Contacts of the helix formed by residues 1272 - 1291 (chain C) in PDB entry 3B13
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 THR1272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254C SER 3.6 12.7 + - - -
1255C ASP* 2.9 42.8 + - + +
1256C GLU 3.6 3.8 - - - -
1257C GLN* 4.1 8.7 - - - +
1258C CYS* 3.8 4.2 - - - -
1271C GLN* 1.3 75.3 - - - +
1273C HIS* 1.3 68.1 + - - +
1274C ARG* 4.0 3.5 + - - +
1275C GLN* 2.9 47.3 + - - +
1276C LEU 3.2 8.3 + - - -
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Residues in contact with HIS1273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250C LEU 4.4 8.5 - - - -
1251C LEU* 3.9 16.3 - - + +
1252C LYS* 3.1 45.1 + - + +
1254C SER* 3.7 8.7 + - - +
1256C GLU* 3.0 42.9 + - - +
1257C GLN 3.8 7.5 + - - -
1258C CYS* 3.6 28.9 - - - -
1259C ALA* 4.7 3.0 + - - +
1262C VAL* 4.6 9.1 - - + +
1272C THR* 1.3 72.3 - - - +
1274C ARG* 1.3 58.1 + - - +
1276C LEU* 3.3 2.3 + - - +
1277C LYS* 2.9 30.7 + - - +
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Residues in contact with ARG1274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252C LYS 3.8 2.2 + - - -
1253C TRP* 3.8 38.1 + - + +
1254C SER* 3.0 26.9 + - - +
1255C ASP* 3.3 34.3 + - - -
1272C THR* 4.3 4.9 - - - +
1273C HIS* 1.3 80.8 - - - +
1275C GLN* 1.3 60.9 + - + +
1277C LYS* 3.7 0.7 - - - +
1278C GLU* 2.9 37.9 + - - +
1307C GLN* 3.0 30.9 + - - -
1311C GLU* 3.9 20.1 + - - +
1312C ILE* 3.5 30.0 - - - +
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Residues in contact with GLN1275 (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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1270C PRO 4.7 1.2 - - - +
1271C GLN* 3.5 23.3 - - + +
1272C THR* 2.9 48.1 + - - +
1274C ARG* 1.3 80.2 - - + +
1276C LEU* 1.3 58.3 + - - +
1278C GLU* 3.6 10.8 - - - +
1279C THR* 3.0 31.4 + - - -
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Residues in contact with LEU1276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247C HIS* 4.3 15.5 - - + -
1251C LEU* 3.7 20.9 - - + -
1258C CYS* 4.0 17.7 - - - -
1262C VAL 4.4 9.2 - - - +
1263C MET* 4.4 5.2 - - + -
1267C GLN* 3.5 31.4 - - - +
1271C GLN* 3.5 25.4 - - - +
1272C THR 3.2 6.8 + - - +
1273C HIS 3.7 6.1 - - - +
1275C GLN* 1.3 76.4 - - - +
1277C LYS* 1.3 66.0 + - - +
1279C THR* 3.1 8.6 + - + -
1280C LEU* 2.9 37.4 + - + +
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Residues in contact with LYS1277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248C THR* 3.8 15.1 + - - -
1249C TRP* 5.9 0.2 - - - +
1251C LEU* 3.1 44.7 + - + +
1252C LYS* 4.3 4.0 - - - +
1253C TRP* 3.6 57.9 - - + +
1273C HIS 2.9 17.2 + - - +
1274C ARG* 4.3 0.2 - - - -
1276C LEU* 1.3 77.0 - - - +
1278C GLU* 1.3 64.1 + - - +
1280C LEU* 3.2 4.2 + - - +
1281C TYR* 2.8 54.5 + - + +
1303C GLU* 4.8 1.4 + - - -
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Residues in contact with GLU1278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253C TRP* 3.8 5.2 - - + -
1274C ARG* 2.9 29.5 + - - +
1275C GLN* 3.6 10.5 - - - +
1277C LYS* 1.3 72.7 - - - +
1279C THR* 1.3 64.4 + - - +
1281C TYR* 3.1 2.9 + - - +
1282C GLU* 2.9 34.6 + - - +
1304C LEU* 3.7 21.3 - - + +
1308C TYR* 2.8 42.5 + - - +
1312C ILE* 5.0 7.4 - - - +
1317C LEU* 3.4 12.3 - - - +
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Residues in contact with THR1279 (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 GLN* 4.3 8.3 + - - +
1275C GLN 3.0 16.5 + - - -
1276C LEU* 3.1 16.6 + - + -
1278C GLU* 1.3 75.1 - - - +
1280C LEU* 1.3 67.7 + - + +
1282C GLU* 3.3 16.1 + - - +
1283C THR* 3.1 25.6 + - - +
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Residues in contact with LEU1280 (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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1225C TYR* 3.5 19.5 - - + +
1244C LEU* 4.6 16.2 - - + +
1247C HIS* 3.5 31.2 - - + +
1248C THR* 3.5 30.1 - - + -
1251C LEU* 4.1 6.3 - - + -
1267C GLN* 4.9 4.5 - - - +
1276C LEU* 2.9 35.8 + - + +
1277C LYS 3.6 0.4 - - - +
1279C THR* 1.3 76.9 - - + +
1281C TYR* 1.3 60.5 + - - +
1283C THR* 3.1 9.2 + - - +
1284C ILE* 2.8 37.7 + - + +
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Residues in contact with TYR1281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245C LEU* 4.5 7.4 - - + +
1248C THR* 3.7 33.3 + - + -
1253C TRP* 4.0 7.2 - + - -
1277C LYS* 2.8 42.8 + - + +
1278C GLU* 3.4 5.4 - - - +
1280C LEU* 1.3 76.4 - - - +
1282C GLU* 1.3 58.2 + - - +
1284C ILE* 3.7 7.8 - - + +
1285C ILE* 2.9 37.6 + - - +
1300C LEU* 3.9 30.6 - - + +
1303C GLU* 2.7 45.2 + - + -
1304C LEU* 3.7 27.8 - - + -
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Residues in contact with GLU1282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278C GLU* 2.9 30.2 + - - +
1279C THR* 3.5 16.5 + - - +
1280C LEU 3.2 0.2 - - - -
1281C TYR* 1.3 76.9 - - - +
1283C THR* 1.3 64.0 + - - +
1285C ILE* 3.4 7.5 + - + +
1286C GLY* 3.1 18.4 + - - -
1304C LEU* 4.5 9.9 - - + -
1308C TYR* 3.7 16.8 + - - -
1317C LEU* 5.0 4.9 - - - +
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Residues in contact with THR1283 (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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1228C ARG* 5.9 0.9 - - - +
1244C LEU* 4.0 10.1 - - + -
1279C THR* 3.1 18.1 + - - +
1280C LEU* 3.1 13.3 + - + +
1282C GLU* 1.3 75.9 - - - +
1284C ILE* 1.3 64.1 + - - +
1286C GLY* 2.9 5.9 + - - -
1287C TYR* 2.9 56.5 + - + +
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Residues in contact with ILE1284 (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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1241C ALA* 3.9 10.1 - - + +
1244C LEU* 3.7 33.0 - - + -
1245C LEU* 3.7 30.3 - - + +
1248C THR* 4.3 10.3 - - + -
1280C LEU* 2.8 27.0 + - + +
1281C TYR* 3.7 7.2 - - + +
1283C THR* 1.3 67.8 - - - +
1285C ILE* 1.3 69.4 + - - +
1286C GLY 2.9 1.3 - - - -
1287C TYR* 2.7 23.3 + - - +
1288C PHE* 2.9 32.8 + - + +
1300C LEU* 3.3 22.2 - - + -
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Residues in contact with ILE1285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281C TYR 2.9 30.0 + - - +
1282C GLU* 3.7 7.4 - - + +
1284C ILE* 1.3 74.2 - - - +
1286C GLY* 1.3 57.4 + - - +
1288C PHE* 3.6 7.6 + - - +
1289C ASP* 3.0 26.5 + - - +
1297C ALA* 4.0 12.1 - - + +
1300C LEU* 3.6 34.8 - - + -
1301C CYS* 3.9 18.4 - - - +
1304C LEU* 3.9 19.1 - - + -
1321C ASN* 5.8 0.2 - - - +
1324C GLN* 4.3 10.1 - - - +
1328C PHE* 4.1 26.7 - - + -
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Residues in contact with GLY1286 (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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1282C GLU 3.1 9.7 + - - -
1283C THR 2.9 8.3 + - - -
1284C ILE 2.8 2.2 + - - -
1285C ILE* 1.3 76.4 - - - +
1287C TYR* 1.3 65.6 + - - -
1289C ASP* 3.0 10.2 + - - +
1290C LYS* 3.0 29.2 + - - +
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Residues in contact with TYR1287 (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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1228C ARG* 3.4 24.0 + - - -
1232C LEU* 3.6 21.6 - - + +
1237C TYR* 3.4 41.0 - + - +
1240C ALA* 3.7 14.8 - - + -
1241C ALA* 3.4 27.6 - - + -
1244C LEU* 3.8 21.5 - - + -
1283C THR* 2.9 33.4 + - + +
1284C ILE* 2.7 13.8 + - - +
1286C GLY* 1.3 71.0 - - - +
1288C PHE* 1.3 56.9 + - - +
1290C LYS* 3.0 14.6 + - - +
1291C GLY* 2.8 24.6 + - - -
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Residues in contact with PHE1288 (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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1238C THR* 3.7 16.2 - - + +
1241C ALA* 3.5 17.7 - - + -
1242C TYR* 3.7 42.2 - + - -
1245C LEU* 3.9 11.7 - - + -
1284C ILE* 2.9 40.2 + - + +
1285C ILE 3.8 4.3 - - - +
1287C TYR* 1.3 72.2 - - - +
1289C ASP* 1.3 63.9 + - - +
1291C GLY* 3.3 1.7 + - - +
1292C LYS 2.9 3.1 + - - -
1293C MET* 2.8 53.9 + - + -
1296C GLU* 3.7 24.5 - - + -
1297C ALA* 4.2 18.6 - - + +
1300C LEU* 4.5 6.5 - - + -
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Residues in contact with ASP1289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285C ILE 3.0 15.5 + - - +
1286C GLY* 3.0 14.3 + - - +
1288C PHE* 1.3 76.1 - - - +
1290C LYS* 1.3 56.6 + - + +
1292C LYS* 2.8 28.1 + - - +
1294C TRP* 2.9 31.1 + - - +
1297C ALA* 4.8 0.4 - - - +
1324C GLN* 4.5 3.9 + - - +
1327C LYS* 4.2 16.9 + - - -
1328C PHE* 3.4 23.0 - - + -
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Residues in contact with LYS1290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237C TYR* 3.6 57.7 + - + +
1286C GLY 3.0 17.0 + - - +
1287C TYR* 3.0 16.2 + - - +
1289C ASP* 1.3 78.0 - - + +
1291C GLY* 1.3 58.7 + - - +
1292C LYS* 3.2 11.5 + - - +
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Residues in contact with GLY1291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237C TYR* 4.2 2.4 - - - +
1238C THR* 3.6 24.4 + - - -
1287C TYR 2.8 12.6 + - - -
1288C PHE 3.3 3.3 + - - -
1289C ASP 3.1 0.4 - - - -
1290C LYS* 1.3 74.7 - - - +
1292C LYS* 1.3 71.1 - - - +
1293C MET* 3.1 15.4 + - - +
1364C ARG* 5.4 1.9 + - - -
1367C GLU* 5.7 0.3 - - - +
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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
------------------------------------------------------------
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