Contacts of the strand formed by residues 587 - 592 (chain B) in PDB entry 4P3N
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 587 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ILE 3.1 13.5 - - - +
466B PHE* 3.6 2.4 - - - -
467B CYS* 2.8 27.0 + - - +
469B MET* 3.5 41.1 - - + +
472B ILE* 3.9 22.0 - - + -
511B VAL* 5.6 0.2 - - + -
563B LEU* 4.2 8.3 - - + -
564B ASP 4.1 3.4 - - - +
565B PHE* 3.8 29.2 - - + -
585B ARG 5.3 1.3 - - - +
586B PRO* 1.3 75.8 - - - +
588B ILE* 1.3 74.0 + - - +
589B VAL* 4.6 3.6 - - + -
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B CYS* 3.7 22.7 - - - -
464B HIS* 4.0 30.1 - - + -
465B ILE 3.6 2.9 - - - +
466B PHE* 3.7 24.9 - - + -
562B GLN 3.6 0.3 - - - +
563B LEU* 3.4 4.5 - - - -
564B ASP* 2.8 41.7 + - + +
567B LEU* 3.5 27.1 - - + -
568B PRO* 3.7 17.5 - - + -
573B LEU* 3.9 4.9 - - + -
586B PRO 5.1 0.4 - - - +
587B VAL* 1.3 76.7 - - - +
589B VAL* 1.3 64.5 + - - +
590B HIS* 4.0 14.4 - - + +
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Residues in contact with VAL 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ALA 3.5 1.0 - - - +
464B HIS* 3.2 8.4 - - - -
465B ILE* 2.9 59.4 + - + +
467B CYS* 4.7 10.5 - - - -
472B ILE* 5.6 2.9 - - + -
475B GLU* 5.8 2.9 - - + -
476B ILE* 4.7 6.7 - - + -
479B CYS* 5.0 0.2 - - - -
561B ILE* 3.7 30.3 - - + -
562B GLN 3.4 2.7 - - - +
563B LEU* 3.6 22.2 - - + -
587B VAL* 4.6 8.3 - - + +
588B ILE* 1.3 81.2 - - - +
590B HIS* 1.3 65.8 + - - +
591B ARG* 3.5 9.2 + - + +
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Residues in contact with HIS 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B MET* 5.4 3.4 - - + +
413B CYS* 3.4 23.7 - - - -
462B ASP* 5.4 2.0 - - - +
464B HIS* 2.9 31.4 + + + +
540B TYR* 4.8 3.1 - + - -
560B THR* 3.6 4.6 - - + +
561B ILE* 3.6 1.9 - - - -
562B GLN* 2.9 66.0 + - + +
564B ASP* 3.0 33.2 + - + +
567B LEU* 3.6 19.5 - - + -
588B ILE* 4.1 2.2 - - + +
589B VAL* 1.3 71.9 - - - +
591B ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B TYR* 3.8 14.3 + - - -
369B PHE* 3.5 17.5 - - - -
461B ASP* 3.5 4.0 + - - +
462B ASP* 3.7 5.4 + - - +
463B ALA* 2.9 64.6 + - - +
465B ILE* 4.3 5.6 - - + -
479B CYS* 4.2 21.5 - - + -
482B PHE* 3.3 36.8 - - - -
560B THR* 3.4 12.6 - - - +
561B ILE* 4.6 9.2 - - + -
589B VAL* 4.0 12.3 - - + +
590B HIS* 1.3 75.7 - - - +
592B ALA* 1.3 64.9 + - - +
593B ILE* 3.7 16.6 - - + +
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Residues in contact with ALA 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B GLN* 4.3 12.6 - - - +
461B ASP* 3.1 26.9 - - - +
483B LEU* 4.9 0.2 - - - +
558B CYS 5.1 2.7 - - - +
559B ALA* 3.2 5.1 - - - +
560B THR* 3.2 35.9 + - + +
591B ARG* 1.3 74.5 - - - +
593B ILE* 1.3 65.6 + - - +
595B GLY* 4.2 17.0 - - - +
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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