Contacts of the helix formed by residues 793 - 805 (chain G) in PDB entry 6V3O
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 GLY 793 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611G LEU* 5.3 0.2 - - - -
724G ALA* 3.2 41.5 - - - +
727G GLU* 3.9 16.0 - - - +
728G TYR 4.5 0.9 - - - -
791G TRP* 3.3 0.8 + - - -
792G LEU* 1.3 81.2 - - - +
794G VAL* 1.3 62.1 + - - +
795G GLY 3.4 3.0 - - - +
796G ALA* 3.8 3.1 + - - +
797G ALA* 3.2 16.1 + - - +
867G THR* 5.8 0.2 + - - -
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Residues in contact with VAL 794 (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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610G ARG* 5.8 0.4 - - + -
611G LEU* 3.9 31.0 - - + +
790G VAL 4.7 2.7 - - - +
791G TRP* 3.0 21.4 + - - +
792G LEU 4.7 1.1 - - - +
793G GLY* 1.3 76.8 - - - +
795G GLY* 1.3 59.0 + - - +
797G ALA* 3.2 5.3 + - - +
798G PHE* 2.8 66.0 + - + -
829G LEU* 4.0 27.1 - - + -
867G THR* 3.9 11.2 - - + -
871G LEU* 5.8 0.2 - - + -
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Residues in contact with GLY 795 (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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791G TRP 4.4 0.2 + - - -
793G GLY 3.4 1.4 - - - +
794G VAL* 1.3 78.9 - - - +
796G ALA* 1.3 62.2 + - - +
798G PHE* 4.7 1.1 - - - -
799G LYS* 3.1 25.8 + - - +
866G GLU* 4.2 12.2 - - - +
867G THR* 3.4 35.7 + - - +
870G LEU* 3.6 11.0 - - - +
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Residues in contact with ALA 796 (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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723G VAL* 3.7 12.5 - - + +
727G GLU* 3.7 42.9 + - + +
793G GLY* 3.8 4.1 + - - +
794G VAL 3.3 0.2 - - - -
795G GLY* 1.3 76.8 - - - +
797G ALA* 1.3 62.2 + - - +
799G LYS* 3.9 3.9 - - - +
800G PHE* 2.9 25.3 + - - +
866G GLU* 4.3 5.5 + - - -
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Residues in contact with ALA 797 (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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611G LEU* 3.6 25.8 - - + -
720G MET* 3.7 32.6 - - + +
723G VAL* 4.1 11.8 - - - +
724G ALA* 4.1 0.7 - - + -
793G GLY 3.2 16.1 + - - +
794G VAL 3.2 5.7 + - - +
796G ALA* 1.3 78.9 - - - +
798G PHE* 1.3 63.2 + - + +
800G PHE* 3.2 4.2 + - - +
801G ALA* 3.0 19.2 + - - +
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Residues in contact with PHE 798 (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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611G LEU* 4.9 8.3 - - + -
720G MET* 3.3 25.6 - - + -
794G VAL* 2.8 47.4 + - + +
795G GLY* 4.0 3.6 - - - +
797G ALA* 1.3 72.9 - - + +
799G LYS* 1.3 62.0 + - - +
801G ALA* 3.2 4.5 + - - +
802G ILE* 3.0 29.1 + - + +
812G LEU* 5.0 0.4 - - - -
822G PHE* 4.2 14.1 - + - -
826G LEU* 3.7 35.9 - - + -
867G THR 5.0 1.3 - - - -
870G LEU* 4.0 27.1 - - + -
871G LEU* 4.1 12.1 - - + -
874G ILE* 3.5 32.5 - - + -
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Residues in contact with LYS 799 (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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795G GLY 3.1 16.9 + - - +
796G ALA* 4.1 3.8 - - - +
798G PHE* 1.3 74.0 - - - +
800G PHE* 1.3 66.9 + - - +
802G ILE* 4.3 6.7 - - + -
803G ASP* 2.9 50.3 + - - +
866G GLU* 4.7 14.4 - - + +
870G LEU* 4.2 16.1 - - + +
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Residues in contact with PHE 800 (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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716G LEU* 5.8 2.0 - - + -
719G GLU* 3.9 42.0 - - + -
720G MET* 4.8 3.8 - - + -
723G VAL* 3.6 37.0 - - + -
796G ALA 2.9 19.5 + - - +
797G ALA 3.5 6.7 - - - +
799G LYS* 1.3 77.1 - - - +
801G ALA* 1.3 68.0 + - + +
803G ASP* 3.9 4.2 - - - +
804G LYS* 3.0 43.5 + - + +
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Residues in contact with ALA 801 (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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716G LEU* 4.1 18.2 - - + -
720G MET* 3.7 28.7 - - + -
797G ALA 3.0 6.2 + - - +
798G PHE 3.2 8.0 + - - +
800G PHE* 1.3 83.7 - - + +
802G ILE* 1.3 63.4 + - - +
804G LYS* 3.3 6.9 + - - -
805G ASP 3.7 0.2 + - - -
808G ASN* 3.0 32.7 + - + +
812G LEU* 4.1 10.8 - - + -
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Residues in contact with ILE 802 (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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798G PHE* 3.0 18.1 + - + +
799G LYS* 3.3 7.4 + - + +
801G ALA* 1.3 76.6 - - - +
803G ASP* 1.3 67.3 + - - +
805G ASP 3.4 18.3 + - - +
806G VAL* 4.3 4.6 + - - +
808G ASN* 4.7 1.1 - - - -
809G PHE* 3.4 49.6 - - + +
812G LEU* 3.6 26.7 - - + -
870G LEU* 4.7 12.8 - - + -
874G ILE* 5.3 2.5 - - + -
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Residues in contact with ASP 803 (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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799G LYS* 2.9 59.4 + - - +
800G PHE* 4.0 4.4 - - - +
802G ILE* 1.3 82.5 - - - +
804G LYS* 1.3 66.9 + - - +
805G ASP* 3.4 1.2 + - - -
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Residues in contact with LYS 804 (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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715G LYS* 4.6 11.5 - - - +
716G LEU* 5.8 1.1 - - + +
719G GLU* 3.0 38.5 + - - +
800G PHE* 3.0 37.3 + - + +
801G ALA* 3.3 6.6 + - - +
803G ASP* 1.3 77.7 - - - +
805G ASP* 1.3 63.6 + - + +
808G ASN* 4.1 13.2 - - - +
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Residues in contact with ASP 805 (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 ALA 3.7 2.0 + - - -
802G ILE 3.4 10.7 - - - +
803G ASP 3.3 2.1 - - - -
804G LYS* 1.3 85.5 - - + +
806G VAL* 1.3 94.0 + - - +
807G ARG* 3.7 21.1 + - - +
808G ASN* 2.9 34.5 + - - +
809G PHE 4.4 0.2 + - - -
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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