Contacts of the helix formed by residues 638 - 656 (chain G) in PDB entry 4P6X
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 CYS 638 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556G THR* 4.4 9.0 - - + -
560G MET* 4.3 1.8 - - - +
636G LEU 3.3 2.0 + - - -
637G PRO* 1.3 77.8 - - - +
639G MET* 1.3 63.6 + - - +
640G TYR 3.5 1.8 - - - -
641G ASP* 3.8 24.1 + - + +
642G GLN* 3.9 21.8 + - - +
735G TYR* 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 639 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556G THR* 4.2 15.0 - - + +
559G ILE* 4.1 28.7 - - + -
560G MET* 4.4 16.6 - - + -
563G LEU* 5.7 2.5 - - - -
629G ILE* 4.2 19.7 - - + -
633G ARG 3.5 17.5 - - - +
634G MET* 4.2 6.7 - - - +
636G LEU* 3.1 41.1 + - + +
637G PRO 3.1 3.8 + - - +
638G CYS* 1.3 78.5 - - - +
640G TYR* 1.3 60.2 + - - +
642G GLN* 3.2 6.1 + - - +
643G CYS* 2.9 53.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 640 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634G MET* 3.8 36.6 + - + +
636G LEU 4.4 1.2 + - - -
638G CYS 3.5 0.6 - - - +
639G MET* 1.3 74.5 - - - +
641G ASP* 1.3 64.2 + - - +
642G GLN 3.0 2.7 - - - -
643G CYS* 4.2 3.8 - - - +
644G LYS* 2.8 68.6 + - + +
647G LEU* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 641 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638G CYS* 3.8 20.8 + - - +
639G MET 3.4 0.8 - - - -
640G TYR* 1.3 80.3 - - - +
642G GLN* 1.3 56.8 + - - +
644G LYS* 3.7 21.6 + - - +
645G HIS* 3.2 26.0 + - - -
735G TYR* 3.3 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 642 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560G MET* 3.2 31.7 - - + +
638G CYS* 3.9 13.9 + - - +
639G MET 3.2 6.8 + - - +
640G TYR 3.0 0.4 - - - -
641G ASP* 1.3 75.6 - - - +
643G CYS* 1.3 63.3 + - - +
644G LYS 3.0 5.6 + - - -
645G HIS* 3.3 16.6 + - - +
646G MET* 3.2 22.7 + - + +
732G LEU* 4.0 1.4 - - + +
735G TYR* 3.4 50.3 - - + +
739G THR* 4.3 12.1 - - - +
900G HCY 2.7 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 643 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560G MET* 6.0 0.4 - - - -
563G LEU* 6.2 0.4 - - - -
621G LEU* 3.5 24.7 - - + -
623G PHE* 4.9 3.8 - - - -
629G ILE* 4.5 7.9 - - - -
634G MET* 3.8 21.3 - - + -
639G MET* 2.9 45.5 + - - +
640G TYR 4.3 1.1 - - - +
642G GLN* 1.3 74.7 - - - +
644G LYS* 1.3 55.2 + - - +
645G HIS 3.3 0.2 - - - -
646G MET* 3.1 15.9 + - - +
647G LEU* 2.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 644 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640G TYR* 2.8 52.2 + - + +
641G ASP* 3.7 36.6 + - - +
643G CYS* 1.3 76.0 - - - +
645G HIS* 1.3 82.1 + - + +
647G LEU* 3.4 4.6 + - - +
648G TYR* 3.2 20.3 + - - +
735G TYR* 5.1 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 645 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641G ASP 3.2 27.3 + - - -
642G GLN 3.7 5.4 - - - -
643G CYS 3.3 0.6 - - - -
644G LYS* 1.3 93.0 + - + +
646G MET* 1.3 65.4 + - - +
648G TYR* 3.3 19.2 - - - +
649G VAL* 3.6 9.0 - - - +
728G VAL* 4.1 17.4 - - + +
731G ASN* 3.3 47.8 + - + +
732G LEU* 3.8 20.1 - - + +
735G TYR* 4.0 15.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 646 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605G ALA* 5.2 2.0 - - + -
608G LEU* 3.6 20.6 - - + +
609G GLY* 4.9 2.9 - - - -
621G LEU* 3.8 15.5 - - + +
623G PHE* 3.6 32.3 - - + -
642G GLN* 3.2 38.6 + - + +
643G CYS* 3.1 13.3 + - - +
645G HIS* 1.3 74.5 - - - +
647G LEU* 1.3 65.3 + - - +
649G VAL* 3.1 23.2 + - - +
650G SER* 3.5 7.4 + - - -
732G LEU* 3.8 29.8 - - + -
900G HCY 3.9 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 647 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619G ASN* 3.3 38.4 - - + +
620G LEU 3.3 21.3 - - - +
621G LEU* 3.6 15.9 - - + +
634G MET* 3.6 19.7 - - + -
640G TYR* 3.9 26.0 - - + +
643G CYS 2.7 23.7 + - - +
644G LYS* 3.7 4.5 - - - +
646G MET* 1.3 72.9 - - - +
648G TYR* 1.3 56.8 + - - +
650G SER* 3.3 7.6 + - - +
651G SER* 2.8 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 648 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644G LYS 3.2 11.9 + - - +
645G HIS* 3.3 13.0 - - - +
646G MET 3.1 0.2 - - - -
647G LEU* 1.3 76.9 - - - +
649G VAL* 1.3 70.0 + - + +
651G SER* 3.0 12.1 + - - -
652G GLU* 2.9 57.1 + - + +
721G LEU* 4.5 4.8 - - + +
724G SER* 3.5 29.8 + - - -
725G MET* 5.6 0.7 - - - -
728G VAL* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 649 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605G ALA* 4.0 20.2 - - + +
606G PHE* 4.2 23.8 - - + -
609G GLY* 3.8 18.2 - - - -
645G HIS 3.6 11.4 - - - +
646G MET* 3.1 20.2 - - - +
648G TYR* 1.3 85.1 - - + +
650G SER* 1.3 62.6 + - - +
652G GLU* 3.2 5.6 + - - +
653G LEU* 3.0 28.3 + - + +
721G LEU* 5.2 2.6 - - + +
725G MET* 4.1 22.7 - - + -
728G VAL* 4.9 3.8 - - + -
732G LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 650 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609G GLY* 3.7 26.7 - - - -
612G SER* 3.6 22.4 - - - -
613G TYR* 3.7 13.3 + - - +
620G LEU 4.6 3.1 + - - -
621G LEU* 4.9 1.3 - - - -
646G MET 3.5 5.3 + - - -
647G LEU* 3.3 16.8 + - - +
648G TYR 3.2 0.2 - - - -
649G VAL* 1.3 81.1 - - - +
651G SER* 1.3 61.8 + - - +
653G LEU* 3.3 3.9 + - - +
654G HIS* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 651 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619G ASN* 6.3 1.1 - - - -
647G LEU 2.8 17.2 + - - -
648G TYR* 3.2 14.9 - - - -
650G SER* 1.3 73.3 + - - +
652G GLU* 1.3 65.6 + - - +
654G HIS* 3.3 8.0 + - - +
655G ARG* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 652 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648G TYR* 2.9 54.4 + - + +
649G VAL 3.2 7.8 + - - +
651G SER* 1.3 81.8 + - - +
653G LEU* 1.3 66.9 + - - +
655G ARG* 2.6 46.2 + - - +
656G LEU* 2.9 31.6 + - + +
721G LEU* 3.9 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 653 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606G PHE* 4.1 23.6 - - + +
609G GLY* 3.6 7.0 - - - -
610G TRP* 3.4 49.4 - - + +
613G TYR* 3.8 17.8 - - + -
649G VAL* 3.0 24.1 + - + +
650G SER 3.7 5.2 - - - +
652G GLU* 1.3 75.4 - - - +
654G HIS* 1.3 57.9 + - - +
657G GLN* 3.1 20.4 + - - -
658G VAL* 3.1 42.7 + - + -
663G TYR* 4.9 2.2 - - + -
666G MET* 5.3 0.2 - - + -
721G LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 654 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613G TYR* 3.4 30.9 - + + -
617G SER* 4.5 21.4 + - - -
650G SER 3.1 11.2 + - - +
651G SER* 3.5 10.2 + - - +
653G LEU* 1.3 76.4 - - - +
655G ARG* 1.3 68.9 + - - +
657G GLN* 2.5 50.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 655 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651G SER* 2.9 19.2 + - - +
652G GLU* 2.6 39.5 + - - +
654G HIS* 1.3 82.8 + - - +
656G LEU* 1.3 95.8 + - - +
657G GLN* 3.4 5.0 + - - +
717G GLN* 4.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 656 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652G GLU* 2.9 18.9 + - - +
655G ARG* 1.3 113.8 - - - +
657G GLN* 1.3 70.2 + - - +
658G VAL* 3.3 9.4 - - + -
714G ARG* 2.8 32.8 + - - +
717G GLN* 3.9 49.4 - - + +
718G LEU* 4.2 14.1 - - + -
721G LEU* 4.2 20.0 - - + -
----------------------------------------------------------
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