Contacts of the helix formed by residues 902 - 912 (chain A) in PDB entry 3DPK
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 THR 902 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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834A VAL* 6.1 2.7 - - - -
838A VAL* 4.7 2.5 - - - -
900A ARG 5.2 2.2 - - - +
901A PRO* 1.3 75.0 - - - +
903A PHE* 1.3 65.0 + - - +
904A GLN* 3.4 8.8 + - - +
905A GLN* 3.0 39.7 + - - +
906A ILE* 3.0 26.2 + - - +
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Residues in contact with PHE 903 (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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763A ALA* 4.0 9.1 - - - +
766A MET* 3.5 52.7 - - + -
767A ALA* 3.7 23.1 - - + +
770A ALA* 4.4 3.1 - - + -
834A VAL* 3.9 28.2 - - + +
837A ASP* 3.7 7.6 - - + -
838A VAL* 3.6 35.0 - - + +
841A TYR* 3.7 29.4 - + + -
902A THR* 1.3 74.7 - - - +
904A GLN* 1.3 57.9 + - - +
906A ILE* 3.2 15.7 + - + +
907A CYS* 2.9 31.7 + - - -
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Residues in contact with GLN 904 (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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767A ALA* 4.0 19.6 - - + +
902A THR* 3.2 8.2 + - - +
903A PHE* 1.3 79.3 - - - +
905A GLN* 1.3 55.8 + - + +
907A CYS* 3.3 16.8 + - - +
908A SER* 2.9 38.1 + - - +
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Residues in contact with GLN 905 (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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900A ARG 4.8 0.3 - - - +
901A PRO* 3.4 15.3 - - + +
902A THR* 3.0 47.0 + - - +
904A GLN* 1.3 75.2 - - + +
906A ILE* 1.3 57.9 + - - +
908A SER* 3.4 6.5 + - - -
909A PHE* 3.0 30.8 + - - +
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Residues in contact with ILE 906 (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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763A ALA* 3.9 7.2 - - + -
838A VAL* 4.4 5.6 - - + -
841A TYR* 3.8 27.4 - - + -
888A ILE* 4.4 14.8 - - + -
892A CYS* 4.0 19.1 - - - -
901A PRO* 3.9 26.0 - - + -
902A THR 3.0 16.5 + - - +
903A PHE* 3.4 21.5 - - + +
905A GLN* 1.3 72.5 - - - +
907A CYS* 1.3 65.1 + - - +
909A PHE* 3.4 5.1 + - - +
910A LEU* 2.9 44.5 + - + +
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Residues in contact with CYS 907 (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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760A SER* 4.7 2.7 - - - +
763A ALA* 3.5 37.0 - - - -
764A GLN* 3.7 20.4 - - + +
767A ALA* 4.3 7.6 - - - -
903A PHE 2.9 17.7 + - - -
904A GLN* 3.6 19.5 - - - +
906A ILE* 1.3 76.1 - - - +
908A SER* 1.3 63.8 + - - +
910A LEU* 3.2 6.4 + - - +
911A GLN* 2.8 36.9 + - + +
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Residues in contact with SER 908 (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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904A GLN* 2.9 25.3 + - - +
905A GLN* 3.6 8.1 - - - -
907A CYS* 1.3 78.3 - - - +
909A PHE* 1.3 61.8 + - - +
911A GLN* 3.3 8.4 + - - +
912A GLU* 3.2 34.2 + - - +
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Residues in contact with PHE 909 (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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884A ASN* 3.6 43.7 - - + -
885A ILE* 5.8 1.6 - - + -
887A SER* 5.4 5.2 - - - -
888A ILE* 3.7 26.2 - - + -
905A GLN 3.0 17.2 + - - +
906A ILE* 3.8 4.7 - - - +
908A SER* 1.3 73.8 + - - +
910A LEU* 1.3 65.4 + - + +
912A GLU* 3.3 39.9 + - + +
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Residues in contact with LEU 910 (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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756A LEU* 4.7 10.8 - - + +
759A SER* 3.8 9.4 - - - +
760A SER* 3.4 40.1 + - - +
763A ALA* 4.2 3.1 - - + -
841A TYR* 3.7 23.1 - - - +
845A LEU* 5.9 1.3 - - + -
885A ILE* 3.9 18.4 - - + -
888A ILE* 3.5 28.0 - - + -
906A ILE* 2.9 29.7 + - + +
907A CYS* 3.6 4.7 - - - +
909A PHE* 1.3 77.5 - - + +
911A GLN* 1.3 64.1 + - - +
912A GLU 3.4 6.6 + - - -
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Residues in contact with GLN 911 (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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760A SER* 4.9 6.8 + - - +
764A GLN* 4.0 21.0 + - - +
907A CYS* 2.8 35.6 + - + +
908A SER* 3.6 8.3 - - - +
909A PHE 3.3 0.2 - - - -
910A LEU* 1.3 72.4 - - + +
912A GLU* 1.3 65.8 + - + +
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Residues in contact with GLU 912 (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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908A SER* 3.2 23.3 + - - +
909A PHE* 3.4 39.1 - - + +
910A LEU 3.5 6.1 - - - -
911A GLN* 1.3 83.5 - - + +
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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