Contacts of the helix formed by residues 912 - 917 (chain A) in PDB entry 6DBV
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 LYS 912 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819A ASP* 4.2 17.9 - - - +
877A ARG* 5.5 14.9 - - - +
880A MET* 4.4 13.9 - - + +
908A TYR* 2.9 42.7 + - + +
909A LEU* 4.7 12.9 + - + +
911A MET* 1.3 74.6 - - + +
913A PRO* 1.3 67.2 - - + +
914A VAL 2.6 17.4 + - - -
915A TRP* 3.2 59.2 + - + +
916A ARG* 5.0 9.9 - - + +
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Residues in contact with PRO 913 (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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909A LEU 3.2 20.4 - - - +
910A GLN 4.0 8.5 - - - +
911A MET 3.5 2.5 - - - -
912A LYS* 1.3 100.3 - - + +
914A VAL* 1.3 62.0 + - + +
915A TRP 3.5 0.4 - - - -
916A ARG* 4.0 15.9 - - + -
917A SER* 3.1 22.9 + - - -
923A ASP* 5.4 0.7 - - - +
924A CYS* 4.5 13.8 - - - -
927A GLN* 5.3 8.5 - - + +
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Residues in contact with VAL 914 (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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910A GLN 4.7 0.7 - - - +
911A MET* 3.1 20.9 - - - +
912A LYS 2.6 6.7 + - - -
913A PRO* 1.3 74.4 - - - +
915A TRP* 1.3 58.8 + - + +
917A SER* 3.3 20.5 - - - +
920A PRO* 4.1 15.6 - - + +
924A CYS* 5.3 4.9 - - - +
927A GLN* 3.8 28.7 - - + -
928A LEU* 4.5 19.3 - - + +
931A TYR* 3.7 28.7 - - + -
965A VAL* 4.4 11.9 - - + -
969A VAL* 4.6 12.3 - - + +
975A ILE* 4.7 2.0 - - - +
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Residues in contact with TRP 915 (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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813A LEU* 6.2 4.7 - - + -
815A ALA* 4.4 12.6 - - + +
818A CYS* 3.4 35.9 - - - -
819A ASP* 4.2 15.5 - - - -
822A ASN* 4.3 7.0 - - - -
908A TYR* 4.0 15.9 - + - -
911A MET* 4.3 3.8 + - - +
912A LYS* 3.2 54.3 + - + +
914A VAL* 1.3 73.5 - - + +
916A ARG* 1.3 95.3 + - + +
917A SER 3.1 1.3 - - - -
931A TYR* 4.3 5.9 + - - -
961A THR* 3.2 19.3 + - - -
965A VAL* 3.7 30.7 - - + -
975A ILE* 3.1 45.6 - - + +
976A GLY* 3.3 11.8 - - - -
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Residues in contact with ARG 916 (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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669A ASN* 5.4 10.1 + - - +
815A ALA* 4.7 15.2 + - - +
816A LEU* 5.0 10.3 - - - +
819A ASP* 2.5 40.4 + - - +
877A ARG* 3.0 43.8 - - - +
912A LYS* 3.6 8.5 + - + +
913A PRO* 4.0 18.2 - - + -
914A VAL 3.5 0.2 - - - -
915A TRP* 1.3 96.3 - - + +
917A SER* 1.3 62.9 + - - +
918A THR* 3.5 3.5 + - - -
976A GLY* 4.8 5.1 - - - -
981A GLU* 6.4 0.4 - - - +
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Residues in contact with SER 917 (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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913A PRO 3.1 21.7 + - - -
914A VAL 3.3 11.7 - - - -
915A TRP 3.1 1.4 - - - +
916A ARG* 1.3 80.0 - - - +
918A THR* 1.3 59.1 + - - +
919A CYS 3.0 6.9 + - - -
920A PRO* 2.9 30.0 - - - +
923A ASP* 3.3 23.6 - - - +
924A CYS* 5.2 0.9 - - - -
975A ILE 2.7 28.6 - - - +
977A ALA 3.9 1.7 + - - -
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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