Contacts of the helix formed by residues 910 - 917 (chain A) in PDB entry 5Y36
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 GLU 910 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A GLN* 3.1 39.4 + - + +
895A ARG* 5.6 4.2 - - - +
898A ASP* 3.0 22.0 - - - +
905A ARG* 3.6 18.2 + - - -
908A LEU 3.5 8.8 + - - +
909A SER* 1.4 77.3 - - - +
911A LEU* 1.3 62.8 + - - +
912A ASP 3.5 0.9 + - - -
913A LYS* 3.6 7.2 + - + +
977A GLU* 3.1 15.6 - - - +
1307A GLU 5.0 2.5 - - - +
1308A ASN* 3.8 11.6 - - - +
1310A ILE* 3.9 11.9 - - + -
1311A HIS* 2.7 31.9 + - - +
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Residues in contact with LEU 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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766A GLU* 5.6 6.3 - - + -
768A GLN* 5.4 8.7 - - - +
849A ASP* 5.1 8.5 - - - +
893A THR* 6.1 0.9 - - - -
894A GLN* 5.0 5.0 + - - +
895A ARG* 4.0 41.2 + - + +
909A SER* 3.5 9.2 - - - +
910A GLU* 1.3 78.1 - - - +
912A ASP* 1.4 53.6 + - - -
913A LYS* 3.2 5.8 + - - +
914A ALA* 4.7 3.5 + - - +
977A GLU* 3.0 4.9 + - - -
34D A 3.7 25.7 + - + +
35D T 2.5 51.2 + - + +
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Residues in contact with ASP 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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911A LEU* 1.4 69.3 - - - +
913A LYS* 1.4 62.6 + - - +
914A ALA* 3.2 1.8 - - - +
915A GLY* 3.4 9.8 + - - -
916A PHE* 5.1 6.6 - - - -
919A ARG* 2.9 33.8 + - - -
975A VAL* 3.4 23.6 - - + +
977A GLU* 2.6 22.9 + - - +
33D C 2.6 38.5 + - + +
34D A 4.2 3.1 - - - +
35D T 3.2 19.3 - - + +
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Residues in contact with LYS 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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887A LEU* 3.7 18.9 - - + +
888A ASN* 6.0 0.4 + - - -
894A GLN* 3.3 52.3 + - + +
910A GLU* 3.6 3.2 + - + +
911A LEU 3.2 5.6 + - - +
912A ASP* 1.4 72.0 - - - +
914A ALA* 1.4 65.1 + - - +
915A GLY 2.9 4.5 + - - -
916A PHE* 3.1 25.4 + - + +
917A ILE* 3.7 26.2 + - + +
977A GLU* 5.5 0.9 - - - -
1303A ARG* 5.6 1.3 - - - +
1307A GLU* 3.1 48.5 + - + +
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Residues in contact with ALA 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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890A LYS* 6.2 0.4 - - + -
911A LEU 4.7 2.8 + - - +
912A ASP* 4.0 7.2 - - - +
913A LYS* 1.4 75.3 - - - +
915A GLY* 1.3 55.3 + - - +
916A PHE 2.9 2.9 + - - -
917A ILE* 3.6 13.3 - - - +
918A LYS 2.6 50.6 + - - +
919A ARG* 3.2 14.8 - - + -
33D C 4.1 5.4 - - - +
34D A 6.1 0.4 - - - +
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Residues in contact with GLY 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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912A ASP* 3.4 14.7 + - - -
913A LYS 2.9 3.4 + - - -
914A ALA* 1.3 75.3 - - - +
916A PHE* 1.4 69.0 + - - +
919A ARG* 3.3 28.8 + - - +
975A VAL* 5.9 0.4 - - - -
1237A TYR* 3.7 17.4 + - - -
1241A HIS* 4.6 6.4 + - - -
31D T 3.9 11.1 + - - -
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Residues in contact with PHE 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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912A ASP 5.1 7.6 - - - -
913A LYS* 3.1 24.5 + - + +
915A GLY* 1.4 83.8 - - - +
917A ILE* 1.3 68.4 + - + +
918A LYS 3.8 0.4 - - - -
975A VAL* 6.2 0.4 - - + -
1236A LEU 5.0 0.4 - - - -
1237A TYR* 3.1 64.8 - + - -
1240A SER* 3.6 29.6 - - - +
1241A HIS* 4.1 22.8 + - + +
1245A LEU* 5.8 3.1 - - - +
1303A ARG* 5.5 8.3 - - + -
1306A ALA* 5.2 10.5 - - + -
1307A GLU* 5.7 6.3 - - + -
1310A ILE* 5.9 6.5 - - + -
31D T 5.6 0.4 - - - -
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Residues in contact with ILE 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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887A LEU* 3.3 47.6 - - + +
888A ASN* 5.1 13.0 - - - +
890A LYS* 3.1 34.2 + - + +
913A LYS* 3.7 23.3 - - + +
914A ALA* 3.6 22.4 - - - +
916A PHE* 1.3 88.7 - - + +
918A LYS* 1.3 71.0 + - - +
1303A ARG* 5.5 7.6 - - - -
30D G 3.8 11.7 + - - -
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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