T ARG* 2.8 33.4 + - - +
686T VAL* 1.3 72.2 - - - +
688T ILE* 1.3 63.7 + - - +
689T LEU* 3.3 6.8 + - + +
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Residues in contact with ILE 688 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586T ILE* 4.7 6.7 - - + -
587T TYR 3.9 7.0 - - - +
588T LEU* 4.2 5.6 - - + -
634T TRP* 4.2 16.6 - - + -
646T VAL* 3.7 27.6 - - + -
647T ILE 3.1 13.6 + - - +
648T ASP* 4.6 3.6 - - + +
649T GLN* 3.0 29.8 + - - +
650T THR* 3.4 21.3 + - + -
656T LEU* 5.9 0.9 - - + -
663T VAL* 3.8 24.0 - - + -
686T VAL* 4.8 3.6 - - + -
687T ASN* 1.3 71.6 - - - +
689T LEU* 1.3 60.3 + - - +
690T ASP 4.2 2.0 - - - +
691T VAL* 3.7 20.4 - - + -
709T MET* 4.7 9.9 - - + -
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Residues in contact with LEU 689 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574T THR* 3.9 17.3 - - + +
587T TYR* 2.8 17.2 + - + +
588T LEU* 4.3 3.6 - - - -
589T LYS* 3.7 36.6 - - + +
649T GLN* 3.5 42.3 - - + +
650T THR* 3.8 6.4 - - - -
651T LYS 4.9 0.9 + - - -
687T ASN* 3.9 13.2 - - + +
688T ILE* 1.3 76.3 - - - +
690T ASP* 1.3 65.7 + - + +
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Residues in contact with ASP 690 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587T TYR* 2.8 49.4 + - + +
650T THR* 3.8 7.5 - - - +
651T LYS 5.5 1.7 + - - -
652T ALA 5.8 0.9 + - - -
653T VAL* 3.8 10.0 - - - +
688T ILE* 3.6 1.4 - - - +
689T LEU* 1.3 84.2 - - + +
691T VAL* 1.3 80.6 + - - +
692T THR* 4.0 16.6 - - - +
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Residues in contact with VAL 691 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585T ARG 3.5 11.0 - - - +
586T ILE* 4.3 17.0 - - + -
587T TYR* 4.9 0.2 - - - -
650T THR* 4.2 6.7 - - + -
653T VAL* 3.4 31.4 - - + +
656T LEU* 4.6 4.7 - - + -
659T ILE* 3.7 19.7 - - + -
688T ILE* 3.7 22.9 - - + -
690T ASP* 1.3 88.6 + - - +
692T THR* 1.3 67.3 + - - +
693T LEU* 3.5 31.4 + - + -
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Residues in contact with THR 692 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583T HIS 3.8 3.8 + - - +
584T ASN* 3.3 6.8 - - - +
585T ARG* 3.0 46.7 + - - +
587T TYR* 4.3 12.4 + - + +
690T ASP* 4.0 15.7 - - - +
691T VAL* 1.3 78.5 - - - +
693T LEU* 1.3 62.5 + - - +
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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