Contacts of the helix formed by residues 1328 - 1346 (chain C) in PDB entry 2OM2
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 ASP1328 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052C GLN* 3.6 1.8 - - - -
1325C CYS* 2.8 26.9 + - - +
1327C THR* 1.3 77.6 + - - +
1329C THR* 1.3 64.9 + - - +
1330C LYS* 3.0 23.7 + - - +
1331C ASN* 3.0 18.6 + - + +
1332C VAL* 2.9 23.0 + - - +
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Residues in contact with THR1329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052C GLN* 2.8 35.3 + - - +
1055C ILE* 4.2 15.7 - - + +
1056C ILE* 3.7 21.2 - - + +
1171C GLN* 5.8 2.1 - - - +
1172C GLN* 4.7 4.1 + - - +
1175C LEU* 3.8 9.5 - - - +
1327C THR 3.6 2.0 + - - -
1328C ASP* 1.3 71.8 + - - +
1330C LYS* 1.3 58.3 + - - +
1332C VAL* 3.3 0.4 + - - -
1333C GLN* 2.9 31.9 + - + +
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Residues in contact with LYS1330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1328C ASP* 3.0 12.1 + - - +
1329C THR* 1.3 78.8 - - - +
1331C ASN* 1.3 63.6 - - - +
1333C GLN* 3.4 10.2 + - - +
1334C PHE* 3.1 22.6 + - + +
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Residues in contact with ASN1331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271C LYS* 3.3 27.1 - - - +
1323C PHE 4.0 1.4 + - - +
1324C THR* 3.3 13.2 - - - -
1325C CYS* 2.9 28.6 + - + +
1328C ASP* 3.0 31.1 + - + +
1330C LYS* 1.3 77.5 - - - +
1332C VAL* 1.3 57.6 + - - +
1334C PHE* 3.2 11.5 + - - +
1335C VAL* 2.9 37.7 + - - +
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Residues in contact with VAL1332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049C ILE* 4.4 14.8 - - + -
1052C GLN* 3.8 17.7 - - + -
1053C MET* 3.8 26.9 - - + -
1056C ILE* 3.9 4.5 - - + -
1267C PHE* 6.1 1.8 - - + -
1324C THR* 5.7 3.4 - - + -
1325C CYS 3.8 3.1 - - - +
1326C ALA* 3.5 35.7 - - - +
1328C ASP 2.9 18.8 + - - +
1329C THR 3.7 4.7 - - - +
1331C ASN* 1.3 75.0 - - - +
1333C GLN* 1.3 60.9 + - - +
1335C VAL* 4.0 4.9 - - - +
1336C PHE* 2.8 29.6 + - + +
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Residues in contact with GLN1333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056C ILE* 3.4 40.9 + - + +
1057C HIS* 5.3 3.4 - - - +
1191C PHE* 6.0 1.3 - - + -
1329C THR* 2.9 20.3 + - - +
1330C LYS* 3.7 9.4 - - - +
1332C VAL* 1.3 77.0 - - - +
1334C PHE* 1.3 61.8 + - - +
1336C PHE* 3.9 3.3 - - - +
1337C ASP* 3.0 28.5 + - + +
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Residues in contact with PHE1334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1330C LYS* 3.1 11.5 + - + +
1331C ASN* 3.2 14.1 + - - +
1333C GLN* 1.3 80.2 - - - +
1335C VAL* 1.3 71.9 + - + +
1337C ASP* 3.5 7.1 + - + +
1338C ALA* 3.3 26.3 + - + +
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Residues in contact with VAL1335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267C PHE* 3.8 22.9 - - + -
1322C HIS* 3.7 35.7 - - + +
1323C PHE 4.2 5.6 - - - +
1324C THR* 3.8 22.0 - - + -
1331C ASN* 2.9 34.0 + - - +
1332C VAL* 4.0 5.2 - - + +
1334C PHE* 1.3 83.3 - - + +
1336C PHE* 1.3 66.1 + - - +
1338C ALA* 3.1 8.7 + - - +
1339C VAL* 3.0 19.8 + - - +
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Residues in contact with PHE1336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C LEU* 3.9 20.4 - - + -
1049C ILE* 6.0 1.6 - - + -
1053C MET* 3.8 19.5 - - + -
1057C HIS* 3.7 22.0 - + + -
1189C PHE* 3.6 36.3 - + - -
1191C PHE* 4.2 4.7 - + - -
1196C PHE* 4.2 8.3 - + - -
1198C MET* 3.8 21.3 - - + -
1222C ILE* 4.6 9.6 - - + -
1267C PHE* 5.2 8.7 - + + -
1332C VAL* 2.8 24.0 + - + +
1333C GLN* 4.1 2.7 - - - +
1335C VAL* 1.3 74.4 - - - +
1337C ASP* 1.3 57.4 + - - +
1339C VAL* 3.2 14.9 + - + +
1340C THR* 2.9 49.0 + - - -
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Residues in contact with ASP1337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191C PHE* 4.0 20.2 - - + -
1192C LYS* 3.2 26.7 + - - -
1333C GLN* 3.0 20.6 + - + +
1334C PHE* 3.7 7.5 - - - +
1335C VAL 3.2 0.2 - - - -
1336C PHE* 1.3 76.2 - - - +
1338C ALA* 1.3 63.7 + - - +
1340C THR* 3.5 1.9 + - - -
1341C ASP* 3.1 34.8 + - - +
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Residues in contact with ALA1338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322C HIS* 4.0 18.4 - - + -
1334C PHE* 3.3 17.9 + - + +
1335C VAL* 3.1 11.0 + - - +
1337C ASP* 1.3 80.9 + - - +
1339C VAL* 1.3 63.4 + - - +
1341C ASP* 3.6 6.1 + - - +
1342C VAL* 3.1 28.1 + - - +
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Residues in contact with VAL1339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C LEU* 5.8 0.4 - - + -
1222C ILE* 5.2 4.0 - - + -
1265C ILE* 3.6 30.1 - - + -
1267C PHE* 4.1 19.5 - - + -
1322C HIS* 3.5 29.8 - - + +
1335C VAL 3.0 17.9 + - - +
1336C PHE* 3.5 22.7 - - + +
1338C ALA* 1.3 78.1 - - - +
1340C THR* 1.3 57.1 + - - +
1342C VAL* 3.3 7.9 + - - +
1343C ILE* 3.0 39.2 + - + +
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Residues in contact with THR1340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191C PHE* 3.5 26.3 - - + -
1192C LYS* 3.9 25.1 - - + -
1194C LEU* 4.1 16.4 - - + -
1196C PHE* 3.7 6.4 - - + -
1336C PHE* 2.9 30.5 + - - -
1337C ASP 3.7 5.4 - - - -
1339C VAL* 1.3 75.6 - - - +
1341C ASP* 1.3 60.4 + - - +
1343C ILE* 3.2 9.8 + - - +
1344C ILE* 2.9 35.5 + - + +
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Residues in contact with ASP1341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192C LYS* 2.6 33.4 + - - +
1337C ASP* 3.1 26.9 + - - +
1338C ALA* 3.6 7.4 + - - +
1339C VAL 3.4 0.2 - - - -
1340C THR* 1.3 75.9 - - - +
1342C VAL* 1.3 58.1 + - + +
1344C ILE* 3.3 11.1 + - - +
1345C LYS* 3.0 29.9 + - - +
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Residues in contact with VAL1342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320C TYR* 3.7 45.3 - - + -
1322C HIS* 5.8 4.0 - - + +
1338C ALA* 3.1 16.4 - - + +
1339C VAL* 3.3 10.5 + - - +
1340C THR 3.2 0.4 - - - -
1341C ASP* 1.3 76.9 - - + +
1343C ILE* 1.3 67.2 + - + +
1345C LYS* 3.2 28.1 - - - +
1346C ASN* 2.8 35.4 + - - +
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Residues in contact with ILE1343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C ARG* 3.8 28.7 + - - +
1034C VAL* 4.3 10.5 - - + -
1036C LEU* 4.2 24.2 - - + -
1194C LEU* 5.1 5.4 - - + -
1196C PHE* 4.3 15.7 - - + -
1219C THR* 4.2 19.7 - - + -
1220C ALA* 5.0 2.5 - - + -
1265C ILE* 4.9 8.1 - - + -
1339C VAL* 3.0 35.4 + - + +
1340C THR* 3.2 10.1 + - - +
1342C VAL* 1.3 79.2 - - + +
1344C ILE* 1.3 61.2 + - - +
1346C ASN* 3.6 8.3 + - - +
1347C ASN 3.3 12.8 + - - +
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Residues in contact with ILE1344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032C ARG* 5.2 4.9 - - - +
1192C LYS* 4.3 22.2 - - + +
1194C LEU* 4.1 21.8 - - + -
1340C THR* 2.9 33.0 + - + +
1341C ASP* 3.5 13.2 - - - +
1342C VAL 3.1 0.2 - - - -
1343C ILE* 1.3 74.6 - - - +
1345C LYS* 1.3 62.4 + - - +
1346C ASN 3.1 1.6 - - - -
1347C ASN* 2.7 26.7 + - - +
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Residues in contact with LYS1345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320C TYR* 5.4 3.7 - - - -
1341C ASP 3.0 14.0 + - - +
1342C VAL* 3.2 42.8 - - - +
1344C ILE* 1.3 73.1 - - - +
1346C ASN* 1.3 69.5 + - - +
1347C ASN* 2.9 18.3 + - - +
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Residues in contact with ASN1346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263C SER* 4.9 5.9 + - - -
1318C GLU* 4.8 3.2 + - - -
1320C TYR* 2.7 32.7 + - - -
1342C VAL* 2.8 30.9 + - - +
1343C ILE* 3.8 7.4 - - - +
1344C ILE 3.1 0.4 - - - -
1345C LYS* 1.3 87.5 - - - +
1347C ASN* 1.3 82.7 + - - +
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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
------------------------------------------------------------
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