Contacts of the helix formed by residues 830 - 844 (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 SER 830 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829G LEU* 1.3 81.7 - - - +
831G GLY* 1.3 63.7 + - - +
832G GLY* 3.0 10.6 + - - -
833G GLN* 3.1 22.5 + - - -
834G ARG* 3.1 8.5 + - - -
2001G ADP 5.0 21.0 + - - -
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Residues in contact with GLY 831 (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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776G PRO* 4.2 3.8 - - - +
829G LEU 3.6 1.6 + - - -
830G SER* 1.3 71.9 - - - +
832G GLY* 1.3 57.6 + - - +
834G ARG* 3.4 28.0 - - - +
835G GLN* 2.8 28.9 + - - +
858G ALA* 3.8 9.8 - - - +
1427G ASP* 5.4 9.0 + - - -
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Residues in contact with GLY 832 (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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830G SER* 3.0 7.0 - - - -
831G GLY* 1.3 73.8 - - - +
833G GLN* 1.3 64.9 + - - +
835G GLN* 3.2 3.3 + - - +
836G ARG* 3.0 43.8 + - - +
858G ALA* 4.2 16.2 - - - +
859G LEU* 4.2 3.9 - - - +
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Residues in contact with GLN 833 (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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807G LEU* 4.3 7.2 - - + -
810G ASP* 3.2 39.0 + - + +
813G ILE* 4.6 7.1 - - - +
814G LEU* 4.6 8.7 - - - +
829G LEU* 3.4 42.8 - - + +
830G SER* 3.1 11.2 + - - +
832G GLY* 1.3 74.4 - - - +
834G ARG* 1.3 63.7 + - - +
836G ARG* 3.0 27.1 + - - +
837G ILE* 2.9 35.2 + - + +
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Residues in contact with ARG 834 (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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775G LYS* 5.7 3.2 - - - +
776G PRO* 2.6 62.1 + - + +
777G TRP* 4.6 3.7 - - - +
778G LEU* 4.1 25.2 - - + +
829G LEU* 3.5 27.4 - - + -
830G SER 3.1 9.9 + - - +
831G GLY* 3.4 24.4 - - - +
832G GLY 3.1 0.2 - - - -
833G GLN* 1.3 77.2 - - - +
835G GLN* 1.3 56.6 + - - +
837G ILE* 3.3 5.9 + - - +
838G SER* 2.9 23.7 + - - -
841G ARG* 4.5 2.6 + - - -
1427G ASP* 5.3 7.1 + - - -
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Residues in contact with GLN 835 (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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772G ALA* 5.1 2.1 - - - +
773G SER 4.7 5.5 + - - +
774G GLN 4.3 8.3 + - - -
776G PRO* 3.7 26.3 - - + +
831G GLY 2.8 17.6 + - - +
832G GLY 3.7 3.8 - - - +
834G ARG* 1.3 75.2 - - - +
836G ARG* 1.3 65.2 + - - +
838G SER* 3.2 11.5 + - - -
839G VAL* 2.9 33.8 + - + +
853G ASP 4.8 1.5 + - - +
854G ASP 3.5 15.2 + - - -
855G PRO* 3.4 31.9 - - - +
857G SER* 5.2 2.2 - - - -
858G ALA* 4.0 21.9 - - + +
859G LEU* 4.9 6.5 - - + -
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Residues in contact with ARG 836 (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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805G CYS* 3.3 45.4 + - + +
806G SER 4.6 2.2 + - - -
807G LEU* 3.7 17.0 - - + +
810G ASP* 2.2 32.6 + - - -
832G GLY* 3.0 35.3 + - - +
833G GLN* 3.0 26.8 - - - +
835G GLN* 1.3 75.5 - - - +
837G ILE* 1.3 57.9 + - - +
839G VAL* 3.3 6.4 + - - +
840G ALA* 2.9 24.1 + - - +
859G LEU* 3.3 27.7 - - + +
863G LEU* 3.2 33.6 - - - +
867G LEU* 4.7 3.1 - - + -
1380G THR* 6.0 1.4 + - - +
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Residues in contact with ILE 837 (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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778G LEU* 5.6 4.3 - - + -
783G VAL* 5.2 13.5 - - + -
786G ASN* 3.9 18.2 - - - +
787G ILE* 4.1 11.4 - - + +
807G LEU* 3.9 26.5 - - + -
822G ILE* 5.7 4.9 - - + -
829G LEU* 5.0 12.6 - - + -
833G GLN* 2.9 32.3 + - + +
834G ARG* 3.7 6.5 - - - +
836G ARG* 1.3 73.5 - - - +
838G SER* 1.3 65.0 + - - +
840G ALA* 3.1 8.7 + - - +
841G ARG* 2.9 50.9 + - - +
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Residues in contact with SER 838 (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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772G ALA* 3.2 30.9 - - - +
773G SER 4.1 5.5 + - - -
776G PRO* 4.2 16.4 - - - +
777G TRP 4.6 3.0 + - - -
834G ARG 2.9 14.0 + - - -
835G GLN* 3.2 17.2 + - - -
837G ILE* 1.3 76.1 - - - +
839G VAL* 1.3 62.5 + - - +
841G ARG* 3.1 36.0 + - - +
842G ALA 3.6 3.1 + - - -
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Residues in contact with VAL 839 (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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772G ALA* 5.2 0.4 - - + -
805G CYS* 4.3 2.2 - - - -
835G GLN* 2.9 28.1 + - + +
836G ARG 3.6 7.2 - - - +
838G SER* 1.3 75.5 - - - +
840G ALA* 1.3 63.2 + - - +
842G ALA* 3.1 7.1 + - - +
843G LEU* 2.9 46.9 + - + +
852G LEU* 4.2 23.6 - - + -
855G PRO* 3.6 31.6 - - + +
867G LEU* 4.1 27.6 - - + -
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Residues in contact with ALA 840 (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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787G ILE* 4.6 20.8 - - + +
801G VAL* 3.7 24.7 - - + -
802G ILE* 6.0 2.0 - - + -
805G CYS* 3.9 7.6 - - + -
807G LEU* 6.1 2.2 - - + -
836G ARG 2.9 14.9 + - - +
837G ILE* 3.1 13.0 + - - +
839G VAL* 1.3 77.1 - - - +
841G ARG* 1.3 63.4 + - - +
843G LEU* 3.9 3.6 - - - -
844G TYR* 2.9 28.4 + - - +
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Residues in contact with ARG 841 (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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771G TYR 4.8 8.1 - - - +
777G TRP* 2.8 27.9 + - - -
778G LEU* 3.1 23.3 - - - +
779G LEU* 3.6 10.5 - - - +
786G ASN* 2.8 59.9 + - - +
787G ILE* 4.4 10.7 - - - +
789G PHE* 5.5 8.4 - - + +
834G ARG 4.5 1.0 + - - -
837G ILE* 2.9 40.6 + - + +
838G SER* 3.2 26.6 - - - +
839G VAL 3.1 0.2 - - - -
840G ALA* 1.3 79.0 - - - +
842G ALA* 1.3 58.5 + - - +
844G TYR 4.1 0.7 - - - -
845G GLN* 3.2 29.3 + - - +
1216G PHE* 4.9 11.7 - - + -
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Residues in contact with ALA 842 (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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770G ALA* 3.6 22.4 - - + +
771G TYR 4.0 17.6 + - - +
838G SER 3.6 2.7 + - - +
839G VAL 3.1 7.6 + - - +
841G ARG* 1.3 77.9 - - - +
843G LEU* 1.3 54.8 + - + +
845G GLN* 3.1 14.0 - - - +
850G VAL* 4.0 14.2 - - + +
851G PHE 4.0 9.0 - - - +
852G LEU* 4.4 8.5 - - + -
881G ARG* 2.6 28.6 + - - -
1216G PHE* 5.1 0.4 - - - -
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Residues in contact with LEU 843 (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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801G VAL* 3.7 20.3 - - + +
804G ALA* 4.5 14.6 - - + -
805G CYS* 3.7 21.3 - - - -
839G VAL* 2.9 39.9 + - + +
840G ALA* 3.1 4.9 + - - +
842G ALA* 1.3 76.8 - - + +
844G TYR* 1.3 59.1 + - - +
845G GLN 3.0 0.3 + - - -
846G HIS* 3.6 0.3 + - - -
850G VAL* 5.6 1.8 - - + -
852G LEU* 5.6 3.8 - - + -
867G LEU* 5.3 4.0 - - + -
871G GLY* 4.8 11.7 - - - +
872G ILE* 5.4 3.1 - - + -
874G GLU* 5.6 1.3 - - - +
875G LEU* 3.8 35.7 - - + -
881G ARG* 2.4 35.2 + - - +
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Residues in contact with TYR 844 (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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787G ILE* 3.5 28.3 - - + +
788G ILE* 3.6 32.8 - - + -
791G SER* 3.7 16.1 + - - -
792G PRO 2.8 27.2 + - - -
793G PHE* 3.1 19.6 - + - -
794G ASN* 3.1 9.1 + - + -
797G ARG* 3.8 39.7 - - + -
798G TYR* 4.0 14.4 - + - -
801G VAL* 3.6 16.0 - - + +
840G ALA 2.9 17.9 + - - +
841G ARG 4.1 0.2 - - - -
843G LEU* 1.3 71.3 - - - +
845G GLN* 1.3 63.3 + - - +
846G HIS* 3.1 6.8 + - - +
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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
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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