Contacts of the helix formed by residues 860 - 869 (chain A) in PDB entry 4YOZ
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 860 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A TYR* 4.3 1.3 - - - -
859A ARG* 1.3 73.0 - - - +
861A PHE* 1.3 58.2 + - - +
862A GLN* 3.5 5.9 + - - +
863A GLU* 2.9 39.6 + - - +
864A ILE* 2.9 28.8 + - - +
866A LYS* 5.2 0.7 + - - -
26B GLU* 3.3 24.5 - - - +
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Residues in contact with PHE 861 (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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845A LEU* 3.6 22.2 - - + -
846A CYS* 3.7 21.8 - - - -
849A TYR* 3.3 49.5 - + + -
860A THR* 1.3 71.3 - - - +
862A GLN* 1.3 56.7 + - - +
864A ILE* 3.3 13.5 - - + +
865A MET* 2.8 51.9 + - - +
930A LEU* 3.9 19.3 - - + -
931A ILE* 4.7 14.6 - - + -
934A TYR* 3.7 27.4 - + + -
24B CYS* 3.9 15.9 - - - -
26B GLU* 3.1 16.2 + - - +
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Residues in contact with GLN 862 (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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860A THR* 3.1 6.8 + - - +
861A PHE* 1.3 76.7 - - - +
863A GLU* 1.3 57.6 + - - +
865A MET* 3.3 13.1 + - + +
866A LYS* 3.0 46.8 + - - +
931A ILE* 5.5 4.7 - - + -
26B GLU* 3.2 23.2 + - + +
27B GLN 2.6 31.2 + - - +
28B LEU* 6.1 0.9 - - + -
29B ASN 3.7 23.2 + - - -
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Residues in contact with GLU 863 (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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810A LEU* 3.6 11.0 - - + +
858A GLU 4.6 0.5 - - - +
859A ARG* 3.2 28.7 - - + +
860A THR* 2.9 49.2 + - - +
862A GLN* 1.3 73.9 - - - +
864A ILE* 1.3 63.7 + - - +
866A LYS* 3.3 18.9 - - - +
867A SER* 2.9 31.3 + - - +
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Residues in contact with ILE 864 (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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806A LEU* 3.9 4.2 - - + +
810A LEU* 4.0 14.6 - - + -
845A LEU* 3.7 35.4 - - + +
848A PHE* 3.6 32.1 - - + -
849A TYR* 3.6 35.0 - - + +
852A ALA* 5.7 0.2 - - + -
859A ARG* 4.0 14.4 - - + +
860A THR 2.9 17.5 + - - +
861A PHE* 3.3 16.6 - - + +
863A GLU* 1.3 78.8 - - - +
865A MET* 1.3 57.9 + - + +
867A SER* 3.5 3.6 + - - -
868A TYR* 3.0 23.7 + - - +
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Residues in contact with MET 865 (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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845A LEU* 4.4 12.3 - - + -
861A PHE* 2.8 40.7 + - + +
862A GLN* 3.8 10.8 - - + +
864A ILE* 1.3 72.4 - - + +
866A LYS* 1.3 60.7 + - + +
867A SER 3.2 1.8 - - - -
868A TYR* 3.4 7.9 - - - +
869A ARG* 2.9 35.6 + - - +
879A TYR* 3.5 55.0 - - + +
930A LEU* 4.4 10.1 - - + -
931A ILE* 5.1 9.9 - - + -
28B LEU* 5.0 16.4 - - + -
29B ASN 6.3 1.8 - - - -
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Residues in contact with LYS 866 (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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860A THR* 5.2 0.8 + - - -
862A GLN* 3.0 40.0 + - + +
863A GLU* 3.3 26.6 + - - +
864A ILE 3.5 0.2 - - - -
865A MET* 1.3 76.4 - - - +
867A SER* 1.3 61.0 + - - +
869A ARG* 3.6 34.5 + - - +
870A ASN* 3.8 17.7 + - - -
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Residues in contact with SER 867 (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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805A ASP* 4.9 0.2 - - - +
806A LEU* 3.9 11.1 - - - +
809A LYS* 4.1 30.5 + - - +
810A LEU* 3.3 28.3 - - - +
863A GLU 2.9 18.2 + - - -
864A ILE 3.6 4.3 - - - -
866A LYS* 1.3 78.9 - - - +
868A TYR* 1.3 62.1 + - - +
869A ARG 3.5 0.3 + - - -
870A ASN* 3.7 15.9 + - - +
871A GLN* 4.5 4.3 - - - +
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Residues in contact with TYR 868 (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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802A ARG* 6.3 0.2 - - + -
806A LEU* 3.7 11.6 - - + +
839A HIS* 4.1 0.5 - - - -
841A ASP* 2.5 48.9 + - + +
844A LEU* 6.6 0.7 - - + -
845A LEU* 3.8 32.8 - - + -
864A ILE 3.0 17.3 + - - +
865A MET* 3.1 8.0 + - - +
867A SER* 1.3 78.3 - - - +
869A ARG* 1.3 58.1 + - - +
870A ASN 3.1 0.7 - - - -
871A GLN* 3.0 38.7 + - - +
873A GLN* 3.9 11.3 - - - +
874A ALA* 3.3 30.3 - - + +
875A ASN 4.8 0.2 - - - -
878A VAL* 3.4 27.6 - - + +
879A TYR* 3.9 22.2 - + - -
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Residues in contact with ARG 869 (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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865A MET* 2.9 17.7 + - - +
866A LYS* 3.6 39.3 + - - +
867A SER 3.4 1.0 - - - -
868A TYR* 1.3 76.6 - - - +
870A ASN* 1.3 61.9 + - - +
871A GLN 3.1 8.6 + - - +
874A ALA* 3.7 21.7 - - + +
875A ASN* 5.6 2.2 - - - -
876A SER* 5.6 2.5 - - - +
879A TYR* 2.5 53.0 + - + +
880A ARG* 4.5 12.7 - - - +
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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