Contacts of the helix formed by residues 1254 - 1264 (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 ASP1254 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B ALA 3.4 8.0 - - - +
1254B ASP* 1.3 90.3 - - - +
1256B ASP* 1.3 62.4 + - - +
1258B GLN* 3.5 9.3 + - + +
1259B GLU* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254B ASP* 3.0 10.5 + - - +
1255B PRO* 1.3 82.9 - - - +
1257B ILE* 1.3 56.9 + - - +
1259B GLU* 3.5 18.5 + - - +
1260B ALA* 3.1 26.2 + - - +
1265B THR* 5.8 0.3 - - - +
1266B THR 5.3 0.3 - - - +
1267B ALA* 3.8 12.4 - - + +
1269B LYS* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251B ILE* 3.3 37.0 - - + +
1252B LEU* 4.4 7.0 - - - -
1254B ASP* 3.0 14.6 + - + +
1256B ASP* 1.3 73.7 - - - +
1258B GLN* 1.3 67.4 + - - +
1260B ALA* 3.2 4.3 + - - +
1261B ILE* 3.0 41.2 + - + +
1267B ALA* 4.3 9.2 - - + -
1269B LYS* 3.9 25.8 - - + -
1284B LEU* 4.1 14.6 - - + -
1301B ILE* 4.0 26.9 - - + -
1303B LEU* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B LEU* 2.8 49.0 + - - +
1253B ALA* 5.1 2.2 - - - +
1254B ASP 3.1 12.9 + - - +
1255B PRO* 3.7 11.2 - - + +
1257B ILE* 1.3 77.9 - - - +
1259B GLU* 1.3 56.9 + - - +
1261B ILE* 3.3 8.9 + - - +
1262B ASN* 2.8 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255B PRO 3.0 17.9 + - - +
1256B ASP* 3.7 17.1 - - - +
1257B ILE 3.2 0.2 - - - -
1258B GLN* 1.3 75.5 - - - +
1260B ALA* 1.3 57.9 + - - +
1262B ASN* 4.8 0.7 - - - +
1263B HIS* 2.8 52.9 + - + +
1265B THR* 4.1 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256B ASP 3.1 17.6 + - - +
1257B ILE 3.2 5.4 + - - +
1259B GLU* 1.3 75.5 - - - +
1261B ILE* 1.3 56.9 + - - +
1264B GLN* 2.9 30.0 + - - -
1265B THR* 3.2 28.4 + - - +
1266B THR 4.5 0.9 - - - +
1267B ALA* 3.8 12.8 - - + -
1297B PHE* 3.4 7.3 - - - -
1301B ILE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252B LEU* 3.6 19.5 - - + -
1257B ILE* 3.0 22.1 + - + +
1258B GLN* 3.7 16.6 - - - +
1260B ALA* 1.3 78.6 - - - +
1262B ASN* 1.3 62.6 + - - +
1263B HIS 3.6 0.2 + - - -
1264B GLN 3.7 1.0 + - - -
1284B LEU* 3.6 31.0 - - + -
1287B ALA* 4.5 8.5 - - + +
1288B ILE* 4.2 15.5 - - + -
1291B LYS* 4.5 16.8 - - + +
1292B TYR* 2.6 46.7 + - + -
1297B PHE* 3.6 9.0 - - - -
1301B ILE* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B GLN* 2.8 43.7 + - - +
1259B GLU* 5.1 0.4 - - - +
1261B ILE* 1.3 82.6 - - - +
1263B HIS* 1.3 77.0 + - + +
1264B GLN* 4.8 2.1 + - - +
1291B LYS* 4.9 9.0 - - - +
1292B TYR* 3.4 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259B GLU* 2.8 37.3 + - + +
1262B ASN* 1.3 87.6 - - + +
1264B GLN* 1.3 72.7 + - - +
1265B THR* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260B ALA 2.9 11.9 + - - -
1262B ASN 3.5 1.4 + - - -
1263B HIS* 1.3 81.1 - - - +
1265B THR* 1.3 60.4 + - - +
1292B TYR* 3.5 34.9 + - + +
1296B GLY 3.2 13.7 - - - +
1297B PHE* 3.7 9.6 - - + -
1298B GLU* 2.9 42.4 + - + +
1299B GLY* 3.5 22.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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