Contacts of the strand formed by residues 583 - 592 (chain B) in PDB entry 4NPJ
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 583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A TYR* 4.9 10.5 - - + +
417A ILE* 4.0 24.9 - - + -
424A ILE* 4.3 2.6 - - + +
426A GLN* 2.9 20.0 + - - +
543B ASP* 3.7 10.5 - - - +
544B SER* 3.7 12.8 - - - -
545B ALA 5.7 0.2 - - - +
576B ARG* 2.6 34.8 + - - -
581B GLU 3.7 9.4 - - - +
582B PRO* 1.3 79.0 - - - +
584B TRP* 1.3 61.7 + - - +
585B GLU* 3.8 27.4 - - + +
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Residues in contact with TRP 584 (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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424A ILE* 3.6 19.5 - - - +
542B LEU* 3.8 35.7 - - + +
543B ASP 2.9 6.3 + - - -
544B SER* 3.9 20.4 - - - -
545B ALA* 3.9 22.7 - - + -
560B PRO* 3.7 24.5 + - + -
562B VAL* 3.3 29.2 - - + -
573B SER* 3.3 7.4 + - - -
574B LYS 3.1 28.4 + - - -
576B ARG* 3.8 16.7 + - - +
582B PRO* 3.3 33.4 - - + -
583B VAL* 1.3 77.7 - - - +
585B GLU* 1.3 75.3 + - - +
586B GLU* 3.3 23.7 + - - +
604B VAL* 4.9 5.8 - - + -
646B ILE* 4.6 3.4 - - + -
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Residues in contact with GLU 585 (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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417A ILE* 4.3 8.7 - - - +
419A ARG* 2.9 37.5 + - - +
422A ASN 5.1 1.4 - - - +
424A ILE* 3.5 10.5 - - + +
459A PHE* 6.0 1.2 - - - -
801A CL 3.4 18.0 - - - +
378B LEU* 3.9 8.4 - - + +
380B PHE* 3.7 9.5 - - - -
541B TYR* 3.4 27.1 - - - +
542B LEU 3.0 13.0 + - - -
543B ASP* 3.0 10.9 + - - +
583B VAL* 3.8 24.3 - - + +
584B TRP* 1.3 78.0 - - - +
586B GLU* 1.3 59.4 + - - +
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Residues in contact with GLU 586 (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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422A ASN 4.9 10.5 - - - +
424A ILE* 6.0 0.4 - - + -
380B PHE* 4.6 2.2 - - - -
541B TYR* 3.5 4.5 - - - -
542B LEU* 2.7 38.3 + - + +
572B GLU 4.4 0.9 - - - +
573B SER* 3.5 11.4 - - - -
574B LYS* 2.9 54.3 + - - +
576B ARG* 5.1 0.9 + - - -
584B TRP* 3.7 23.8 - - + +
585B GLU* 1.3 79.4 - - - +
587B ASN* 1.3 59.8 + - - +
588B PHE* 3.6 28.7 - - + -
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Residues in contact with ASN 587 (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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380B PHE* 3.4 54.1 + - + +
381B PRO 4.6 7.9 + - - -
382B VAL* 5.3 1.0 - - - +
539B ILE* 3.8 23.6 - - - +
540B LEU 3.1 21.2 - - - +
541B TYR* 3.3 11.5 + - + +
586B GLU* 1.3 74.2 - - - +
588B PHE* 1.3 73.0 + - - +
589B THR* 4.7 4.6 + - - -
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Residues in contact with PHE 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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538B LEU 3.8 0.4 - - - +
539B ILE* 3.6 3.6 - - - +
540B LEU* 2.8 43.8 + - + +
542B LEU* 4.0 8.3 - - + -
564B MET* 3.5 37.7 - - + -
571B GLN* 3.6 30.5 - - + +
572B GLU 3.6 18.2 - - - -
573B SER* 3.9 8.1 - - - -
586B GLU* 3.6 45.8 - - + -
587B ASN* 1.3 78.9 - - - +
589B THR* 1.3 64.7 + - - +
590B PHE* 3.9 17.3 - - + -
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Residues in contact with THR 589 (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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381B PRO 5.2 4.5 + - - -
382B VAL* 6.0 0.5 - - - +
383B PRO* 4.9 7.4 - - + +
445B LEU* 4.4 22.2 - - + -
447B TYR* 4.4 12.5 + - - +
537B LEU* 4.5 20.6 - - + -
538B LEU 3.4 8.3 - - - +
539B ILE* 4.6 15.4 - - + +
571B GLN* 3.0 21.7 + - - +
587B ASN* 4.7 4.7 + - - -
588B PHE* 1.3 76.6 + - - +
590B PHE* 1.3 68.1 + - - +
591B PHE* 6.0 0.7 - - + -
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Residues in contact with PHE 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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537B LEU* 3.3 10.4 - - - +
538B LEU* 2.8 62.2 + - + +
540B LEU* 4.2 18.8 - - + -
564B MET* 3.6 38.1 - - + -
565B SER* 4.2 2.9 - - - -
566B VAL* 4.3 12.3 - - + -
569B LYS* 4.1 17.0 - - + -
570B ALA* 4.6 0.2 - - - -
571B GLN* 3.4 31.2 - - + -
588B PHE* 3.9 20.4 - - + -
589B THR* 1.3 77.2 - - - +
591B PHE* 1.3 67.3 - - - +
592B ILE* 4.2 6.1 - - + -
600B LEU* 4.9 2.0 - - + -
702B CL 3.7 10.3 - - + -
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Residues in contact with PHE 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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386B VAL* 4.3 10.3 - - + -
423B GLN* 5.0 2.9 - - - -
443B GLU* 4.0 28.3 - - + -
445B LEU* 3.3 47.8 - - + -
534B SER* 3.4 27.4 - - - +
536B ALA 3.9 1.3 - - - -
537B LEU* 3.7 12.6 - - + -
566B VAL* 5.0 6.4 - - - +
589B THR* 6.5 0.2 - - + -
590B PHE* 1.3 75.2 - - - +
592B ILE* 1.3 64.4 + - - +
593B HIS 4.2 1.1 + - - -
598B GLN* 5.6 0.7 + - - -
655B LEU* 5.1 0.2 - - + -
702B CL 3.1 21.6 - - + +
704B ACT 3.2 34.3 - - + -
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Residues in contact with ILE 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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534B SER* 3.3 5.4 + - - -
535B SER 2.9 23.4 + - - -
536B ALA* 2.8 23.7 + - + +
537B LEU 4.0 2.0 - - - -
538B LEU* 3.6 40.8 - - + +
566B VAL* 3.8 22.7 - - + -
590B PHE* 4.2 2.0 - - + -
591B PHE* 1.3 81.7 - - - +
593B HIS* 1.3 61.5 + - - +
594B ASN 4.0 0.2 - - - -
595B PRO* 3.8 28.3 - - + -
598B GLN* 3.5 11.4 - - - +
620B LEU* 3.7 27.6 - - + -
652B LEU* 4.3 3.1 - - + -
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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