Contacts of the helix formed by residues 794 - 806 (chain G) in PDB entry 6C3P
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 ASN 794 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792G PRO* 3.2 21.9 + - - +
793G PHE* 1.3 81.0 - - - +
795G LYS* 1.3 56.6 + - - +
796G GLN* 3.1 3.1 - - + +
797G ARG* 3.7 24.0 - - + +
798G TYR* 2.5 39.7 + - - +
844G TYR* 3.1 11.2 + - - +
846G HIS* 6.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 795 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793G PHE* 3.6 28.6 + - + -
794G ASN* 1.3 69.6 - - - +
796G GLN* 1.3 62.8 + - - +
798G TYR* 4.1 3.5 - - - -
799G LYS* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 796 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794G ASN* 3.1 2.6 - - + -
795G LYS* 1.3 79.7 - - - +
797G ARG* 1.3 58.4 + - - +
799G LYS* 3.6 8.4 - - - +
800G MET* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 797 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794G ASN* 3.1 26.0 + - + +
796G GLN* 1.3 78.8 - - - +
798G TYR* 1.3 58.0 + - - +
800G MET* 3.6 18.1 - - + +
801G VAL* 2.9 37.5 + - + +
844G TYR* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 798 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783G VAL* 4.9 0.5 - - - +
784G GLU* 3.6 12.2 + - + +
787G ILE* 3.8 34.4 - - + +
788G ILE* 4.7 5.8 - - + -
793G PHE* 3.4 38.1 - + + -
794G ASN 2.5 22.3 + - - +
795G LYS* 3.6 3.6 - - - +
797G ARG* 1.3 74.6 - - - +
799G LYS* 1.3 67.2 + - + +
801G VAL* 3.2 2.6 + - + +
802G ILE* 3.0 49.1 + - + +
811G ILE* 5.6 0.5 - - - +
818G ASP* 2.5 43.9 + - - -
844G TYR* 4.0 13.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 799 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795G LYS* 2.9 47.7 + - - +
796G GLN* 3.6 7.6 - - - +
798G TYR* 1.3 78.6 - - + +
800G MET* 1.3 59.8 + - - +
802G ILE* 3.8 11.8 - - + +
803G GLU* 2.9 49.6 + - + +
808G GLN* 5.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 800 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796G GLN 2.9 21.9 + - - +
797G ARG* 3.6 22.4 - - + +
799G LYS* 1.3 78.9 - - - +
801G VAL* 1.3 67.2 + - + +
803G GLU* 3.8 6.5 - - - +
804G ALA* 2.9 30.2 + - + +
874G GLU* 3.6 42.0 - - + +
881G ARG* 6.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 801 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787G ILE* 5.4 2.7 - - + -
797G ARG* 2.9 23.6 + - + +
798G TYR* 3.6 4.5 - - + +
800G MET* 1.3 85.1 - - + +
802G ILE* 1.3 66.0 + - + +
804G ALA* 3.2 8.2 + - - +
805G CYS* 3.0 21.8 + - - +
840G ALA* 3.7 27.8 - - + +
843G LEU* 3.7 28.0 - - + +
844G TYR* 3.6 32.5 - - + +
874G GLU* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 802 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787G ILE* 5.2 11.2 - - + -
798G TYR* 3.0 59.7 + - + +
799G LYS* 3.8 7.0 - - + +
800G MET 3.2 0.2 - - - -
801G VAL* 1.3 80.7 - - + +
803G GLU* 1.3 52.0 + - - +
805G CYS* 3.0 7.0 + - - +
806G SER 2.5 31.9 + - - -
807G LEU* 3.3 9.8 + - + -
808G GLN* 3.1 40.2 - - + +
811G ILE* 3.6 22.9 - - + -
840G ALA* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 803 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799G LYS* 2.9 35.7 + - + +
800G MET* 4.0 5.3 - - - +
802G ILE* 1.3 72.1 - - - +
804G ALA* 1.3 64.4 + - - +
806G SER* 3.3 10.8 + - - +
808G GLN* 4.4 21.1 + - + +
866G HIS* 3.5 22.0 + - - -
870G ALA* 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 804 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800G MET* 2.9 16.2 + - + +
801G VAL* 3.2 13.2 - - - +
802G ILE 3.1 0.2 - - - -
803G GLU* 1.3 78.6 - - - +
805G CYS* 1.3 60.8 + - - +
806G SER* 3.4 1.7 + - - -
843G LEU* 4.5 7.6 - - + -
866G HIS* 4.0 4.0 - - - +
867G LEU* 3.4 27.2 + - + -
870G ALA* 3.9 13.0 - - + +
871G GLY* 3.8 28.7 - - - +
874G GLU* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 805 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801G VAL 3.0 13.0 + - - +
802G ILE* 3.7 5.8 - - - +
804G ALA* 1.3 75.0 - - - +
806G SER* 1.3 74.6 + - - +
807G LEU* 4.5 8.5 - - + +
836G ARG* 3.3 52.9 - - + +
839G VAL* 4.3 0.7 - - - -
840G ALA* 3.9 9.6 - - + -
843G LEU* 3.7 28.0 - - - -
863G LEU* 4.8 0.3 - - - +
867G LEU* 4.1 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 806 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802G ILE 2.5 14.0 + - - -
803G GLU* 3.3 8.4 + - - +
804G ALA 3.2 2.8 - - - -
805G CYS* 1.3 82.2 + - - +
807G LEU* 1.3 58.1 + - - +
808G GLN* 3.4 4.0 - - - +
809G PRO* 3.6 14.5 - - - +
810G ASP* 5.0 2.4 - - - +
836G ARG* 4.6 3.8 + - - -
863G LEU* 4.1 22.7 + - - +
866G HIS* 3.3 36.7 + - - +
867G LEU* 5.6 0.5 + - - +
----------------------------------------------------------
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