Contacts of the helix formed by residues 1249 - 1256 (chain B) in PDB entry 2O8C
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 TYR1249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A THR* 3.6 23.6 - - + -
1214B GLU* 5.5 2.5 - - + -
1215B LEU 3.3 24.7 - - - -
1216B GLY 3.1 24.5 + - - -
1220B ALA 4.1 3.3 + - - -
1221B THR* 4.0 9.2 - - + -
1224B GLY* 3.3 33.4 - - - -
1225B THR* 3.4 27.6 - - + -
1228B ALA* 5.1 1.8 - - + -
1245B PHE* 6.0 0.2 - + - -
1247B THR* 2.9 25.4 + - - +
1248B HIS* 1.3 78.1 - - + +
1250B HIS* 1.3 65.7 + - - +
1251B SER* 3.2 3.8 - - - +
1252B LEU* 3.2 34.4 + - + +
1253B VAL* 3.4 13.2 - - - +
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Residues in contact with HIS1250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A SER* 4.9 3.8 - - - -
756A THR* 3.7 5.3 + - - +
757A TYR* 3.5 35.4 - + + -
1248B HIS 2.9 9.8 + - - +
1249B TYR* 1.3 70.3 - - - +
1251B SER* 1.3 62.6 + - - +
1253B VAL* 3.2 24.7 + - + +
1254B GLU* 3.2 37.8 + - + +
1294B CYS 5.9 1.8 - - - -
1296B LYS* 3.6 37.0 - - + +
1324B GLU* 5.1 5.6 + - + -
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Residues in contact with SER1251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A THR* 4.5 3.2 + - - -
757A TYR* 4.0 23.4 - - - -
1225B THR* 3.5 28.6 - - - +
1249B TYR* 4.5 2.9 - - - +
1250B HIS* 1.3 78.6 - - - +
1252B LEU* 1.3 62.8 + - - +
1254B GLU* 3.5 12.9 + - - +
1255B ASP* 3.4 26.7 + - - +
1327B ASN* 6.1 0.9 - - - -
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Residues in contact with LEU1252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131B LEU* 4.8 7.1 - - + +
1225B THR* 5.9 4.0 - - - +
1228B ALA* 4.0 20.0 - - + +
1229B ASN* 3.4 40.4 - - + +
1232B VAL* 4.7 5.4 - - + -
1245B PHE* 4.0 28.3 - - + -
1247B THR* 4.1 19.1 - - + +
1249B TYR* 3.2 18.8 + - + +
1250B HIS 3.2 0.2 - - - -
1251B SER* 1.3 80.7 + - - +
1253B VAL* 1.3 61.4 + - - +
1255B ASP* 3.5 4.5 + - - +
1256B TYR* 3.3 38.0 + - + +
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Residues in contact with VAL1253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131B LEU* 4.6 14.1 - - + -
1133B THR* 4.2 25.4 - - + -
1247B THR* 4.8 6.5 - - + -
1249B TYR 3.4 15.7 - - - +
1250B HIS* 3.2 18.8 + - + +
1252B LEU* 1.3 73.7 - - - +
1254B GLU* 1.3 64.5 + - + +
1255B ASP 3.4 0.2 - - - -
1256B TYR 3.2 18.2 - - - +
1257B SER* 3.4 5.4 + - - -
1264B LEU* 4.0 24.5 - - + -
1293B ALA* 5.2 11.9 - - + -
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Residues in contact with GLU1254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A TYR* 5.1 4.1 + - - -
1250B HIS* 3.2 39.8 + - + +
1251B SER* 3.6 15.0 - - - +
1252B LEU 3.2 0.2 - - - -
1253B VAL* 1.3 77.3 - - + +
1255B ASP* 1.3 65.8 + - - +
1256B TYR 3.4 0.3 + - - -
1257B SER* 3.6 17.4 + - - -
1324B GLU* 5.6 5.0 - - - +
1327B ASN* 4.2 25.3 - - - +
1328B GLN* 6.1 0.5 - - - +
1331B ARG* 4.0 28.3 + - - +
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Residues in contact with ASP1255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847A LYS* 4.0 14.6 - - - +
1229B ASN* 3.5 34.1 + - - +
1251B SER 3.4 15.9 + - - +
1252B LEU* 3.9 7.6 - - - +
1253B VAL 3.4 0.4 - - - -
1254B GLU* 1.3 80.4 - - - +
1256B TYR* 1.3 63.3 + - + +
1257B SER* 3.7 1.2 + - - -
1259B ASN* 3.4 13.9 + - - +
1330B LEU* 6.1 1.0 - - - +
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Residues in contact with TYR1256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131B LEU* 4.0 17.5 - - + +
1229B ASN* 3.2 42.3 + - - -
1232B VAL* 3.8 20.4 - - + -
1233B LYS* 3.3 25.4 + - - +
1236B ALA* 5.8 0.4 - - + -
1252B LEU* 3.3 30.7 + - + +
1253B VAL 3.2 8.4 - - - +
1254B GLU 3.2 0.2 - - - -
1255B ASP* 1.3 82.0 - - + +
1257B SER* 1.3 63.2 + - - +
1258B GLN 3.7 0.9 - - - -
1259B ASN* 3.1 36.9 + - - +
1262B VAL* 3.9 28.4 - - + +
1264B LEU* 3.8 14.2 - - - +
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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
------------------------------------------------------------
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