Contacts of the strand formed by residues 587 - 592 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A ILE 3.2 14.4 - - - +
466A PHE* 3.7 2.9 - - - -
467A CYS* 2.8 24.5 + - - +
469A MET* 3.6 42.6 - - + +
472A ILE* 3.7 28.7 - - + -
563A LEU* 4.4 8.1 - - + -
564A ASP 4.1 4.5 - - - +
565A PHE* 4.0 22.0 - - + -
585A ARG 5.4 1.3 - - - +
586A PRO* 1.3 77.6 - - - +
588A ILE* 1.3 73.8 + - - +
589A VAL* 4.7 3.4 - - + -
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Residues in contact with ILE 588 (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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417A CYS* 3.6 23.1 - - - -
464A HIS* 4.0 19.3 - - + -
465A ILE 3.6 2.7 - - - +
466A PHE* 3.7 25.4 - - + -
562A GLN 3.7 0.5 - - - +
563A LEU* 3.5 4.3 - - - -
564A ASP* 2.8 42.7 + - + +
567A LEU* 3.5 26.7 - - + -
568A PRO* 3.8 15.5 - - + -
573A LEU* 4.1 4.9 - - + -
586A PRO* 4.2 0.9 + - + -
587A VAL* 1.3 73.8 - - - +
589A VAL* 1.3 64.5 + - - +
590A HIS* 3.9 28.5 - - + +
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Residues in contact with VAL 589 (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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463A ALA 3.3 1.2 - - - +
464A HIS* 3.2 6.9 - - - -
465A ILE* 2.9 64.2 + - + +
467A CYS* 4.5 16.2 - - - -
472A ILE* 5.4 2.7 - - + -
475A GLU* 5.8 2.9 - - + -
476A ILE* 4.9 5.2 - - + -
479A CYS* 4.9 1.1 - - - -
561A ILE* 3.8 30.3 - - + -
562A GLN 3.5 2.7 - - - +
563A LEU* 3.6 22.9 - - + -
587A VAL* 4.6 3.8 - - + +
588A ILE* 1.3 80.9 - - - +
590A HIS* 1.3 64.0 + - - +
591A ARG* 3.6 2.2 + - + -
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Residues in contact with HIS 590 (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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411A MET* 6.3 0.4 - - + +
413A CYS* 3.5 23.0 - - - -
462A ASP* 5.4 2.0 - - - +
463A ALA 3.8 3.8 - - - -
464A HIS* 2.9 29.1 + + + +
540A TYR* 4.7 4.2 - + - -
560A THR* 3.7 4.8 - - + +
561A ILE* 3.5 2.3 - - - -
562A GLN* 2.9 67.1 + - + +
564A ASP* 2.9 37.1 + - + +
567A LEU* 3.7 12.8 - - + -
588A ILE* 3.9 2.9 - - + -
589A VAL* 1.3 73.9 - - - +
591A ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 591 (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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360A ILE* 5.9 0.4 - - - +
364A TYR* 3.7 13.9 + - - -
369A PHE* 3.6 33.1 - - - -
461A ASP* 3.7 2.3 + - - +
462A ASP* 3.8 4.7 + - - +
463A ALA* 2.8 52.0 + - + +
465A ILE* 3.9 16.6 - - + -
479A CYS* 4.2 15.3 - - - +
482A PHE* 3.7 16.6 - - - -
560A THR* 3.2 10.5 - - - +
561A ILE* 4.8 3.4 - - + -
589A VAL* 4.2 9.6 - - + +
590A HIS* 1.3 77.2 - - - +
592A ALA* 1.3 61.3 + - - +
593A ILE* 3.3 38.9 - - + +
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Residues in contact with ALA 592 (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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460A GLN* 4.7 15.5 - - + +
461A ASP* 3.2 25.1 - - - +
462A ASP* 4.9 1.6 - - - +
483A LEU* 5.1 0.2 - - - +
558A CYS 4.9 1.6 - - - +
559A ALA* 3.0 6.6 - - - +
560A THR* 2.9 43.4 + - + +
591A ARG* 1.3 75.4 - - - +
593A ILE* 1.3 62.8 + - - +
595A GLY* 4.3 14.4 - - - +
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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