Contacts of the helix formed by residues 1209 - 1212 (chain D) in PDB entry 6OVR
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 LEU1209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770D LEU* 3.6 9.7 - - - +
771D SER 3.5 9.6 - - - +
772D PRO* 3.3 23.0 + - - +
773D ALA 3.5 18.6 - - - +
774D SER 4.2 3.8 - - - +
775D GLY* 3.6 18.8 - - - +
1145D TYR* 3.7 36.8 + - + +
1205D TYR* 5.5 1.1 - - - +
1207D TYR* 3.4 9.1 + - + +
1208D ASP* 1.3 71.7 + - - +
1210D SER* 1.3 60.6 + - - +
1211D MET 3.1 1.0 + - - -
1212D ALA* 3.6 9.1 + - - +
1364D HIS* 3.8 19.3 - - + -
1366D LYS* 3.8 26.0 - - - +
1367D HIS* 3.6 10.3 - - + +
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Residues in contact with SER1210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710D ARG* 2.9 28.5 + - - -
767D HIS 5.0 4.3 + - - +
768D ASN* 4.5 8.1 + - - -
769D LEU 4.8 2.6 + - - -
770D LEU* 3.2 45.3 + - - +
771D SER 3.7 3.2 + - - -
772D PRO* 4.0 11.6 - - - +
919D PHE* 4.2 5.5 - - - -
1208D ASP* 2.8 17.5 + - - -
1209D LEU* 1.3 75.5 - - - +
1211D MET* 1.3 68.7 + - - +
16E LYS* 4.5 0.7 + - - -
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Residues in contact with MET1211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767D HIS 5.5 4.3 - - - +
919D PHE* 3.7 15.2 - - - -
924D MET* 5.3 6.5 - - + -
1208D ASP* 2.6 38.8 + - + +
1210D SER* 1.3 87.8 - - - +
1212D ALA* 1.3 69.2 + - - +
1213D ARG* 3.0 46.1 + - + +
1214D PRO 4.5 2.5 - - - +
1216D SER* 3.9 10.3 - - - +
10E PHE* 4.5 20.0 - - - -
16E LYS* 3.4 37.2 - - + +
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Residues in contact with ALA1212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770D LEU* 4.0 9.9 - - + -
919D PHE* 3.9 16.6 - - + -
920D LEU* 3.9 23.5 - - + +
1145D TYR* 3.8 22.7 - - - +
1207D TYR* 3.8 22.0 + - + -
1208D ASP 3.1 4.6 + - - -
1209D LEU 3.6 5.8 + - - -
1210D SER 3.7 0.2 - - - -
1211D MET* 1.3 78.3 - - - +
1213D ARG* 1.3 58.8 + - - +
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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