Contacts of the strand formed by residues 1226 - 1230 (chain A) in PDB entry 6A5T
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 LEU1226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1218A ILE* 4.6 4.9 - - + -
1222A PHE* 3.6 50.2 + - + +
1223A SER 4.4 3.5 - - - +
1225A ASP* 1.3 82.9 - - + +
1227A PHE* 1.3 66.7 + - - +
1228A VAL* 3.2 12.4 + - + +
1242A CYS* 3.5 37.5 - - + -
1243A ARG 3.0 32.8 - - - +
1244A VAL* 4.0 11.0 - - + +
1245A ILE* 3.5 6.1 - - - +
1263A LEU* 5.3 3.6 - - + -
1266A ILE* 4.7 18.8 - - + -
1270A MET* 4.7 6.3 - - + -
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Residues in contact with PHE1227 (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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1175A TYR* 3.6 28.5 - + - -
1194A LEU* 6.3 0.2 - - + -
1226A LEU* 1.3 70.6 - - - +
1228A VAL* 1.3 78.3 + - - +
1229A MET* 3.4 29.2 - - + -
1241A ARG 4.8 0.4 - - - -
1242A CYS* 3.1 8.8 - - - +
1243A ARG* 2.8 64.5 + - + +
1245A ILE* 3.0 20.3 - - + +
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Residues in contact with VAL1228 (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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1175A TYR* 3.9 4.2 + - - -
1215A ALA* 3.8 32.8 - - + +
1218A ILE* 4.0 23.6 - - + -
1219A SER* 3.4 24.0 - - - +
1222A PHE 4.8 1.6 - - - +
1226A LEU* 3.2 14.8 + - + +
1227A PHE* 1.3 94.5 - - - +
1229A MET* 1.3 67.7 + - - +
1230A TRP* 4.8 3.4 - - + -
1240A ILE* 5.0 5.2 - - + -
1241A ARG 4.1 1.3 - - - -
1242A CYS* 4.5 11.4 - - - -
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Residues in contact with MET1229 (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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1172A VAL* 5.1 10.1 - - + -
1175A TYR* 3.5 39.3 - - + -
1176A PHE* 5.8 10.3 - - + -
1194A LEU* 5.5 3.6 - - + -
1227A PHE* 3.4 26.7 - - + -
1228A VAL* 1.3 77.1 - - - +
1230A TRP* 1.3 67.3 + - - +
1231A SER* 5.2 0.4 - - - +
1240A ILE* 3.7 3.3 - - - +
1241A ARG* 2.8 78.5 + - + +
1243A ARG* 4.8 14.1 - - - +
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Residues in contact with TRP1230 (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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1175A TYR* 4.9 18.7 - + - -
1211A MET* 3.5 19.3 - - + -
1212A ASN* 4.5 26.6 + - + +
1215A ALA* 3.7 30.3 - - + +
1228A VAL* 4.8 3.8 - - + -
1229A MET* 1.3 81.3 - - - +
1231A SER* 1.3 80.9 + - - +
1232A GLU* 3.8 20.0 - - + +
1233A ASP* 3.8 17.9 - - - -
1239A ILE 4.1 8.5 - - - +
1240A ILE* 4.7 7.6 - - + -
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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