Contacts of the helix formed by residues 802 - 810 (chain A) in PDB entry 6CNC
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 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A VAL* 5.7 4.7 - - - +
795A ALA* 3.6 22.8 + - - +
801A GLY* 1.3 75.9 - - - -
803A THR* 1.3 73.9 + - - +
804A LEU* 3.1 8.0 - - - +
805A ASN* 2.7 30.4 + - - +
806A VAL* 3.2 10.7 + - - +
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Residues in contact with THR 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778A GLY* 4.4 11.1 + - - -
781A CYS* 5.3 1.9 - - - -
782A ILE* 4.4 31.5 + - + +
795A ALA* 4.5 1.8 - - - +
802A SER* 1.3 86.2 + - - +
804A LEU* 1.3 55.1 + - + +
806A VAL* 3.6 14.1 - - - +
807A SER* 2.7 47.0 + - - -
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Residues in contact with LEU 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774A ARG* 3.2 54.1 + - - +
802A SER* 3.0 5.7 + - - +
803A THR* 1.3 85.3 - - + +
805A ASN* 1.3 62.1 + - + +
807A SER* 4.3 2.5 - - - -
808A GLN* 3.6 8.3 + - - +
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Residues in contact with ASN 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801A GLY* 4.6 5.7 - - - -
802A SER 2.7 25.3 + - - +
804A LEU* 1.3 71.4 - - - +
806A VAL* 1.3 56.8 + - - +
807A SER 3.1 1.1 - - - -
808A GLN* 2.7 37.0 + - - +
809A MET* 3.6 2.1 + - - +
950B PRO* 2.8 30.4 + - - +
951B SER* 3.3 24.0 + - - +
953B MET* 3.2 23.5 - - - +
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Residues in contact with VAL 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781A CYS* 5.6 4.7 - - - -
782A ILE* 6.5 1.1 - - + -
785A LEU* 5.7 6.7 - - + -
791A PRO* 3.4 39.0 - - + +
795A ALA* 4.9 7.9 - - + -
802A SER 3.2 4.8 + - - +
803A THR* 3.6 24.2 - - - +
805A ASN* 1.3 78.5 + - - +
807A SER* 1.3 60.7 + - - +
809A MET* 2.8 33.3 + - + +
810A VAL* 2.9 29.9 + - + +
950B PRO* 5.9 2.5 - - + -
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Residues in contact with SER 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774A ARG* 4.7 9.5 + - - +
775A GLU* 6.0 0.2 - - - -
778A GLY* 3.9 17.6 + - - -
781A CYS* 4.0 16.8 - - - -
803A THR* 2.7 29.2 + - - -
804A LEU* 4.3 5.6 - - - -
806A VAL* 1.3 77.4 - - - +
808A GLN* 1.3 56.9 + - - +
811A ALA* 3.0 18.5 + - - +
812A VAL* 2.9 33.9 + - - +
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Residues in contact with GLN 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774A ARG* 3.0 33.9 - - - +
804A LEU* 3.6 9.4 - - - +
805A ASN* 2.7 13.4 + - - +
807A SER* 1.3 77.4 - - - +
809A MET* 1.3 63.5 + - - +
810A VAL 3.5 0.2 + - - -
812A VAL 3.5 6.5 - - - +
813A VAL* 3.5 38.1 - - + +
814A GLY 5.8 0.2 + - - -
851A SER* 3.6 7.3 + - - -
852A PHE* 3.3 19.7 + - + -
864A HIS* 5.9 1.9 - - - -
953B MET* 3.1 33.7 - - - +
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Residues in contact with MET 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717A VAL* 3.6 32.5 - - + -
791A PRO* 4.8 6.3 - - - -
805A ASN* 3.6 0.8 + - - +
806A VAL* 2.8 28.6 + - - +
808A GLN* 1.3 73.1 - - - +
810A VAL* 1.3 58.8 + - + +
851A SER* 3.2 17.0 - - - -
852A PHE* 4.0 9.8 - - + -
853A PHE* 3.4 19.5 + - - +
949B PHE* 3.2 34.5 - - + +
950B PRO* 3.6 17.5 - - + +
953B MET* 3.5 28.9 - - + -
954B THR 4.3 0.7 - - - +
955B VAL* 4.0 19.3 - - + -
958B MET* 6.0 0.7 - - + -
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Residues in contact with VAL 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A ASP 5.1 1.1 - - - +
717A VAL* 3.2 36.8 - - + +
718A THR 5.0 0.2 - - - -
719A PRO* 3.8 32.8 - - + +
723A LEU* 3.6 25.1 - - + -
727A LYS* 5.2 1.4 - - - +
781A CYS* 4.4 7.6 - - - -
785A LEU* 5.2 13.5 - - + -
791A PRO* 6.0 0.4 - - + -
806A VAL* 2.9 27.0 + - + +
809A MET* 1.3 74.9 - - - +
811A ALA* 1.3 59.7 + - - +
851A SER* 2.6 22.8 + - - -
853A PHE* 5.4 0.9 - - - +
854A SER* 5.2 0.5 + - - -
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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