Contacts of the helix formed by residues 860 - 876 (chain H) 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 ASP 860 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858H ALA 3.6 1.8 + - - +
859H LEU* 1.3 73.2 - - - +
861H ILE* 1.3 65.0 + - + +
862H HIS* 3.4 8.6 + - - -
863H LEU* 3.2 26.2 + - - +
864H SER* 2.7 29.9 + - - -
1378H GLY 5.0 4.9 - - - +
1379H ARG* 3.2 15.7 - - - +
1380H THR* 2.8 40.7 + - - +
1537H HIS* 5.5 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 861 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860H ASP* 1.3 74.0 - - + +
862H HIS* 1.3 106.3 + - + +
864H SER* 4.1 5.4 - - - -
865H ASP* 2.9 39.8 + - - +
889H LYS* 4.8 10.8 - - + +
891H GLN* 5.8 0.2 - - - +
1537H HIS 4.9 11.8 + - - +
1538H ARG* 5.3 9.2 - - - +
1539H VAL* 6.2 3.4 - - + -
1576H PHE* 4.4 23.3 - - + +
1579H ALA* 5.2 8.7 - - + -
1580H ASP* 3.6 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 862 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860H ASP* 3.3 8.7 + - - +
861H ILE* 1.3 101.4 - - + +
863H LEU* 1.3 66.1 + - + +
865H ASP* 3.8 3.6 - - - +
866H HIS* 3.0 26.4 + - - +
1379H ARG* 3.3 43.7 - - + +
1380H THR* 6.1 0.2 - - - +
1576H PHE* 3.3 30.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 863 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805H CYS 5.6 0.2 - - - +
806H SER* 4.1 19.1 + - - +
810H ASP* 5.4 0.9 - - - +
836H ARG* 3.2 47.1 - - - +
859H LEU* 3.7 19.3 - - + -
860H ASP* 3.2 18.0 + - - +
862H HIS* 1.3 85.0 - - + +
864H SER* 1.3 61.7 + - - +
866H HIS* 4.5 5.8 - - - +
867H LEU* 2.8 34.1 + - - +
1380H THR* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 864 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856H PHE* 4.0 21.2 + - - +
859H LEU* 3.5 25.0 + - - +
860H ASP 2.7 24.8 + - - -
861H ILE* 3.9 3.6 - - - -
863H LEU* 1.3 76.7 - - - +
865H ASP* 1.3 58.8 + - - +
867H LEU* 3.9 0.9 - - - +
868H MET* 2.9 33.4 + - - +
889H LYS* 3.3 28.0 + - - -
892H TYR* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 865 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861H ILE* 2.9 30.8 + - - +
862H HIS* 3.8 3.9 - - - +
864H SER* 1.3 74.6 - - - +
866H HIS* 1.3 65.7 + - - +
868H MET* 4.1 0.2 - - - +
869H GLN* 2.9 31.9 + - - +
889H LYS* 4.1 4.6 + - - -
891H GLN* 5.3 3.3 - - - +
892H TYR* 2.0 39.2 + - - +
1579H ALA* 4.8 14.7 - - - +
1580H ASP* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 866 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803H GLU 3.5 16.2 + - - -
804H ALA 4.5 0.7 - - - -
806H SER* 3.3 34.0 - - - +
862H HIS 3.0 17.4 + - - +
863H LEU* 4.0 6.1 - - - +
865H ASP* 1.3 76.2 - - - +
867H LEU* 1.3 63.8 + - - +
869H GLN* 4.7 7.4 - - + -
870H ALA* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 867 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804H ALA 3.4 17.2 + - - +
805H CYS* 4.1 30.5 - - + +
806H SER* 5.6 0.4 + - - -
836H ARG* 4.7 5.8 - - + -
839H VAL* 4.1 29.8 - - + -
843H LEU* 5.3 4.7 - - + -
852H LEU* 5.9 1.3 - - + -
855H PRO* 5.2 1.8 - - + +
856H PHE* 4.2 16.6 - - + -
859H LEU* 3.7 25.6 - - + -
863H LEU 2.8 21.3 + - - +
864H SER* 3.9 2.2 - - - +
866H HIS* 1.3 74.8 - - - +
868H MET* 1.3 68.5 + - - +
871H GLY* 2.8 27.7 + - - -
872H ILE* 5.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 868 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708H LEU* 4.4 15.0 - - + -
710H MET* 3.9 17.0 - - + -
856H PHE* 3.6 22.0 - - + -
864H SER 2.9 21.7 + - - +
865H ASP 4.1 1.1 - - - +
867H LEU* 1.3 75.3 - - - +
869H GLN* 1.3 68.1 + - - +
872H ILE* 2.8 47.6 + - + +
873H LEU 3.5 0.2 + - - -
885H LEU* 5.7 3.6 - - + -
892H TYR* 3.2 61.0 - - + -
895H HIS* 4.0 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 869 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865H ASP* 2.9 26.0 + - - +
866H HIS* 3.9 7.0 - - + +
868H MET* 1.3 77.5 - - - +
870H ALA* 1.3 59.6 + - - +
873H LEU* 2.7 47.8 - - + +
892H TYR* 5.5 3.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 870 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803H GLU 4.7 0.9 - - - +
804H ALA* 3.9 21.1 - - + -
866H HIS* 2.9 34.3 + - + +
869H GLN* 1.3 76.6 - - + +
871H GLY* 1.3 58.0 + - - +
873H LEU* 3.8 4.4 - - - +
874H GLU* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 871 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804H ALA* 3.8 18.6 - - - +
843H LEU* 4.8 11.6 - - - +
867H LEU* 2.8 18.9 + - - -
870H ALA* 1.3 76.5 - - - +
872H ILE* 1.3 57.2 + - - -
874H GLU* 3.0 9.9 + - - +
875H LEU* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 872 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708H LEU* 3.5 36.1 - - + -
843H LEU* 5.4 2.2 - - + -
852H LEU* 4.3 13.7 - - + -
856H PHE* 5.4 2.0 - - + -
867H LEU* 3.7 8.5 + - + +
868H MET* 2.8 50.0 + - + +
871H GLY* 1.3 72.9 - - - -
873H LEU* 1.3 56.4 + - - +
875H LEU* 3.2 23.2 + - + +
876H LEU* 2.9 33.0 + - + +
883H VAL* 4.7 4.0 - - + -
885H LEU* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 873 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868H MET 3.5 0.2 + - - -
869H GLN* 2.7 39.6 + - + +
870H ALA* 4.8 2.9 - - - +
872H ILE* 1.3 78.5 - - - +
874H GLU* 1.3 58.0 + - - +
876H LEU* 3.7 7.7 - - - +
877H ARG* 2.8 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 874 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800H MET* 3.6 42.9 - - + +
801H VAL* 6.0 1.0 - - - +
804H ALA* 6.2 0.4 - - + -
843H LEU* 5.6 1.7 - - - +
870H ALA 2.9 16.0 + - - +
871H GLY* 3.0 11.3 + - - +
873H LEU* 1.3 76.7 - - - +
875H LEU* 1.3 78.3 + - - +
877H ARG* 3.0 19.1 + - + +
878H ASP* 2.8 31.0 + - - +
881H ARG* 4.3 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 875 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843H LEU* 3.8 23.8 - - + -
850H VAL* 4.8 4.3 - - + -
852H LEU* 5.4 0.9 - - + -
871H GLY 2.9 14.9 + - - +
872H ILE* 3.2 27.8 + - + +
874H GLU* 1.3 82.4 - - - +
876H LEU* 1.3 58.3 + - - +
878H ASP* 2.9 30.4 + - - +
881H ARG* 3.4 56.8 + - + +
883H VAL* 3.6 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 876 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706H GLY 4.3 13.5 - - - +
707H GLN 4.5 0.7 - - - -
708H LEU* 3.6 52.5 - - + +
872H ILE* 2.9 21.4 + - + +
873H LEU* 3.7 7.2 - - - +
875H LEU* 1.3 75.4 - - - +
877H ARG* 1.3 59.1 + - - +
878H ASP 3.3 7.6 - - - +
881H ARG 5.4 2.7 - - - +
883H VAL* 5.0 5.2 - - + -
895H HIS 5.1 3.4 - - - +
897H ASP* 3.8 15.7 - - - +
----------------------------------------------------------
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