Contacts of the helix formed by residues 649 - 670 (chain J) in PDB entry 6PSS
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 LYS 649 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647J PRO* 3.3 1.8 - - - +
648J GLU* 1.3 94.8 + - + +
650J LYS* 1.3 58.7 + - - +
651J HIS 3.3 1.8 - - - -
652J GLU* 2.4 51.5 + - + +
653J ILE* 3.0 45.1 + - + +
692J ARG* 6.0 0.4 - - - +
696J ALA* 4.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 650 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646J ILE* 3.8 17.0 - - + -
647J PRO* 3.3 25.9 + - + +
648J GLU 3.1 1.6 - - - -
649J LYS* 1.3 75.3 - - - +
651J HIS* 1.3 68.9 + - + +
653J ILE* 3.9 1.1 - - - +
654J ILE* 2.9 42.2 + - + +
693J VAL* 3.8 27.1 - - + -
741J ALA 4.3 4.0 + - - +
743J MET* 4.2 12.8 - - - +
760J THR 3.3 27.1 + - - -
761J ALA* 4.1 0.6 - - - +
762J ASN* 3.5 21.4 + - - +
765J GLU* 3.5 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 651 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646J ILE* 6.4 0.9 - - + -
648J GLU 4.1 8.0 + - - +
649J LYS 3.3 0.4 - - - -
650J LYS* 1.3 87.4 - - + +
652J GLU* 1.3 56.7 + - + +
654J ILE* 3.8 11.7 - - + +
655J SER* 2.3 40.9 + - - +
765J GLU* 5.0 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 652 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648J GLU 4.5 3.4 - - - +
649J LYS* 2.4 57.1 + - + +
651J HIS* 1.3 78.6 - - + +
653J ILE* 1.3 61.1 + - + +
655J SER* 3.8 5.1 - - - -
656J GLU* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 653 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649J LYS* 3.0 31.3 + - + +
652J GLU* 1.3 75.0 - - + +
654J ILE* 1.3 60.7 + - - +
656J GLU* 3.6 5.7 - - + +
657J ALA* 2.9 28.8 + - - +
689J ALA* 3.5 37.2 - - + +
692J ARG* 3.5 57.0 - - + +
693J VAL* 3.8 23.6 - - + -
696J ALA* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 654 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650J LYS* 2.9 40.6 + - + +
651J HIS* 3.8 11.7 - - + +
653J ILE* 1.3 77.5 - - - +
655J SER* 1.3 59.1 + - - +
657J ALA 3.4 0.9 + - - -
658J GLU* 2.9 49.3 + - - +
686J TRP* 3.7 13.0 - - + -
689J ALA* 6.5 0.2 - - + -
693J VAL* 5.2 1.8 - - + -
743J MET* 4.8 10.5 - - + -
760J THR* 3.4 48.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 655 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651J HIS* 2.3 31.0 + - - +
652J GLU* 3.9 5.7 - - - -
654J ILE* 1.3 77.8 - - - +
656J GLU* 1.3 57.7 + - - +
658J GLU* 3.7 8.7 - - - +
659J ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 656 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652J GLU* 2.8 27.9 + - + +
653J ILE* 3.6 6.1 - - - +
654J ILE 3.3 0.2 - - - -
655J SER* 1.3 77.2 - - - +
657J ALA* 1.3 57.4 + - - +
659J ALA* 3.3 7.7 + - - +
660J GLU* 2.9 34.2 + - + +
692J ARG* 2.5 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 657 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653J ILE 2.9 17.2 + - - +
656J GLU* 1.3 73.6 - - - +
658J GLU* 1.3 61.1 + - - +
660J GLU* 3.3 3.2 + - - +
661J VAL* 2.9 34.3 + - - +
685J ILE* 4.1 17.0 - - + -
686J TRP* 3.6 29.6 - - + -
689J ALA* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 658 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654J ILE* 2.9 39.3 + - - +
655J SER* 3.8 8.1 - - - +
656J GLU 3.3 0.2 - - - -
657J ALA* 1.3 77.5 - - - +
659J ALA* 1.3 57.0 + - - +
661J VAL* 3.4 9.7 - - + +
662J ALA* 2.9 28.8 + - - +
686J TRP* 3.6 18.9 - - + -
760J THR* 4.7 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 659 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655J SER 2.9 16.7 + - - +
656J GLU* 3.6 7.4 - - - +
657J ALA 3.3 0.2 - - - -
658J GLU* 1.3 76.6 - - - +
660J GLU* 1.3 63.8 + - - +
662J ALA* 3.3 7.1 + - - +
663J GLU* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 660 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656J GLU* 2.9 21.6 + - + +
657J ALA* 3.3 6.3 + - - +
659J ALA* 1.3 82.8 - - - +
661J VAL* 1.3 57.8 + - - +
663J GLU* 3.1 35.0 + - - +
664J ILE* 3.0 37.5 + - - +
685J ILE* 4.0 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 661 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657J ALA 2.9 20.4 + - - +
658J GLU* 3.4 14.8 - - + +
660J GLU* 1.3 73.7 - - - +
662J ALA* 1.3 62.1 + - - +
664J ILE* 4.4 2.4 - - - +
665J GLN* 2.9 29.3 + - - +
678J ARG* 5.3 1.3 + - - +
682J VAL* 3.7 33.3 - - + +
685J ILE* 3.9 16.4 - - + -
686J TRP* 3.5 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 662 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658J GLU 2.9 18.9 + - - +
659J ALA* 3.5 9.4 - - - +
660J GLU 3.2 0.2 - - - -
661J VAL* 1.3 78.5 - - - +
663J GLU* 1.3 56.2 + - - +
665J GLN* 3.3 8.8 + - - +
666J GLU* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 663 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659J ALA 3.0 13.8 + - - +
660J GLU* 3.1 33.5 + - - +
662J ALA* 1.3 77.9 - - - +
664J ILE* 1.3 70.3 + - + +
666J GLU* 3.1 15.9 + - - +
667J GLN* 3.0 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 664 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660J GLU* 3.0 29.9 + - - +
661J VAL* 4.4 4.0 - - - +
663J GLU* 1.3 88.2 - - - +
665J GLN* 1.3 60.2 + - - +
667J GLN* 3.7 19.3 - - - +
668J PHE* 2.9 28.6 + - - +
673J VAL* 4.6 8.2 - - + +
678J ARG* 3.8 25.1 - - + +
681J LYS* 3.8 34.3 - - + -
682J VAL* 4.6 4.7 - - + -
685J ILE* 3.7 24.5 - - + -
51N ILE* 5.1 7.6 - - + -
52N PHE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 665 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661J VAL 2.9 20.6 + - - +
662J ALA* 3.5 9.2 - - - +
663J GLU 3.3 0.2 - - - -
664J ILE* 1.3 76.6 - - - +
666J GLU* 1.3 57.7 + - + +
668J PHE* 3.5 10.0 + - - -
669J GLN* 2.9 51.2 + - - +
678J ARG* 3.8 34.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 666 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662J ALA* 2.9 23.2 + - - +
663J GLU* 3.1 15.6 + - - +
665J GLN* 1.3 77.2 - - + +
667J GLN* 1.3 54.8 + - + +
669J GLN* 2.9 17.8 + - - +
670J SER* 2.6 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 667 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663J GLU* 3.0 38.7 + - - +
664J ILE* 3.4 22.6 + - - +
666J GLU* 1.3 76.6 - - + +
668J PHE* 1.3 57.0 + - - +
670J SER* 3.9 10.5 - - - -
672J LEU* 2.9 37.3 + - + +
673J VAL* 3.2 11.7 + - + +
51N ILE* 3.3 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 668 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664J ILE 2.9 16.6 + - - +
665J GLN* 3.9 16.2 - - - +
667J GLN* 1.3 76.4 - - - +
669J GLN* 1.3 67.6 + - + +
670J SER 3.2 1.6 - - - -
671J GLY* 3.1 12.0 + - - -
673J VAL* 3.2 26.7 - - + +
674J THR* 3.5 10.8 - - - -
675J ALA* 3.3 33.0 - - + -
678J ARG* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 669 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665J GLN* 2.9 38.9 + - - +
666J GLU* 2.9 18.9 + - - +
668J PHE* 1.3 80.3 - - + +
670J SER* 1.3 58.7 + - - +
671J GLY* 3.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 670 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666J GLU* 2.6 21.2 + - - +
667J GLN* 4.1 7.6 - - - -
668J PHE 3.2 0.2 - - - -
669J GLN* 1.3 71.2 - - - +
671J GLY* 1.3 62.2 + - - +
672J LEU* 3.3 23.2 + - - +
----------------------------------------------------------
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