Contacts of the helix formed by residues 1266 - 1269 (chain A) in PDB entry 4YKN
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 PRO1266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175A PRO* 3.9 19.5 - - + -
1214A ASP* 3.2 40.2 - - + +
1215A CYS 4.2 1.8 - - - +
1216A VAL* 4.6 3.6 - - + -
1264A LYS 3.5 4.2 - - - +
1265A TYR* 1.3 85.9 - - + +
1267A LEU* 1.3 66.8 + - - +
1268A SER* 3.2 5.8 - - - +
1269A GLN* 2.9 42.1 + - + +
1270A TYR* 3.8 5.2 - - - -
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Residues in contact with LEU1267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190A ILE* 5.3 3.1 - - + -
1192A VAL* 4.3 13.5 - - + -
1211A ILE* 4.3 13.7 - - + -
1213A HIS 3.6 7.0 + - - +
1215A CYS* 3.2 22.5 + - - +
1217A PRO* 4.5 13.9 - - + -
1220A VAL* 4.0 25.4 - - + -
1252A LEU* 4.8 0.2 - - + -
1261A PHE* 3.7 35.0 - - + -
1265A TYR 3.5 1.2 + - - -
1266A PRO* 1.3 73.5 - - - +
1268A SER* 1.3 61.3 + - - +
1269A GLN 3.1 1.6 + - - -
1270A TYR* 3.2 17.5 + - + +
1273A ILE* 3.2 39.7 - - + +
1285A LEU* 4.6 7.9 - - + -
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Residues in contact with SER1268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A PRO 4.4 5.7 + - - -
1177A LEU* 4.2 11.8 - - - +
1213A HIS* 2.9 51.6 + - - -
1214A ASP* 4.5 2.6 - - - -
1266A PRO* 4.7 3.6 - - - +
1267A LEU* 1.3 75.8 - - - +
1269A GLN* 1.3 60.1 + - - +
1270A TYR 3.3 0.4 - - - -
1273A ILE* 3.5 12.3 - - - +
1274A ARG* 3.0 33.7 + - - +
1277A ILE* 4.1 12.8 - - - -
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Residues in contact with GLN1269 (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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1171A VAL* 3.2 18.0 - - + +
1172A GLU* 2.7 59.4 + - + +
1173A SER 3.9 5.9 + - - -
1174A SER 3.6 23.1 - - - +
1175A PRO* 3.3 29.5 - - + +
1265A TYR* 3.6 18.2 - - + -
1266A PRO* 2.9 34.5 + - + +
1268A SER* 1.3 79.5 + - - +
1270A TYR* 1.3 58.3 + - - +
1274A ARG* 4.2 5.4 - - - +
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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