Contacts of the helix formed by residues 1281 - 1293 (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 GLY1281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1248B ASP* 3.0 20.8 + - - -
1251B ILE* 5.6 0.6 - - - +
1280B VAL* 1.3 73.9 - - - +
1282B THR* 1.3 55.1 + - - +
1284B LEU* 3.2 12.4 + - - +
1285B SER* 3.0 29.4 + - - -
1303B LEU* 4.9 7.9 - - - -
1305B PHE* 5.3 0.2 - - - -
1314B GLY* 5.6 0.7 - - - -
1315B ALA 4.9 1.1 - - - -
1317B ASN* 5.6 0.9 - - - -
1321B MET* 4.5 3.0 - - - +
1323B LEU* 4.5 21.1 - - - -
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Residues in contact with THR1282 (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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1021B ASP 4.2 3.8 - - - +
1024B GLN* 3.9 1.1 - - - -
1025B ILE* 3.7 34.5 - - + +
1248B ASP* 3.3 0.4 + - - -
1279B THR* 3.2 39.5 + - + +
1280B VAL 3.2 0.2 - - - -
1281B GLY* 1.3 76.0 - - - +
1283B ARG* 1.3 64.9 + - - +
1285B SER* 3.3 4.4 + - - -
1286B GLY 3.0 18.0 + - - -
1315B ALA* 2.8 35.6 + - - +
1316B PHE* 4.3 10.1 - - + -
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Residues in contact with ARG1283 (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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1023B HIS* 3.1 22.2 + - - +
1024B GLN* 3.0 49.0 + - + +
1025B ILE* 4.5 2.3 - - - +
1027B PRO* 4.0 25.8 - - + +
1243B ASN* 3.8 16.6 - - - +
1244B GLY 4.9 3.8 + - - -
1246B VAL* 4.0 4.8 - - - +
1248B ASP* 3.0 23.2 + - + +
1249B ASP* 2.9 36.0 + - - -
1252B LEU* 3.8 18.3 - - + +
1282B THR* 1.3 77.9 - - - +
1284B LEU* 1.3 59.0 + - - +
1286B GLY* 3.4 1.9 + - - -
1287B ALA* 3.0 26.9 + - - +
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Residues in contact with LEU1284 (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* 3.3 8.2 + - - +
1251B ILE* 4.7 10.5 - - + -
1252B LEU* 3.8 18.7 - - + +
1257B ILE* 4.1 5.4 - - + -
1261B ILE* 3.6 31.9 - - + -
1281B GLY* 3.2 11.2 + - - +
1283B ARG* 1.3 76.5 - - - +
1285B SER* 1.3 66.7 + - - +
1287B ALA* 3.1 2.3 + - - +
1288B ILE* 3.1 35.1 + - + +
1301B ILE* 4.1 24.5 - - + -
1303B LEU* 3.9 28.0 - - + -
1321B MET* 4.5 11.2 - - + -
1323B LEU* 5.8 0.4 - - + -
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Residues in contact with SER1285 (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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954B PRO* 5.2 0.7 - - - -
1025B ILE* 4.8 3.1 - - - -
1281B GLY 3.0 13.9 + - - -
1282B THR* 3.3 10.6 + - - -
1284B LEU* 1.3 74.8 - - - +
1286B GLY* 1.3 57.5 + - - +
1288B ILE* 3.3 1.1 + - - -
1289B ALA* 2.9 27.0 + - - +
1315B ALA 4.1 0.4 + - - -
1316B PHE* 3.1 28.4 + - - -
1317B ASN* 3.6 3.1 - - - -
1318B LEU* 3.2 15.8 - - - +
1321B MET* 2.8 35.7 - - - +
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Residues in contact with GLY1286 (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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958B MET* 3.4 16.2 - - - +
1025B ILE* 3.5 34.5 - - - +
1282B THR 3.0 10.3 + - - -
1283B ARG 3.7 1.6 - - - -
1284B LEU 3.2 0.4 - - - -
1285B SER* 1.3 77.6 - - - +
1287B ALA* 1.3 55.6 + - - +
1289B ALA* 3.5 0.4 + - - -
1290B LYS* 2.9 32.1 + - - +
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Residues in contact with ALA1287 (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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958B MET* 5.4 0.2 - - - -
1252B LEU* 4.1 23.8 - - + -
1261B ILE* 4.5 10.1 - - + -
1283B ARG 3.0 13.8 + - - +
1284B LEU 3.1 8.0 + - - +
1286B GLY* 1.3 77.9 - - - +
1288B ILE* 1.3 61.7 + - - +
1290B LYS* 3.5 2.4 + - - -
1291B LYS* 2.7 44.7 + - - +
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Residues in contact with ILE1288 (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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1261B ILE* 4.2 15.7 - - + -
1284B LEU* 3.1 33.2 + - + +
1285B SER 3.7 6.3 - - - +
1287B ALA* 1.3 74.3 - - - +
1289B ALA* 1.3 57.5 + - - +
1291B LYS 3.1 2.6 + - - -
1292B TYR* 2.8 37.7 + - + +
1293B GLY 5.0 1.6 - - - +
1297B PHE* 3.6 51.8 - - + -
1301B ILE* 4.2 5.4 - - + -
1318B LEU* 3.9 14.4 - - + -
1321B MET* 3.9 28.7 - - + -
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Residues in contact with ALA1289 (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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954B PRO* 3.9 19.1 - - + -
955B GLU* 4.0 11.4 - - - +
958B MET* 4.0 14.1 - - + +
1285B SER 2.9 20.8 + - - +
1286B GLY 4.0 2.7 - - - +
1288B ILE* 1.3 70.4 - - - +
1290B LYS* 1.3 64.3 + - - +
1293B GLY* 2.8 38.1 + - - +
1318B LEU* 3.8 11.4 - - + -
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Residues in contact with LYS1290 (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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958B MET* 4.0 29.5 - - + +
1028B GLU* 3.9 28.6 + - - -
1286B GLY 2.9 19.2 + - - +
1287B ALA* 3.6 7.2 - - - +
1288B ILE 3.3 0.2 - - - -
1289B ALA* 1.3 77.2 - - - +
1291B LYS* 1.3 78.6 + - - +
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Residues in contact with LYS1291 (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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1261B ILE* 4.5 15.3 - - + +
1262B ASN* 4.9 7.9 - - - +
1287B ALA* 2.7 44.5 + - - +
1288B ILE 3.1 3.8 + - - +
1290B LYS* 1.3 103.5 - - - +
1292B TYR* 1.3 86.1 + - + +
1293B GLY 3.9 0.2 - - - -
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Residues in contact with TYR1292 (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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1261B ILE* 2.6 38.0 + - + -
1262B ASN* 3.4 15.2 + - - -
1264B GLN* 3.5 27.7 + - + +
1288B ILE* 2.8 28.2 + - + +
1291B LYS* 1.3 92.9 - - + +
1293B GLY* 1.3 65.2 + - - +
1295B ASN 4.1 0.3 + - - -
1296B GLY* 3.2 32.0 + - - -
1297B PHE* 3.5 37.9 - + + +
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Residues in contact with GLY1293 (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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955B GLU* 3.4 29.6 - - - -
1288B ILE* 4.2 1.6 - - - +
1289B ALA* 2.8 32.0 + - - +
1291B LYS 3.9 0.4 - - - -
1292B TYR* 1.3 87.3 - - - +
1294B ASN* 1.3 63.0 + - - -
1296B GLY 4.4 0.3 + - - -
1297B PHE* 5.3 0.5 + - - +
1318B LEU* 4.3 4.2 - - - +
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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
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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