Contacts of the strand formed by residues 645 - 657 (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 THR 645 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B ALA* 3.4 6.1 - - - +
546B ARG* 3.1 47.1 + - - +
547B ASN* 5.6 0.8 + - - +
548B LEU* 5.2 0.2 - - - +
634B ARG* 4.0 25.3 - - + +
635B PHE 3.1 13.9 - - - +
636B GLN* 4.4 15.7 - - + +
637B LEU* 4.0 6.8 - - - +
643B ASN* 3.4 13.2 - - - +
644B SER* 1.3 79.7 - - - +
646B ILE* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 3.7 17.3 - - + -
544B SER 3.7 11.2 - - - +
545B ALA* 4.4 4.9 - - + -
562B VAL* 4.4 9.4 - - + -
584B TRP* 4.6 3.6 - - + -
602B VAL* 4.4 4.5 - - + -
604B VAL* 4.3 21.5 - - + -
616B LEU* 4.1 18.6 - - + -
634B ARG* 4.4 2.5 - - - -
635B PHE* 2.9 41.7 + - + +
637B LEU* 4.2 16.4 - - + -
645B THR* 1.3 74.5 - - - +
647B LYS* 1.3 63.7 + - - +
648B MET* 3.4 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B TYR* 6.2 0.4 - - - -
542B LEU* 4.3 1.0 - - - +
543B ASP* 3.1 51.5 + - + +
544B SER* 2.8 26.3 + - - +
545B ALA* 4.6 1.2 - - - +
632B SER* 5.0 9.1 + - - -
633B GLN* 3.6 16.2 - - - +
634B ARG* 4.2 41.7 - - + +
646B ILE* 1.3 71.0 - - - +
648B MET* 1.3 68.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 4.2 18.4 - - + -
541B TYR* 3.3 12.3 - - - +
542B LEU* 3.9 15.7 - - + -
543B ASP* 4.7 1.3 - - - +
562B VAL* 5.0 0.9 - - + -
564B MET* 5.1 0.7 - - + -
600B LEU* 4.8 0.4 - - - -
602B VAL* 3.7 33.9 - - + -
616B LEU* 4.7 4.5 - - + -
631B VAL 4.0 1.0 - - - +
632B SER* 3.4 3.8 + - - -
633B GLN 3.2 31.6 + - - +
635B PHE* 4.0 16.7 - - + -
646B ILE* 3.4 41.4 + - + +
647B LYS* 1.3 80.9 - - - +
649B LYS* 1.3 59.9 + - - +
650B ILE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 649 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ILE 3.8 1.2 - - - +
540B LEU* 3.7 1.6 - - - -
541B TYR* 2.7 64.0 + - + +
630B THR* 4.2 21.5 - - + -
631B VAL 3.6 2.7 - - - -
632B SER* 3.6 24.5 - - - +
648B MET* 1.3 73.5 - - - +
650B ILE* 1.3 62.6 + - - +
651B ALA* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 650 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B LEU* 3.5 32.1 - - + -
539B ILE 3.4 4.9 - - - +
540B LEU* 4.4 9.9 - - + -
600B LEU* 3.7 23.3 - - + -
618B VAL* 4.7 12.8 - - + -
620B LEU* 5.3 0.9 - - + -
623B LEU* 3.6 16.0 - - + +
629B MET 3.9 0.5 - - - +
630B THR* 3.2 6.2 - - - +
631B VAL* 2.9 41.7 + - + +
635B PHE* 4.1 23.6 - - + -
648B MET* 4.3 18.4 - - + -
649B LYS* 1.3 78.9 - - - +
651B ALA* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LEU 4.0 0.3 - - - +
538B LEU* 3.6 5.0 - - - +
539B ILE* 2.7 58.4 + - + +
629B MET 3.5 4.3 - - - -
630B THR* 3.3 21.5 - - + +
649B LYS* 5.8 2.0 - - + -
650B ILE* 1.3 73.4 - - - +
652B LEU* 1.3 60.9 + - - +
653B ARG* 4.6 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 652 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B ALA* 3.9 16.8 - - + -
537B LEU 3.4 17.7 - - - +
538B LEU* 4.1 15.5 - - + -
592B ILE* 4.3 8.3 - - + -
595B PRO* 3.7 20.4 - - + -
620B LEU* 4.3 6.7 - - + +
623B LEU* 3.8 23.7 - - + +
624B LEU* 3.6 31.0 - - + -
629B MET* 3.0 39.0 + - + +
651B ALA* 1.3 73.3 - - - +
653B ARG* 1.3 80.0 + - - +
654B VAL* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 5.8 3.2 - - - +
508B LEU* 3.9 40.3 + - + +
509B MET 3.3 21.3 - - - +
510B PRO* 3.7 19.4 - - - +
536B ALA* 3.0 5.3 - - - -
537B LEU* 2.7 44.6 + - + +
539B ILE* 4.7 16.5 - - + +
628B ASP* 3.8 32.3 + - - +
629B MET* 4.8 0.2 - - - -
630B THR* 4.2 6.9 + - - -
651B ALA* 4.6 9.3 - - - +
652B LEU* 1.3 85.0 + - - +
654B VAL* 1.3 62.8 + - - +
655B LEU* 4.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B THR 3.2 4.3 - - - +
508B LEU* 3.5 1.4 - - - -
509B MET* 2.7 45.7 + - + +
511B ASN 3.9 21.3 - - - +
512B ALA* 4.2 11.4 - - - -
514B ASN* 4.7 2.7 - - + -
515B LEU* 3.9 43.3 - - + +
518B VAL* 4.5 4.7 - - + -
535B SER 3.4 11.0 - - - +
536B ALA* 3.9 5.4 - - + -
595B PRO* 5.2 0.2 - - + -
624B LEU* 5.1 2.5 - - + -
629B MET* 4.5 10.1 - - + -
652B LEU* 4.3 2.4 - - + -
653B ARG* 1.3 72.2 - - - +
655B LEU* 1.3 70.9 + - - +
656B HIS* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B VAL* 3.5 41.3 - - + -
443B GLU* 5.5 0.2 - - - +
506B LEU* 4.1 21.6 - - + +
507B THR 3.5 2.9 - - - +
508B LEU* 3.8 25.8 - - + -
518B VAL* 3.2 26.0 - - - +
534B SER* 3.9 20.6 - - - +
535B SER* 2.8 15.8 + - - +
536B ALA* 3.7 34.3 - - - +
537B LEU* 4.2 10.1 - - + -
591B PHE* 5.1 0.4 - - + -
653B ARG 4.7 0.4 - - - +
654B VAL* 1.3 71.8 - - - +
656B HIS* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B LEU* 4.0 6.3 - - - +
507B THR* 2.6 38.2 + - - +
509B MET* 3.7 28.2 - - + -
514B ASN* 3.6 27.4 + - + -
517B LYS* 3.3 40.3 + - - -
518B VAL* 4.4 8.3 - - + -
654B VAL* 4.9 0.7 - - + -
655B LEU* 1.3 75.1 - - - +
657B LEU* 1.3 79.4 + - - +
658B GLU* 3.4 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ARG* 3.3 28.9 - - + +
484B LEU* 4.5 11.4 - - + -
502B ARG* 4.9 1.6 - - - +
504B GLU* 3.7 29.8 - - + +
505B TRP 3.4 18.4 - - - +
506B LEU* 3.9 11.9 - - + +
517B LYS* 4.9 2.9 + - - -
518B VAL* 5.6 0.4 - - - +
656B HIS* 1.3 88.6 + - - +
658B GLU* 1.3 70.7 - - - +
659B LYS* 4.2 25.9 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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