Contacts of the helix formed by residues 1246 - 1254 (chain B) in PDB entry 1OFD
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 VAL1246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020B TYR* 3.0 31.2 - - + +
1024B GLN* 3.6 38.4 - - - +
1243B ASN* 4.4 4.5 - - + +
1244B GLY 3.9 7.4 - - - +
1245B PRO* 1.3 78.4 - - - +
1247B LEU* 1.3 65.6 + - - +
1248B ASP* 3.7 11.7 - - + +
1249B ASP* 2.9 44.7 + - - +
1250B ASP* 3.8 6.3 + - - +
1278B ARG 5.1 2.0 - - - +
1283B ARG* 4.0 5.8 - - - +
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Residues in contact with LEU1247 (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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1246B VAL* 1.3 72.1 - - - +
1248B ASP* 1.3 60.0 + - - +
1250B ASP* 2.9 40.1 + - + +
1251B ILE* 3.1 17.7 + - + +
1271B TYR* 4.3 24.7 - - + -
1272B ARG 4.5 7.6 - - - +
1273B LEU* 3.3 34.3 - - + -
1277B ASP* 4.1 22.0 + - + +
1280B VAL* 4.9 5.8 - - + -
1305B PHE* 4.1 16.4 - - + -
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Residues in contact with ASP1248 (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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1024B GLN* 3.8 11.5 + - - -
1246B VAL* 3.2 9.9 - - + +
1247B LEU* 1.3 73.9 - - - +
1249B ASP* 1.3 57.0 + - - +
1251B ILE* 3.5 15.7 - - + +
1252B LEU* 2.8 35.8 + - + +
1280B VAL* 3.4 14.2 - - - +
1281B GLY* 3.0 35.1 + - - -
1283B ARG* 3.0 40.4 + - + -
1284B LEU* 3.3 8.7 + - + +
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Residues in contact with ASP1249 (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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1244B GLY 4.1 1.6 - - - +
1245B PRO* 4.0 7.3 - - + +
1246B VAL* 2.9 32.7 + - - +
1248B ASP* 1.3 77.7 - - - +
1250B ASP* 1.3 59.4 + - - +
1252B LEU* 3.6 5.8 + - - +
1253B ALA* 3.1 27.2 + - - +
1283B ARG* 2.9 38.9 + - - -
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Residues in contact with ASP1250 (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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1246B VAL 4.1 4.5 - - - +
1247B LEU* 2.9 32.0 + - + +
1249B ASP* 1.3 76.0 - - - +
1251B ILE* 1.3 68.4 + - + +
1253B ALA* 3.3 7.6 + - - +
1254B ASP* 3.3 18.2 + - - +
1271B TYR* 4.9 5.9 + - + -
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Residues in contact with ILE1251 (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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1247B LEU* 3.1 23.2 + - + +
1248B ASP* 3.5 22.7 - - + +
1250B ASP* 1.3 76.7 - - - +
1252B LEU* 1.3 63.1 + - - +
1254B ASP* 3.2 11.4 + - - +
1257B ILE* 3.3 45.2 - - + +
1271B TYR* 3.6 44.0 - - + +
1280B VAL* 5.4 0.2 - - + -
1281B GLY 5.6 0.9 - - - +
1284B LEU* 4.7 10.3 - - + -
1303B LEU* 4.2 18.8 - - + -
1305B PHE* 4.2 18.2 - - + -
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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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1248B ASP 2.8 21.3 + - - +
1249B ASP* 4.2 4.7 - - - +
1251B ILE* 1.3 73.4 - - + +
1253B ALA* 1.3 60.1 + - - +
1254B ASP 3.3 1.2 - - - +
1257B ILE* 4.4 2.7 - - + -
1258B GLN* 2.8 38.8 + - - +
1261B ILE* 3.6 31.0 - - + -
1283B ARG* 3.8 41.5 - - + +
1284B LEU* 3.8 21.1 - - + +
1287B ALA* 4.1 13.2 - - + -
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Residues in contact with ALA1253 (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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1249B ASP 3.1 18.7 + - - +
1250B ASP* 3.7 8.5 - - - +
1251B ILE 3.2 0.6 - - - -
1252B LEU* 1.3 75.5 - - - +
1254B ASP* 1.3 64.5 + - - +
1255B PRO* 3.4 7.8 - - - +
1258B GLN* 5.1 2.3 - - - +
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Residues in contact with ASP1254 (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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1250B ASP 3.3 9.8 + - - +
1251B ILE 3.2 14.1 + - - +
1253B ALA* 1.3 76.1 - - - +
1255B PRO* 1.3 73.3 - - - +
1256B ASP* 3.0 26.7 + - - +
1257B ILE* 3.0 20.6 + - + +
1258B GLN* 3.1 13.0 + - - +
1269B LYS* 2.9 43.1 + - - +
1271B TYR* 4.3 6.0 + - - +
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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