Contacts of the strand formed by residues 1222 - 1226 (chain A) in PDB entry 6BM0
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 ILE1222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176A CYS* 4.9 2.5 - - - -
1178A CYS* 3.6 25.6 - - - -
1183A VAL* 3.7 26.9 - - + -
1192A LEU* 4.0 15.9 - - + -
1215A MET* 4.3 19.7 - - + -
1216A ILE 3.4 13.2 - - - +
1217A SER* 3.8 3.8 - - - -
1220A ASN 4.1 2.0 - - - +
1221A PHE* 1.3 76.5 - - - +
1223A LEU* 1.3 69.1 + - - +
1224A ALA* 5.5 0.2 - - + -
1233A LEU* 3.3 5.5 - - - +
1234A LEU* 2.6 61.7 + - + +
1235A ARG 5.4 0.2 - - - +
1236A TYR* 5.4 1.6 - - + -
1243A LEU* 4.2 10.1 - - + -
1260A PHE* 5.0 0.7 - - - -
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Residues in contact with LEU1223 (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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1215A MET* 3.3 7.6 - - - +
1216A ILE* 2.8 33.8 + - + +
1221A PHE 3.8 0.8 + - - -
1222A ILE* 1.3 77.6 - - - +
1224A ALA* 1.3 68.7 + - - +
1231A ILE* 3.8 24.5 - - + -
1232A SER 4.3 0.7 - - - -
1233A LEU* 3.7 24.9 - - + +
1258A VAL* 3.7 31.0 - - + -
1259A ASP 3.8 9.9 - - - +
1260A PHE* 3.6 33.8 - - + -
1269A PHE* 4.3 22.0 - - + -
1271A VAL* 5.5 0.2 - - + -
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Residues in contact with ALA1224 (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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1190A ILE* 4.5 7.4 - - + -
1212A ILE* 4.0 13.5 - - + -
1214A GLN 3.6 6.3 - - - -
1215A MET* 4.0 16.8 - - + -
1223A LEU* 1.3 78.1 - - - +
1225A ALA* 1.3 62.7 + - - +
1230A SER 3.8 1.0 - - - +
1231A ILE* 3.6 13.9 - - - +
1232A SER* 3.4 47.5 + - - +
1234A LEU* 5.4 2.5 - - + -
1258A VAL* 4.6 1.3 - - - +
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Residues in contact with ALA1225 (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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1212A ILE* 3.3 5.5 - - - +
1213A HIS* 2.9 31.9 + - + -
1214A GLN* 2.8 28.1 + - + +
1224A ALA* 1.3 77.5 - - - +
1226A ASP* 1.3 59.7 + - - +
1230A SER 3.7 4.9 - - - -
1255A VAL* 3.7 26.2 - - + -
1258A VAL* 3.7 15.3 - - + -
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Residues in contact with ASP1226 (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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1209A GLN* 3.2 34.6 - - + +
1210A LEU* 3.6 11.4 + - - +
1211A TYR* 2.9 29.2 + - - +
1212A ILE* 3.9 3.0 - - + +
1213A HIS* 3.2 13.5 - - - -
1225A ALA* 1.3 74.4 - - - +
1227A VAL* 1.3 83.1 + - - +
1228A MET* 3.2 6.5 + - - +
1229A LYS* 3.1 20.4 + - - +
1230A SER* 3.4 26.6 - - - +
1231A ILE 4.4 0.4 - - - +
1255A VAL* 3.5 14.9 - - - +
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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