Contacts of the strand formed by residues 536 - 546 (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 ALA 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534A SER* 3.4 4.9 - - - -
535A SER* 1.3 82.3 - - - +
537A LEU* 1.3 67.1 + - - +
591A PHE* 3.8 0.3 - - - -
592A ILE* 2.7 40.4 + - + +
595A PRO* 3.8 25.4 - - + -
652A LEU* 4.3 7.2 - - + -
653A ARG 3.2 17.9 - - - +
654A VAL* 4.1 3.8 - - + -
655A LEU* 3.8 7.1 - - - +
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Residues in contact with LEU 537 (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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383A PRO* 4.0 18.4 - - + -
386A VAL* 4.0 11.2 - - + -
445A LEU* 3.8 23.6 - - + -
508A LEU* 4.2 18.2 - - + -
536A ALA* 1.3 76.7 - - - +
538A LEU* 1.3 59.8 + - - +
539A ILE* 4.0 11.3 + - + +
589A THR* 4.6 7.0 - - + -
590A PHE 3.3 12.1 - - - +
591A PHE* 3.6 37.5 - - + -
592A ILE* 4.0 2.9 - - - -
651A ALA 4.0 0.3 - - - +
652A LEU* 3.5 6.2 - - - +
653A ARG* 2.8 39.5 + - + +
655A LEU* 4.0 10.7 - - + +
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Residues in contact with LEU 538 (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* 1.3 72.8 - - - +
539A ILE* 1.3 60.7 + - - +
540A LEU* 4.1 23.8 - - + -
566A VAL* 3.9 25.8 - - + -
588A PHE 3.8 0.5 - - - +
589A THR* 3.3 4.0 - - - +
590A PHE* 2.7 46.5 + - + +
592A ILE* 3.6 18.5 - - + +
600A LEU* 4.2 8.5 - - + -
620A LEU* 3.7 26.0 - - + -
623A LEU* 3.9 2.0 - - + -
650A ILE* 3.7 22.4 - - + -
651A ALA 3.6 13.7 - - - +
652A LEU* 3.8 10.1 - - + -
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Residues in contact with ILE 539 (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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382A VAL* 3.9 29.2 - - + -
383A PRO* 4.3 10.1 - - + -
508A LEU* 4.6 12.6 - - + -
537A LEU* 4.6 10.5 - - + +
538A LEU* 1.3 78.2 - - - +
540A LEU* 1.3 65.2 + - - +
587A ASN* 3.6 23.6 - - - +
588A PHE 3.4 4.3 - - - +
589A THR* 4.1 16.4 - - + +
649A LYS 4.2 0.3 - - - +
650A ILE* 4.6 0.2 - - - +
651A ALA* 2.8 43.6 + - + +
653A ARG* 5.0 10.5 - - + -
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Residues in contact with LEU 540 (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* 4.1 14.4 - - + -
539A ILE* 1.3 77.1 - - - +
541A TYR* 1.3 70.0 + - - +
542A LEU* 4.1 3.4 - - + +
564A MET* 3.6 25.8 - - - -
587A ASN* 3.3 9.0 - - - +
588A PHE* 2.8 52.0 + - + +
590A PHE* 4.2 16.8 - - + -
600A LEU* 3.7 32.5 - - + -
648A MET* 5.1 7.0 - - - -
649A LYS 3.1 12.3 - - - +
650A ILE* 4.2 10.8 - - + -
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Residues in contact with TYR 541 (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* 3.4 11.1 - - + +
380A PHE* 3.9 20.2 - + - -
540A LEU* 1.3 74.9 - - - +
542A LEU* 1.3 58.6 + - - +
543A ASP* 3.3 33.2 + - + -
585A GLU* 3.2 52.2 - - - +
586A GLU 3.5 10.5 - - - -
587A ASN* 3.5 15.9 - - - +
648A MET* 3.1 10.1 - - - +
649A LYS* 2.7 74.0 + - + -
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Residues in contact with LEU 542 (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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540A LEU* 4.1 7.4 - - + +
541A TYR* 1.3 70.6 - - - +
543A ASP* 1.3 59.2 + - - +
544A SER 4.8 0.2 - - - +
562A VAL* 3.8 21.8 - - + -
564A MET* 4.5 2.7 - - + -
573A SER* 3.8 14.8 - - - -
584A TRP* 3.6 41.7 - - + -
585A GLU* 3.0 7.9 + - - -
586A GLU 2.7 38.1 + - - +
588A PHE* 4.0 17.3 - - + -
646A ILE* 3.7 35.0 - - + -
647A LYS 4.3 0.9 - - - +
648A MET* 4.2 12.8 - - + -
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Residues in contact with ASP 543 (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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541A TYR* 3.3 35.6 + - + -
542A LEU* 1.3 70.5 - - - +
544A SER* 1.3 83.7 + - - +
583A VAL* 3.7 2.8 - - - +
584A TRP* 2.8 27.2 + - - -
585A GLU* 3.1 13.5 + - - +
647A LYS* 3.0 45.2 + - + +
648A MET* 5.0 0.2 - - - -
703B ACT 4.1 11.4 - - - +
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Residues in contact with SER 544 (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* 3.9 0.6 - - - +
543A ASP* 1.3 99.4 + - - +
545A ALA* 1.3 60.7 + - - +
546A ARG* 6.1 0.2 - - - +
582A PRO 3.1 17.3 - - - -
583A VAL* 3.9 14.4 - - - -
584A TRP* 3.9 11.5 - - - -
634A ARG* 4.4 7.7 + - - -
646A ILE* 3.5 5.4 - - - +
647A LYS* 2.7 38.2 + - - +
703B ACT 4.5 7.2 + - - -
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Residues in contact with ALA 545 (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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544A SER* 1.3 79.2 - - - +
546A ARG* 1.3 62.8 + - - +
548A LEU* 4.1 16.2 - - + -
581A GLU* 3.4 27.5 - - - +
582A PRO* 3.0 25.9 + - + +
584A TRP* 3.9 9.6 - - + -
604A VAL* 5.7 0.9 - - + -
634A ARG* 3.9 3.6 - - - +
637A LEU* 5.3 0.2 - - + -
645A THR 3.2 14.8 - - - +
646A ILE* 4.3 8.3 - - + -
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Residues in contact with ARG 546 (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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544A SER* 6.1 0.2 - - - +
545A ALA* 1.3 75.9 - - - +
547A ASN* 1.3 83.9 + - - +
548A LEU* 3.3 5.6 + - - +
580A ASN 3.8 1.3 - - - -
581A GLU* 4.6 7.9 - - + -
634A ARG* 3.5 52.4 - - - +
643A ASN 4.9 0.4 - - - +
644A SER* 3.5 0.5 - - - -
645A THR* 2.9 36.4 + - - +
463B PRO 4.4 6.0 + - - -
464B ASP* 3.6 17.8 + - - +
465B LYS* 3.5 33.5 - - - +
466B ASP 4.9 0.2 - - - +
701B NA 3.4 23.3 - - - -
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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