Contacts of the strand formed by residues 583 - 592 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543A ASP* 3.8 6.7 - - - +
544A SER* 4.2 4.5 - - - -
576A ARG* 2.5 35.0 + - - -
581A GLU* 4.0 4.3 - - + +
582A PRO* 1.3 77.7 - - - +
584A TRP* 1.3 59.7 + - - +
585A GLU* 3.8 32.1 - - + +
415B TYR* 4.8 3.8 - - - +
417B ILE* 4.0 26.7 - - + -
424B ILE* 4.6 2.5 - - + +
426B GLN* 2.8 27.7 + - - +
703B ACT 4.0 30.1 - - - +
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Residues in contact with TRP 584 (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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542A LEU* 3.6 37.5 - - + +
543A ASP 2.8 10.1 + - - -
544A SER* 3.9 11.0 - - - -
545A ALA* 3.9 22.0 - - + -
560A PRO* 3.9 21.7 + - + -
562A VAL* 3.3 28.7 - - + -
573A SER* 3.4 6.7 + - - -
574A LYS 3.1 27.9 + - - -
576A ARG* 3.7 24.0 + - + +
582A PRO* 3.3 38.6 - - + -
583A VAL* 1.3 73.9 - - - +
585A GLU* 1.3 71.7 + - - +
586A GLU* 3.3 23.1 + - - +
604A VAL* 4.5 4.5 - - + -
646A ILE* 4.4 2.0 - - + -
424B ILE* 3.3 18.9 - - - +
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Residues in contact with GLU 585 (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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378A LEU* 3.7 13.3 - - + +
380A PHE* 3.8 14.7 - - - -
541A TYR* 3.2 30.5 + - - +
542A LEU 3.0 12.8 + - - -
543A ASP* 3.1 10.0 + - - +
583A VAL* 3.8 25.5 - - + +
584A TRP* 1.3 77.2 - - - +
586A GLU* 1.3 59.5 + - - +
417B ILE* 4.6 3.9 - - - +
419B ARG* 3.4 40.5 + - - -
422B ASN* 5.0 2.1 - - - +
424B ILE* 4.0 17.4 - - + +
457B GLU* 5.4 0.2 - - - +
703B ACT 4.7 6.1 - - - +
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Residues in contact with GLU 586 (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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380A PHE* 4.7 2.5 - - - -
541A TYR* 3.5 5.8 - - - -
542A LEU* 2.7 38.5 + - + +
572A GLU 4.2 1.4 - - - +
573A SER* 3.5 24.1 - - - -
574A LYS* 2.9 44.4 + - - +
576A ARG* 4.9 1.7 + - - -
584A TRP* 3.6 25.6 - - + +
585A GLU* 1.3 77.7 - - - +
587A ASN* 1.3 60.1 + - - +
588A PHE* 3.5 23.6 - - + -
422B ASN 5.2 8.1 - - - +
424B ILE* 5.4 1.1 - - + -
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Residues in contact with ASN 587 (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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380A PHE* 3.6 48.6 - - + +
381A PRO 5.3 3.8 + - - -
539A ILE* 3.6 24.4 - - - +
540A LEU 3.3 14.8 + - - +
541A TYR* 3.5 17.7 - - - +
586A GLU* 1.3 74.4 - - - +
588A PHE* 1.3 82.0 + - - +
589A THR* 4.8 2.4 + - - -
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Residues in contact with PHE 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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538A LEU 3.8 1.1 - - - +
539A ILE* 3.4 3.5 - - - -
540A LEU* 2.8 54.8 + - + +
542A LEU* 4.0 9.4 - - + -
564A MET* 3.5 26.9 - - + -
571A GLN* 3.5 29.2 - - + +
572A GLU 3.7 19.1 - - - -
573A SER* 4.1 7.4 - - - -
586A GLU* 3.5 47.3 - - + -
587A ASN* 1.3 81.8 + - - +
589A THR* 1.3 65.0 + - - +
590A PHE* 4.0 16.4 - - + -
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Residues in contact with THR 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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381A PRO 5.4 3.8 + - - -
383A PRO* 4.7 9.6 - - + +
445A LEU* 4.4 23.3 - - + -
447A TYR* 4.8 7.0 + - - -
537A LEU* 4.6 14.6 - - + -
538A LEU 3.3 7.4 - - - +
539A ILE* 4.1 21.1 - - + +
571A GLN* 2.9 22.4 + - - +
587A ASN* 4.8 2.6 + - - -
588A PHE* 1.3 78.9 + - - +
590A PHE* 1.3 71.6 + - - +
591A PHE* 6.4 0.2 - - + -
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Residues in contact with PHE 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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537A LEU* 3.3 9.9 - - - +
538A LEU* 2.7 65.2 + - + +
540A LEU* 4.2 15.0 - - + -
564A MET* 3.7 36.1 - - + -
565A SER* 4.5 2.5 - - - -
566A VAL* 4.4 8.7 - - + -
569A LYS* 3.8 30.7 - - + -
571A GLN* 3.2 42.6 - - + -
588A PHE* 4.0 17.3 - - + -
589A THR* 1.3 78.5 - - - +
591A PHE* 1.3 65.8 + - - +
592A ILE* 4.2 4.9 - - + -
600A LEU* 5.1 1.3 - - + -
802A CL 3.8 3.1 - - + -
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Residues in contact with PHE 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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386A VAL* 4.1 17.7 - - + -
423A GLN* 4.9 2.9 - - - -
443A GLU* 4.1 32.5 - - + -
444A ALA 4.5 0.4 - - - -
445A LEU* 3.5 40.6 - - + -
534A SER* 3.4 26.9 - - - +
536A ALA 4.0 1.3 - - - -
537A LEU* 3.6 19.3 - - + -
566A VAL* 5.1 1.7 - - - +
569A LYS* 4.1 31.3 - - - +
589A THR* 6.4 0.4 - - + -
590A PHE* 1.3 73.9 - - - +
592A ILE* 1.3 65.0 + - - +
593A HIS* 4.3 1.5 + - - -
598A GLN* 5.3 0.2 - - - +
655A LEU* 5.0 0.7 - - + -
802A CL 3.1 22.3 - - + +
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Residues in contact with ILE 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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534A SER* 3.1 7.5 + - - -
535A SER 2.9 24.1 + - - -
536A ALA* 2.7 23.1 + - + +
537A LEU 4.0 2.2 - - - -
538A LEU* 3.6 41.3 - - + +
566A VAL* 3.8 22.0 - - + -
590A PHE* 4.2 2.0 - - + +
591A PHE* 1.3 84.1 - - - +
593A HIS* 1.3 61.9 + - - +
594A ASN 3.9 0.2 - - - +
595A PRO* 3.7 32.5 - - + -
598A GLN* 3.7 10.8 - - - +
620A LEU* 3.7 25.8 - - + -
652A LEU* 4.3 2.9 - - + -
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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