Contacts of the helix formed by residues 1254 - 1264 (chain A) 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 ASP1254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1250A ASP 3.4 9.6 + - - +
1251A ILE* 3.1 17.2 + - - +
1253A ALA* 1.3 75.3 - - - +
1255A PRO* 1.3 69.6 - - - +
1256A ASP* 2.8 28.9 + - - +
1257A ILE* 2.9 26.0 + - + +
1258A GLN* 3.0 12.2 + - - +
1269A LYS* 2.8 41.8 + - - +
1271A TYR* 4.5 4.2 + - - +
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Residues in contact with PRO1255 (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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1253A ALA 3.2 8.7 - - - +
1254A ASP* 1.3 90.2 - - - +
1256A ASP* 1.3 61.8 + - - +
1258A GLN* 3.5 8.8 + - + +
1259A GLU* 3.0 28.8 + - - +
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Residues in contact with ASP1256 (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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1254A ASP* 2.8 13.7 + - - +
1255A PRO* 1.3 76.7 - - - +
1257A ILE* 1.3 57.7 + - - +
1259A GLU* 3.6 16.9 + - - +
1260A ALA* 3.0 26.2 + - - +
1265A THR* 5.5 0.7 - - - +
1267A ALA* 3.8 12.6 - - + +
1269A LYS* 2.8 33.4 + - - +
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Residues in contact with ILE1257 (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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1251A ILE* 3.3 41.1 - - + +
1252A LEU* 4.2 9.2 - - - -
1254A ASP* 2.9 13.4 + - + +
1256A ASP* 1.3 74.9 - - - +
1258A GLN* 1.3 67.3 + - - +
1260A ALA* 3.2 4.3 + - - +
1261A ILE* 2.9 40.1 + - + +
1267A ALA* 4.3 9.9 - - + -
1269A LYS* 4.0 24.2 - - + -
1284A LEU* 4.1 14.1 - - + -
1301A ILE* 3.9 29.6 - - + -
1303A LEU* 4.3 1.1 - - + -
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Residues in contact with GLN1258 (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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1252A LEU* 2.8 48.0 + - - +
1253A ALA* 4.8 3.1 - - - +
1254A ASP 3.0 12.0 + - - +
1255A PRO* 3.7 11.0 - - + +
1257A ILE* 1.3 76.3 - - - +
1259A GLU* 1.3 56.0 + - - +
1261A ILE* 3.3 8.3 + - - +
1262A ASN* 3.0 56.4 + - - +
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Residues in contact with GLU1259 (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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1255A PRO 3.0 19.0 + - - +
1256A ASP* 3.6 16.2 - - - +
1258A GLN* 1.3 73.9 - - - +
1260A ALA* 1.3 59.1 + - - +
1263A HIS* 2.7 56.8 + - + +
1264A GLN 3.7 0.2 + - - -
1265A THR* 3.9 27.7 - - - +
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Residues in contact with ALA1260 (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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1256A ASP 3.0 17.4 + - - +
1257A ILE 3.2 5.1 + - - +
1259A GLU* 1.3 77.0 - - - +
1261A ILE* 1.3 56.7 + - - +
1264A GLN* 2.9 27.5 + - - -
1265A THR* 3.4 28.0 + - - +
1267A ALA* 3.8 12.8 - - + -
1297A PHE* 3.3 9.9 - - - -
1301A ILE* 3.7 23.1 - - + -
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Residues in contact with ILE1261 (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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1252A LEU* 3.6 21.8 - - + -
1257A ILE* 2.9 22.4 + - + +
1258A GLN* 3.7 14.1 - - - +
1260A ALA* 1.3 79.4 - - - +
1262A ASN* 1.3 64.3 + - - +
1263A HIS 3.7 0.2 + - - -
1264A GLN 4.0 0.2 + - - -
1284A LEU* 3.6 32.3 - - + -
1287A ALA* 4.5 12.3 - - + +
1288A ILE* 4.3 12.3 - - + -
1291A LYS* 4.4 18.6 - - + +
1292A TYR* 2.7 43.3 + - + -
1297A PHE* 3.8 7.7 - - - -
1301A ILE* 4.2 6.3 - - + -
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Residues in contact with ASN1262 (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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1258A GLN* 3.0 45.2 + - - +
1261A ILE* 1.3 87.6 - - - +
1263A HIS* 1.3 78.9 + - + +
1264A GLN* 4.9 0.9 + - - +
1291A LYS* 4.4 12.5 - - - +
1292A TYR* 3.6 11.1 + - - -
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Residues in contact with HIS1263 (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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1259A GLU* 2.7 35.1 + - + +
1262A ASN* 1.3 89.7 - - + +
1264A GLN* 1.3 74.6 + - - +
1265A THR* 3.3 12.9 + - - +
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Residues in contact with GLN1264 (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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1260A ALA 2.9 14.5 + - - -
1262A ASN 5.6 0.6 + - - -
1263A HIS* 1.3 81.4 + - - +
1265A THR* 1.3 61.7 + - - +
1292A TYR* 3.4 42.0 + - + +
1296A GLY 3.7 5.4 - - - +
1297A PHE* 3.7 6.0 - - + -
1298A GLU* 2.9 44.6 + - + +
1299A GLY* 3.4 22.3 + - - +
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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