Contacts of the strand formed by residues 585 - 592 (chain T) in PDB entry 2P8W
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 ARG 585 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576T LEU* 3.1 33.1 - - + +
577T SER 3.2 5.8 - - - +
578T LYS* 3.6 40.2 - - + +
582T LYS 5.2 4.7 + - - +
583T HIS 5.2 2.5 - - - +
584T ASN* 1.3 81.2 - - - +
586T ILE* 1.3 66.8 + - - +
587T TYR* 4.3 7.4 - - + -
691T VAL* 3.5 6.3 - - - +
692T THR* 3.0 46.2 + - - +
708T THR* 4.5 0.4 - - - -
840T ASP 2.9 24.3 + - - -
841T LYS 3.0 17.4 + - - -
842T LEU* 3.2 33.6 + - - +
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Residues in contact with ILE 586 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575T ALA 3.4 5.0 - - - +
576T LEU* 3.6 2.6 - - - +
577T SER 2.9 27.7 + - - -
584T ASN* 6.4 0.4 - - + -
585T ARG* 1.3 78.6 - - - +
587T TYR* 1.3 68.4 + - - +
588T LEU* 3.9 28.0 + - + -
659T ILE* 5.6 0.2 - - + -
663T VAL* 4.7 7.2 - - + -
688T ILE* 4.7 10.5 - - + -
690T ASP 3.8 4.3 - - - +
691T VAL* 4.3 17.9 - - + -
705T ILE* 4.5 13.9 - - + -
708T THR* 3.8 15.4 - - + +
709T MET* 3.7 40.8 - - + +
712T ALA* 4.1 9.6 - - + +
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Residues in contact with TYR 587 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574T THR* 3.9 23.6 - - + -
575T ALA 3.2 5.2 - - - -
576T LEU* 3.4 34.0 - - + +
585T ARG* 4.3 14.8 - - + -
586T ILE* 1.3 75.0 - - - +
588T LEU* 1.3 62.4 + - - +
688T ILE* 3.8 3.1 - - - +
689T LEU* 2.8 28.1 + - + -
690T ASP* 2.8 51.3 + - + +
692T THR* 4.3 14.2 + - + +
842T LEU* 3.4 32.4 - - + +
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Residues in contact with LEU 588 (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* 4.1 1.2 - - - +
575T ALA* 2.6 45.3 + - + +
586T ILE* 3.9 11.7 - - + -
587T TYR* 1.3 74.4 - - - +
589T LYS* 1.3 69.4 + - - +
590T ALA* 4.7 0.4 - - + +
686T VAL* 3.7 26.7 - - + -
687T ASN 3.1 19.3 - - - +
688T ILE* 4.2 4.0 - - + -
689T LEU* 4.2 4.3 - - - +
709T MET* 4.0 15.5 - - + -
712T ALA* 3.6 46.0 - - + +
713T THR* 4.0 8.7 - - - +
716T GLY* 4.0 13.9 - - - -
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Residues in contact with LYS 589 (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* 3.6 35.5 + - + +
571T SER* 3.3 17.9 + - - +
573T GLN* 4.2 4.9 - - - +
574T THR* 3.3 38.6 + - - +
588T LEU* 1.3 85.2 - - - +
590T ALA* 1.3 61.8 + - - +
686T VAL* 3.5 2.8 - - - +
687T ASN* 2.8 38.8 + - + +
689T LEU* 3.7 20.4 - - + +
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Residues in contact with ALA 590 (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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567T VAL* 4.7 2.0 - - + -
569T SER 3.7 1.0 - - - +
570T GLU* 3.1 4.6 - - - +
571T SER* 2.6 34.0 + - - -
588T LEU* 5.3 0.7 - - + -
589T LYS* 1.3 74.1 - - - +
591T GLU* 1.3 62.0 + - - +
684T VAL* 4.6 8.3 - - + -
685T ARG 3.1 9.6 - - - +
686T VAL* 4.4 11.9 - - + +
713T THR 5.4 0.2 - - - +
716T GLY* 3.6 27.8 - - - +
717T PHE* 4.0 8.5 - - + +
720T ALA* 3.8 5.6 - - + +
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Residues in contact with GLU 591 (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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567T VAL* 3.6 6.9 - - - +
569T SER 3.9 2.7 - - - -
570T GLU* 4.1 18.7 - - + +
590T ALA* 1.3 76.1 - - - +
592T PRO* 1.3 78.4 - - + +
685T ARG* 2.8 73.3 + - + +
687T ASN* 2.8 26.8 + - - +
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Residues in contact with PRO 592 (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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567T VAL* 3.4 15.0 - - + +
568T GLU* 3.3 35.2 - - - +
569T SER* 3.4 15.7 - - - +
570T GLU 4.0 0.7 - - - +
591T GLU* 1.3 102.6 - - + +
593T ILE* 1.3 64.6 + - - +
594T ASP 4.0 1.0 + - - -
683T SER 3.6 7.9 - - - +
685T ARG* 4.6 1.6 - - - +
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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