Contacts of the helix formed by residues 794 - 806 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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792E PRO* 3.2 22.5 + - - +
793E PHE* 1.3 79.8 - - - +
795E LYS* 1.3 56.8 + - - +
796E GLN* 3.1 3.4 - - + +
797E ARG* 3.1 24.8 + - + +
798E TYR* 2.5 39.9 + - - +
844E TYR* 3.1 11.2 + - - +
846E HIS* 6.2 2.4 - - - -
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Residues in contact with LYS 795 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793E PHE* 3.6 28.1 + - + -
794E ASN* 1.3 69.4 - - - +
796E GLN* 1.3 63.9 + - - +
798E TYR* 3.6 3.7 - - - +
799E LYS* 2.9 49.9 + - - +
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Residues in contact with GLN 796 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794E ASN* 3.1 2.8 - - + -
795E LYS* 1.3 79.2 - - - +
797E ARG* 1.3 58.4 + - - +
799E LYS* 3.6 9.3 - - - +
800E MET* 2.9 34.1 + - - +
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Residues in contact with ARG 797 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794E ASN* 3.1 25.2 + - + +
796E GLN* 1.3 77.9 - - - +
798E TYR* 1.3 57.3 + - - +
800E MET* 3.6 18.1 - - + +
801E VAL* 2.9 36.4 + - + +
844E TYR* 3.8 17.7 - - + -
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Residues in contact with TYR 798 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783E VAL* 4.9 0.5 - - - +
784E GLU* 3.6 11.7 + - + +
787E ILE* 3.8 35.2 - - + +
788E ILE* 4.7 6.1 - - + -
793E PHE* 3.4 41.1 - + + -
794E ASN 2.5 22.7 + - - +
795E LYS* 3.6 4.3 - - - +
797E ARG* 1.3 73.8 - - - +
799E LYS* 1.3 68.0 + - + +
801E VAL* 3.2 2.8 + - - +
802E ILE* 3.0 50.9 + - + +
811E ILE* 5.6 0.5 - - - +
818E ASP* 2.5 44.3 + - - -
844E TYR* 4.0 13.0 - + + -
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Residues in contact with LYS 799 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795E LYS* 2.9 46.3 + - - +
796E GLN* 3.6 7.4 - - - +
798E TYR* 1.3 78.1 - - + +
800E MET* 1.3 60.7 + - + +
802E ILE* 4.3 11.2 - - + -
803E GLU* 2.9 49.8 + - + +
808E GLN* 5.6 4.3 - - - +
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Residues in contact with MET 800 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796E GLN 2.9 21.5 + - - +
797E ARG* 3.6 21.8 - - + +
799E LYS* 1.3 79.3 - - + +
801E VAL* 1.3 66.0 + - + +
803E GLU* 3.8 6.9 - - - +
804E ALA* 2.9 30.0 + - + +
874E GLU* 3.6 42.4 - - + +
881E ARG* 6.2 0.7 - - - +
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Residues in contact with VAL 801 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787E ILE* 5.4 3.1 - - + -
797E ARG* 2.9 23.6 + - + +
798E TYR* 3.6 4.7 - - + +
800E MET* 1.3 85.9 - - + +
802E ILE* 1.3 64.3 + - + +
804E ALA* 3.2 9.2 + - - +
805E CYS* 3.0 21.7 + - - +
840E ALA* 3.7 28.3 - - + +
843E LEU* 3.7 27.6 - - + +
844E TYR* 3.6 31.2 - - + +
874E GLU* 6.0 0.7 - - - +
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Residues in contact with ILE 802 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787E ILE* 5.2 11.4 - - + -
798E TYR* 3.0 59.5 + - + +
799E LYS* 3.8 6.3 - - + +
800E MET 3.2 0.4 - - - -
801E VAL* 1.3 80.0 - - + +
803E GLU* 1.3 50.7 + - - +
805E CYS* 3.0 7.7 + - - +
806E SER 2.5 32.1 + - - -
807E LEU* 3.3 10.7 + - + -
808E GLN* 3.1 40.2 - - + +
811E ILE* 3.6 22.9 - - + -
818E ASP* 5.9 0.2 - - - -
840E ALA* 6.0 2.2 - - + -
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Residues in contact with GLU 803 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799E LYS* 2.9 34.2 + - + +
800E MET* 4.0 5.1 - - - +
802E ILE* 1.3 72.3 - - - +
804E ALA* 1.3 66.5 + - - +
806E SER* 3.3 10.5 + - - +
808E GLN* 4.4 21.5 + - + +
866E HIS* 3.5 21.5 + - - -
870E ALA* 4.7 0.7 - - - +
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Residues in contact with ALA 804 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800E MET* 2.9 16.2 + - + +
801E VAL* 3.2 13.9 - - - +
803E GLU* 1.3 78.9 - - - +
805E CYS* 1.3 60.6 + - - +
806E SER* 3.4 1.7 + - - -
843E LEU* 4.5 8.3 - - + -
866E HIS* 4.0 4.7 - - - +
867E LEU* 3.4 27.9 + - - -
870E ALA* 3.9 13.5 - - + -
871E GLY* 3.8 28.3 - - - +
874E GLU* 6.2 0.7 - - + -
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Residues in contact with CYS 805 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801E VAL 3.0 12.1 + - - +
802E ILE* 3.7 7.4 - - - +
804E ALA* 1.3 73.9 - - - +
806E SER* 1.3 75.8 + - - +
807E LEU* 4.5 8.1 - - + +
836E ARG* 3.3 53.4 - - + +
839E VAL* 4.3 0.4 - - - -
840E ALA* 3.9 11.9 - - + -
843E LEU* 3.7 26.9 - - - -
863E LEU* 5.6 0.3 - - - +
867E LEU* 4.1 21.9 - - + +
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Residues in contact with SER 806 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802E ILE 2.5 13.8 + - - -
803E GLU* 3.3 8.2 + - - +
804E ALA 3.2 2.2 - - - -
805E CYS* 1.3 81.5 + - - +
807E LEU* 1.3 59.1 + - - +
808E GLN* 3.4 3.6 - - - +
809E PRO* 3.6 14.9 - - - +
810E ASP* 5.0 2.4 - - - +
836E ARG* 4.6 4.2 + - - -
863E LEU* 4.1 23.0 + - - +
866E HIS* 3.3 36.4 + - - +
867E LEU* 5.6 0.7 + - - +
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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