Contacts of the strand formed by residues 536 - 546 (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 ALA 536 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534B SER* 3.5 2.3 - - - -
535B SER* 1.3 81.8 - - - +
537B LEU* 1.3 59.9 + - - +
591B PHE* 3.8 0.7 - - - -
592B ILE* 2.8 36.8 + - + +
595B PRO* 4.1 17.0 - - + -
652B LEU* 3.9 19.7 - - + -
653B ARG 3.0 20.2 - - - +
654B VAL* 3.9 3.1 - - + +
655B LEU* 3.7 15.5 - - - +
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Residues in contact with LEU 537 (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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383B PRO* 4.0 27.1 - - + -
386B VAL* 3.9 19.3 - - + -
445B LEU* 3.8 12.3 - - + -
508B LEU* 4.2 17.7 - - + -
536B ALA* 1.3 76.8 - - - +
538B LEU* 1.3 61.0 + - - +
539B ILE* 4.1 5.1 + - + -
589B THR* 4.5 11.2 - - + -
590B PHE 3.3 14.6 - - - +
591B PHE* 3.7 30.3 - - + -
592B ILE* 4.0 3.1 - - - -
651B ALA 4.0 0.3 - - - +
652B LEU* 3.4 4.7 - - - +
653B ARG* 2.7 39.6 + - + +
655B LEU* 4.2 11.9 - - + +
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Residues in contact with LEU 538 (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* 1.3 72.8 - - - +
539B ILE* 1.3 64.4 + - - +
540B LEU* 4.0 4.0 + - + -
566B VAL* 4.2 12.3 - - + -
588B PHE 3.8 0.9 - - - +
589B THR* 3.4 5.0 - - - +
590B PHE* 2.8 46.9 + - + +
592B ILE* 3.6 17.4 - - + +
600B LEU* 4.2 29.8 - - + -
620B LEU* 3.8 29.2 - - + -
623B LEU* 3.8 10.1 - - + -
650B ILE* 3.5 28.5 - - + -
651B ALA 3.6 5.2 - - - +
652B LEU* 4.1 8.1 - - + -
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Residues in contact with ILE 539 (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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382B VAL* 3.6 43.7 - - + -
383B PRO* 5.0 2.7 - - + -
508B LEU* 5.1 2.7 - - + -
537B LEU* 5.0 6.5 - - + +
538B LEU* 1.3 78.1 - - - +
540B LEU* 1.3 62.3 + - - +
541B TYR 5.2 0.2 - - - +
587B ASN* 3.8 26.0 - - - +
588B PHE 3.6 4.5 - - - +
589B THR* 4.6 15.3 - - + +
649B LYS 3.8 1.6 - - - +
650B ILE* 3.4 4.2 - - - +
651B ALA* 2.7 54.8 + - + +
653B ARG* 4.7 19.3 - - + +
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Residues in contact with LEU 540 (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* 4.8 4.9 - - + -
539B ILE* 1.3 72.9 - - - +
541B TYR* 1.3 73.4 + - - +
542B LEU* 3.8 15.7 - - + +
564B MET* 3.8 28.3 - - + -
587B ASN* 3.1 5.4 - - - +
588B PHE* 2.8 46.0 + - + +
590B PHE* 4.2 12.8 - - + -
600B LEU* 3.6 42.0 - - + -
648B MET* 4.2 14.1 - - + -
649B LYS 3.7 2.2 - - - -
650B ILE* 4.4 8.7 - - + +
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Residues in contact with TYR 541 (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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378B LEU* 3.4 14.4 - - + +
380B PHE* 3.9 27.1 - + + -
539B ILE* 4.1 1.0 - - + +
540B LEU* 1.3 73.8 - - - +
542B LEU* 1.3 57.2 + - - +
543B ASP* 2.9 41.7 + - + -
585B GLU* 3.4 38.2 - - - +
586B GLU 3.5 11.0 - - - -
587B ASN* 3.3 10.0 + - - +
647B LYS* 6.2 0.4 - - - -
648B MET* 3.3 7.7 - - - +
649B LYS* 2.7 68.0 + - + +
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Residues in contact with LEU 542 (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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540B LEU* 3.8 12.7 - - + +
541B TYR* 1.3 71.0 - - - +
543B ASP* 1.3 59.6 + - - +
544B SER 4.9 0.4 - - - +
562B VAL* 3.6 31.6 - - + -
564B MET* 4.4 1.6 - - + -
573B SER* 3.8 17.9 - - - -
584B TRP* 3.8 22.9 - - + -
585B GLU* 3.0 6.9 + - - -
586B GLU 2.7 37.7 + - - +
588B PHE* 4.0 12.1 - - + -
646B ILE* 3.7 33.2 - - + -
647B LYS 4.3 1.1 - - - +
648B MET* 3.9 18.4 - - + -
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Residues in contact with ASP 543 (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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541B TYR* 2.9 40.9 + - + -
542B LEU* 1.3 73.1 - - - +
544B SER* 1.3 85.9 + - - +
583B VAL* 3.7 4.9 - - - +
584B TRP* 2.9 23.4 + - - -
585B GLU* 3.0 13.7 + - - +
647B LYS* 3.1 43.8 + - + +
648B MET* 5.2 0.4 - - - -
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Residues in contact with SER 544 (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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542B LEU* 3.9 0.8 - - - +
543B ASP* 1.3 101.5 + - - +
545B ALA* 1.3 67.4 + - - +
582B PRO 3.2 15.3 - - - -
583B VAL* 3.7 17.0 - - - -
584B TRP* 3.9 10.8 - - - -
646B ILE* 3.7 4.3 - - - +
647B LYS* 2.8 34.9 + - - +
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Residues in contact with ALA 545 (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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544B SER* 1.3 80.6 + - - +
546B ARG* 1.3 62.6 + - - +
548B LEU* 4.3 12.6 - - + -
581B GLU* 3.4 21.7 - - - +
582B PRO* 2.8 32.4 + - + +
583B VAL* 5.7 0.2 - - - +
584B TRP* 3.9 10.1 - - + -
604B VAL* 6.2 1.1 - - + -
637B LEU* 5.6 0.2 - - + -
645B THR 3.4 15.0 - - - +
646B ILE* 4.2 9.0 - - + +
647B LYS* 4.6 1.1 - - - +
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Residues in contact with ARG 546 (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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463A PRO 5.0 5.3 + - - +
464A ASP* 3.7 32.2 + - - +
465A LYS* 4.2 9.1 - - - +
466A ASP 5.4 0.2 - - - +
545B ALA* 1.3 78.9 - - - +
547B ASN* 1.3 96.0 + - - +
548B LEU* 3.4 3.6 + - - +
580B ASN 4.2 0.9 + - - -
581B GLU* 4.1 14.1 + - - +
634B ARG* 3.0 50.2 - - - +
643B ASN 4.2 0.3 - - - +
645B THR* 3.1 39.6 + - - +
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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