Contacts of the helix formed by residues 860 - 876 (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 ASP 860 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858G ALA 3.6 2.0 + - - +
859G LEU* 1.3 73.6 - - - +
861G ILE* 1.3 63.3 + - + +
862G HIS* 3.9 7.3 + - - -
863G LEU* 3.2 26.2 + - - +
864G SER* 2.7 30.6 + - - -
1378G GLY 5.0 4.5 - - - +
1379G ARG* 3.2 16.2 - - - +
1380G THR* 2.8 41.5 + - - +
1537G HIS* 5.5 14.4 - - + +
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Residues in contact with ILE 861 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860G ASP* 1.3 73.7 - - + +
862G HIS* 1.3 106.1 + - + +
864G SER* 4.1 5.2 - - - -
865G ASP* 2.9 39.9 + - - +
889G LYS* 4.8 11.4 - - + +
1537G HIS 4.9 11.6 + - - +
1538G ARG* 5.3 10.1 - - - +
1539G VAL* 6.2 3.1 - - + -
1576G PHE* 4.4 24.5 - - + +
1579G ALA* 5.2 9.2 - - + -
1580G ASP* 3.6 31.6 - - - +
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Residues in contact with HIS 862 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860G ASP* 3.3 8.9 - - - +
861G ILE* 1.3 101.4 - - + +
863G LEU* 1.3 67.4 + - + +
865G ASP* 3.8 3.6 - - - +
866G HIS* 3.0 26.1 + - - +
1379G ARG* 3.3 43.9 + - + +
1380G THR* 6.1 0.2 - - - +
1576G PHE* 3.3 31.3 - + - -
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Residues in contact with LEU 863 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805G CYS 5.6 0.2 - - - +
806G SER* 4.1 18.6 + - - +
810G ASP* 5.4 0.7 - - - +
836G ARG* 3.2 47.6 - - - +
859G LEU* 3.7 19.3 - - + -
860G ASP* 3.2 17.5 + - - +
862G HIS* 1.3 86.6 - - + +
864G SER* 1.3 61.3 + - - +
866G HIS* 4.5 5.4 - - - +
867G LEU* 2.8 34.0 + - - +
1380G THR* 4.0 23.1 - - + -
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Residues in contact with SER 864 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856G PHE* 4.0 21.7 + - - +
859G LEU* 3.5 25.2 + - - +
860G ASP 2.7 25.3 + - - -
861G ILE* 3.9 3.4 - - - -
863G LEU* 1.3 77.2 - - - +
865G ASP* 1.3 57.2 + - - +
867G LEU* 3.9 0.7 - - - +
868G MET* 2.9 33.8 + - - +
889G LYS* 3.3 27.2 + - - -
892G TYR* 4.4 1.1 - - - -
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Residues in contact with ASP 865 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861G ILE* 2.9 30.8 + - - +
862G HIS* 3.8 3.0 - - - +
864G SER* 1.3 75.6 - - - +
866G HIS* 1.3 64.8 + - - +
868G MET* 4.1 0.2 - - - +
869G GLN* 2.9 32.3 + - - +
889G LYS* 4.1 5.0 + - - -
891G GLN* 5.3 3.1 - - - +
892G TYR* 2.0 39.4 + - - +
1579G ALA* 4.8 14.4 - - - +
1580G ASP* 5.6 1.0 - - - +
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Residues in contact with HIS 866 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803G GLU 3.5 16.7 + - - -
804G ALA 4.6 0.2 - - - -
806G SER* 3.3 33.7 - - - +
862G HIS 3.0 17.8 + - - +
863G LEU* 4.0 6.1 - - - +
865G ASP* 1.3 75.9 - - - +
867G LEU* 1.3 64.0 + - - +
869G GLN* 3.9 7.4 - - + +
870G ALA* 2.9 35.0 + - + +
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Residues in contact with LEU 867 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804G ALA 3.4 18.4 - - - +
805G CYS* 4.1 28.9 - - + +
806G SER* 5.6 0.6 + - - +
836G ARG* 4.7 5.6 - - + -
839G VAL* 4.1 31.2 - - + -
843G LEU* 5.3 4.3 - - + -
852G LEU* 5.9 1.3 - - + -
855G PRO* 5.2 2.2 - - + +
856G PHE* 4.2 15.9 - - + -
859G LEU* 3.7 24.5 - - + -
863G LEU* 2.8 22.4 + - + +
864G SER* 3.9 2.0 - - - +
866G HIS* 1.3 72.6 - - - +
868G MET* 1.3 69.6 + - - +
871G GLY* 2.8 28.1 + - - -
872G ILE* 3.7 9.8 + - + -
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Residues in contact with MET 868 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708G LEU* 4.4 15.0 - - + -
710G MET* 3.9 16.6 - - + -
856G PHE* 3.6 23.3 - - + -
864G SER 2.9 21.7 + - - +
865G ASP 4.1 1.1 - - - +
867G LEU* 1.3 74.6 - - - +
869G GLN* 1.3 69.4 + - - +
872G ILE* 2.8 46.4 + - + +
873G LEU 3.5 0.3 + - - -
885G LEU* 5.7 3.8 - - + -
892G TYR* 3.2 59.7 - - + -
895G HIS* 4.0 13.7 - - + +
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Residues in contact with GLN 869 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865G ASP* 2.9 26.6 + - - +
866G HIS* 3.9 7.2 - - + +
868G MET* 1.3 76.5 - - - +
870G ALA* 1.3 58.7 + - - +
873G LEU* 2.7 47.9 + - + +
892G TYR* 5.5 2.6 + - + -
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Residues in contact with ALA 870 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803G GLU 4.7 0.7 - - - +
804G ALA* 3.9 21.5 - - + -
866G HIS* 2.9 35.5 + - + +
869G GLN* 1.3 75.7 - - + +
871G GLY* 1.3 58.9 + - - +
873G LEU* 3.8 4.0 - - - +
874G GLU* 2.9 29.4 + - - +
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Residues in contact with GLY 871 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804G ALA* 3.8 19.9 - - - +
843G LEU* 4.8 12.5 - - - +
867G LEU* 2.8 18.7 + - - -
870G ALA* 1.3 74.8 - - - +
872G ILE* 1.3 57.5 + - - -
874G GLU* 3.0 9.5 + - - +
875G LEU* 2.9 33.8 + - - +
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Residues in contact with ILE 872 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708G LEU* 3.5 36.1 - - + -
843G LEU* 5.4 2.0 - - + -
852G LEU* 4.3 13.7 - - + -
856G PHE* 5.4 2.0 - - + -
867G LEU* 3.7 8.5 + - + +
868G MET* 2.8 49.6 + - + +
871G GLY* 1.3 72.2 - - - -
873G LEU* 1.3 56.5 + - - +
875G LEU* 3.2 24.3 + - + +
876G LEU* 2.9 31.8 + - + +
883G VAL* 4.7 4.5 - - + -
885G LEU* 4.2 21.8 - - + -
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Residues in contact with LEU 873 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868G MET 3.5 0.2 + - - -
869G GLN* 2.7 38.8 + - + +
870G ALA* 3.9 3.1 - - - +
872G ILE* 1.3 77.9 - - - +
874G GLU* 1.3 57.4 + - - +
876G LEU* 3.7 8.2 - - - +
877G ARG* 2.8 60.0 + - - +
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Residues in contact with GLU 874 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800G MET* 3.6 43.4 - - + +
801G VAL* 6.0 0.9 - - - +
804G ALA* 6.2 0.7 - - + -
843G LEU* 5.6 1.6 - - - +
870G ALA 2.9 14.8 + - - +
871G GLY* 3.0 12.1 + - - +
873G LEU* 1.3 77.0 - - + +
875G LEU* 1.3 76.6 + - - +
877G ARG* 3.0 19.1 + - + +
878G ASP* 2.8 30.7 + - - +
881G ARG* 4.3 8.5 + - - -
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Residues in contact with LEU 875 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843G LEU* 3.8 23.6 - - + -
850G VAL* 4.8 4.0 - - + -
852G LEU* 5.4 0.9 - - + -
871G GLY 2.9 14.9 + - - +
872G ILE* 3.5 26.7 - - + +
874G GLU* 1.3 83.7 - - - +
876G LEU* 1.3 57.8 + - - +
878G ASP* 2.9 30.7 + - - +
881G ARG* 3.4 57.0 + - + +
883G VAL* 3.6 39.9 - - + -
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Residues in contact with LEU 876 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706G GLY 4.3 14.1 - - - +
707G GLN 4.5 0.9 - - - -
708G LEU* 3.6 51.8 - - + +
872G ILE* 2.9 21.2 + - + +
873G LEU* 3.7 7.0 - - - +
875G LEU* 1.3 75.1 - - - +
877G ARG* 1.3 58.4 + - - +
878G ASP 3.3 7.8 - - - +
881G ARG 5.4 2.2 - - - +
883G VAL* 5.0 5.8 - - + -
895G HIS 5.1 4.3 - - - +
897G ASP* 3.8 15.0 - - - +
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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
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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) + - + + + + + -
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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