Contacts of the helix formed by residues 807 - 813 (chain H) 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 LEU 807 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783H VAL* 5.0 2.9 - - + -
787H ILE* 4.7 13.7 - - + -
802H ILE* 3.3 18.2 + - + +
805H CYS* 4.2 11.0 - - + +
806H SER* 1.3 74.9 - - - +
808H GLN* 1.3 60.6 + - - +
809H PRO* 3.3 3.6 - - - -
810H ASP* 2.8 26.1 + - + +
811H ILE* 2.8 45.7 + - + -
833H GLN* 4.3 13.5 - - + -
836H ARG* 3.7 25.1 - - + +
837H ILE* 3.9 28.3 - - + +
840H ALA* 6.1 2.2 - - + -
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Residues in contact with GLN 808 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799H LYS* 5.6 4.4 - - - +
802H ILE* 3.1 35.2 - - + +
803H GLU* 4.4 25.1 + - + +
806H SER* 5.2 0.9 - - - -
807H LEU* 1.3 76.5 - - - +
809H PRO* 1.3 70.1 - - + +
811H ILE* 3.1 15.7 + - - +
812H ASP* 2.9 23.9 + - - +
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Residues in contact with PRO 809 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806H SER* 3.6 16.4 - - - +
807H LEU 3.4 4.3 - - - -
808H GLN* 1.3 93.2 - - + +
810H ASP* 1.3 65.2 + - - +
812H ASP* 3.5 7.3 + - + +
813H ILE* 3.3 20.4 + - - +
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Residues in contact with ASP 810 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806H SER 5.0 1.9 - - - +
807H LEU* 2.8 20.3 + - + +
809H PRO* 1.3 80.3 - - - +
811H ILE* 1.3 62.9 + - - +
813H ILE* 3.0 25.5 - - - +
814H LEU* 3.2 14.6 - - - +
833H GLN* 3.2 25.8 + - - +
836H ARG* 2.2 36.6 + - - -
863H LEU* 5.4 0.9 - - - +
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Residues in contact with ILE 811 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783H VAL* 5.0 8.5 - - + -
787H ILE* 5.9 0.2 - - + -
798H TYR* 5.6 1.8 - - - +
802H ILE* 3.6 39.5 - - + -
807H LEU* 2.8 33.6 + - + +
808H GLN* 3.1 18.6 + - - +
810H ASP* 1.3 76.3 - - - +
812H ASP* 1.3 65.2 + - - +
814H LEU* 3.1 21.2 + - + +
817H GLY* 3.1 45.7 - - - +
818H ASP* 3.6 12.6 - - + +
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Residues in contact with ASP 812 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808H GLN 2.9 12.0 + - - +
809H PRO* 3.7 10.8 - - + +
810H ASP 3.4 0.2 - - - -
811H ILE* 1.3 78.3 - - - +
813H ILE* 1.3 60.3 + - - +
814H LEU 3.2 8.3 + - - +
817H GLY* 5.3 1.0 - - - -
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Residues in contact with ILE 813 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809H PRO 3.3 7.2 + - - +
810H ASP* 3.0 34.1 - - - +
812H ASP* 1.3 77.2 - - - +
814H LEU* 1.3 65.0 + - + +
815H PRO* 3.7 2.8 - - - +
833H GLN* 4.6 9.2 - - - +
2001H ADP 6.0 1.6 - - - +
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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