Contacts of the helix formed by residues 647 - 661 (chain G) in PDB entry 5LS6
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 SER 647 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G VAL 5.2 0.4 + - - -
124G ASP* 2.5 41.2 + - - -
646G ILE* 1.3 77.7 - - - +
648G GLN* 1.3 65.3 + - - +
649G ASP* 3.7 7.5 + - - -
650G GLU* 3.2 10.2 + - - +
651G ALA* 3.2 21.0 + - - +
672G ASP 3.7 13.0 - - - -
673G PHE* 4.2 7.3 - - - -
674G VAL* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 648 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647G SER* 1.3 70.9 - - - +
649G ASP* 1.3 66.3 + - - +
651G ALA* 4.0 1.9 - - - +
652G ASP* 2.9 34.5 + - - +
668G ASN* 3.6 13.2 + - - +
670G ASN 3.2 26.1 + - - -
671G ASN* 3.4 23.1 + - - +
672G ASP 3.9 5.6 + - - +
673G PHE 3.8 3.8 + - - -
674G VAL* 3.3 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 649 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ASP* 4.1 8.2 - - - +
647G SER* 3.2 5.6 + - - -
648G GLN* 1.3 77.2 - - - +
650G GLU* 1.3 58.4 + - - +
652G ASP* 2.7 31.5 + - - +
653G ARG* 3.2 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 650 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G GLU 4.8 3.8 - - - -
124G ASP* 3.5 14.2 + - - +
125G GLU* 3.1 34.6 + - - +
153G TYR* 5.4 2.2 + - - -
646G ILE* 3.7 23.3 - - + -
647G SER* 3.2 19.6 + - - +
649G ASP* 1.3 77.8 - - - +
651G ALA* 1.3 61.8 + - - +
653G ARG* 2.8 35.6 + - - +
654G ARG* 2.8 64.7 + - - +
679G ARG* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 651 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646G ILE* 3.4 24.8 - - + +
647G SER 3.2 13.1 + - - +
648G GLN* 4.1 3.8 - - - +
649G ASP 3.1 0.8 - - - -
650G GLU* 1.3 78.2 - - - +
652G ASP* 1.3 58.7 + - - +
653G ARG 3.4 0.2 - - - -
654G ARG* 4.4 3.6 - - - -
655G GLY* 3.1 19.6 + - - -
666G LEU* 3.2 20.5 - - + +
674G VAL* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 652 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G ASN* 5.1 3.3 + - - +
648G GLN* 2.9 22.6 + - - +
649G ASP* 2.7 20.9 + - - +
651G ALA* 1.3 71.3 - - - +
653G ARG* 1.3 61.6 + - + -
655G GLY* 3.9 2.3 - - - -
656G LYS* 3.4 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 653 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ASP* 3.6 22.6 + - - +
125G GLU 2.9 23.5 + - - +
126G THR* 5.2 6.3 + - - +
149G LEU* 4.6 4.9 - - - +
152G ASN* 3.4 36.6 + - + +
153G TYR* 3.4 42.4 + - + +
649G ASP* 3.2 21.9 + - - +
650G GLU* 2.8 43.6 + - - +
652G ASP* 1.3 76.0 - - + +
654G ARG* 1.3 61.2 + - - +
655G GLY 3.1 1.1 - - - -
656G LYS* 2.9 21.9 + - - +
657G VAL* 3.3 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 654 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G VAL* 4.2 9.9 - - - +
125G GLU* 6.2 0.2 - - - +
153G TYR* 4.5 4.7 + - - +
644G GLU* 2.6 32.7 + - - -
646G ILE* 3.9 26.9 - - - +
650G GLU* 2.8 38.6 + - - +
651G ALA* 4.2 4.5 - - - +
653G ARG* 1.3 74.9 - - + +
655G GLY* 1.3 61.7 + - - +
657G VAL* 3.2 10.3 - - - +
658G TYR* 2.8 56.5 + - + +
666G LEU* 4.8 1.1 - - + -
676G ASP* 2.6 40.4 + - - +
679G ARG* 3.4 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 655 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651G ALA 3.1 17.7 + - - -
652G ASP* 4.1 2.7 - - - -
653G ARG 3.1 0.6 - - - -
654G ARG* 1.3 77.5 - - - +
656G LYS* 1.3 50.7 + - - +
658G TYR* 2.6 10.3 + - - -
659G ASP* 2.5 46.5 + - - +
664G SER* 5.7 1.1 - - - -
666G LEU* 4.0 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 656 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G PHE* 3.4 35.3 - - - -
148G GLU* 2.7 44.9 + - + +
149G LEU* 4.4 9.9 - - + +
152G ASN* 3.1 30.7 - - - +
652G ASP 3.4 13.6 + - - +
653G ARG 2.9 11.0 + - - +
655G GLY* 1.3 74.1 - - - +
657G VAL* 1.3 61.9 + - - +
659G ASP* 3.5 16.8 + - - +
660G LYS 3.4 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 657 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G PRO* 3.6 27.8 - - + -
134G MET* 5.8 0.4 - - - -
145G PHE* 4.3 9.0 - - + -
149G LEU* 4.4 12.4 - - + +
153G TYR* 5.9 1.8 - - - +
653G ARG 3.3 4.8 + - - +
654G ARG* 3.2 24.9 - - - +
656G LYS* 1.3 77.3 - - - +
658G TYR* 1.3 72.8 + - + +
660G LYS* 3.1 13.0 + - + +
661G TYR* 3.2 26.8 + - + -
809G 74D 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 658 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654G ARG* 2.8 48.6 + - + +
655G GLY 2.6 10.3 + - - +
657G VAL* 1.3 79.6 - - + +
659G ASP* 1.3 62.6 + - - +
660G LYS 3.2 0.2 - - - -
661G TYR 3.4 1.7 + - - +
662G MET* 3.3 15.8 + - - -
663G CYS 3.3 17.9 + - - +
664G SER* 3.8 30.7 - - - -
666G LEU* 3.9 15.3 - - + -
676G ASP* 2.9 29.7 + - - -
678G THR* 3.1 41.7 - - + +
679G ARG* 4.8 3.8 + - - +
809G 74D 3.9 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 659 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G PHE* 5.9 0.4 - - + -
655G GLY* 2.5 35.0 + - - +
656G LYS* 3.5 19.3 + - - +
658G TYR* 1.3 71.6 - - - +
660G LYS* 1.3 62.6 + - - +
662G MET* 3.1 21.0 + - - +
664G SER* 5.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 660 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G MET* 3.7 24.6 - - - -
138G VAL* 5.7 6.9 - - - +
141G GLN 4.9 9.1 + - - -
142G ASP* 5.1 11.1 + - - +
145G PHE* 3.5 61.9 - - + -
656G LYS 3.4 2.2 + - - -
657G VAL* 3.1 10.7 + - + +
659G ASP* 1.3 81.4 - - - +
661G TYR* 1.3 61.6 + - + +
662G MET* 3.2 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 661 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G TYR* 4.2 11.2 - - - -
132G PRO* 4.0 15.1 - - + +
133G TYR 4.2 6.8 + - - -
134G MET* 4.0 26.9 - - + +
657G VAL* 3.2 41.4 + - + -
658G TYR 3.4 2.6 + - - +
659G ASP 3.4 0.4 - - - -
660G LYS* 1.3 75.6 - - - +
662G MET* 1.3 63.9 + - - +
663G CYS* 3.0 10.2 + - - +
809G 74D 3.4 86.1 - + + -
237H ASP* 5.7 0.7 + - - -
----------------------------------------------------------
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