Contacts of the helix formed by residues 1328 - 1346 (chain A) in PDB entry 6CNB
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 ILE1328 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323A PHE* 3.2 35.3 - - + -
1327A GLY* 1.3 68.8 - - - +
1329A GLU* 1.3 65.8 + - + +
1331A ALA* 2.5 30.1 + - - +
1332A ARG 2.9 11.2 + - - -
1363A THR* 4.0 15.5 - - + -
1366A GLY 3.7 8.5 - - - +
177E ARG 4.9 0.9 - - - +
178E ILE* 3.5 38.6 - - + -
179E GLN* 3.9 13.5 - - + +
182E ASP* 3.6 21.5 - - + +
212E ARG* 3.7 33.0 - - - +
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Residues in contact with GLU1329 (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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1327A GLY 2.9 3.5 + - - +
1328A ILE* 1.3 80.3 - - + +
1330A ALA* 1.3 57.7 + - - +
1332A ARG* 3.1 13.8 + - - +
1333A TYR* 3.0 31.9 + - + +
150E VAL* 5.7 0.7 - - + -
151E PRO* 3.6 28.5 - - + -
153E HIS* 4.0 17.7 - - + +
178E ILE* 6.4 0.2 - - + -
198E ILE* 3.5 21.5 - - + +
200E ARG* 2.6 43.3 + - - +
212E ARG* 2.9 30.4 + - - +
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Residues in contact with ALA1330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1322A VAL* 4.3 4.0 - - + -
1326A LEU* 3.6 25.6 - - + -
1327A GLY 3.3 5.3 + - - +
1328A ILE 2.8 3.8 + - - -
1329A GLU* 1.3 73.9 - - - +
1331A ALA* 1.3 67.7 + - - +
1333A TYR* 3.2 4.4 + - - +
1334A SER* 2.9 23.9 + - - -
149E LEU* 4.1 18.9 - - + +
150E VAL* 3.6 31.8 - - + +
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Residues in contact with ALA1331 (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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1319A VAL* 3.6 29.0 - - + +
1322A VAL* 3.8 13.0 - - + +
1323A PHE* 4.0 24.5 - - + +
1327A GLY 4.1 1.2 - - - -
1328A ILE 2.5 24.6 + - - +
1330A ALA* 1.3 72.6 - - - +
1332A ARG* 1.3 63.2 + - - +
1334A SER* 3.1 6.5 + - - -
1335A ILE* 2.9 16.8 + - - +
1368A VAL* 4.0 8.1 - - + -
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Residues in contact with ARG1332 (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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1328A ILE 2.9 6.6 + - - +
1329A GLU* 3.1 18.8 + - - +
1331A ALA* 1.3 74.1 - - - +
1333A TYR* 1.3 77.3 + - - +
1334A SER 2.7 1.7 + - - -
1335A ILE* 2.5 40.2 + - + +
1336A ILE* 3.2 17.3 + - + +
1356A GLN* 4.6 15.8 + - - +
1359A GLY* 3.1 34.1 - - - +
1360A ASP* 4.0 12.2 - - - +
1363A THR* 3.2 29.4 + - + +
200E ARG* 2.7 52.5 - - - +
208E TYR* 5.1 2.6 + - - -
212E ARG* 4.3 6.7 - - - +
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Residues in contact with TYR1333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1329A GLU* 3.0 20.5 + - + +
1330A ALA* 3.8 4.7 - - - +
1332A ARG* 1.3 92.8 - - - +
1334A SER* 1.3 58.2 + - - +
1336A ILE* 3.7 16.5 - - + +
1337A ARG* 3.6 27.8 + - + +
148E GLU* 4.9 8.0 + - - -
149E LEU* 3.4 45.1 - - + +
151E PRO* 6.0 1.3 - - + -
200E ARG* 5.8 4.3 - - + -
201E LYS 4.1 12.7 + - - -
202E SER* 3.4 39.3 + - - -
203E GLU 5.0 1.7 + - - -
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Residues in contact with SER1334 (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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1315A THR* 5.8 2.4 - - - +
1316A THR 4.3 13.5 + - - -
1317A ASN* 5.8 0.2 - - - -
1319A VAL* 4.8 6.3 - - - +
1322A VAL* 5.1 11.7 - - - +
1330A ALA 2.9 12.3 + - - -
1331A ALA* 3.3 12.3 - - - -
1332A ARG 2.7 3.6 + - - -
1333A TYR* 1.3 76.9 - - - +
1335A ILE* 1.3 58.7 + - - -
1336A ILE 3.2 0.2 - - - -
1337A ARG* 2.9 11.3 + - - +
1338A GLU* 2.9 34.8 + - - +
149E LEU* 4.7 16.3 - - - +
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Residues in contact with ILE1335 (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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1129A ILE* 3.6 31.4 - - + +
1130A ILE* 5.2 0.4 - - + +
1132A ALA* 5.9 0.4 - - + -
1319A VAL* 3.8 25.6 - - + -
1331A ALA 2.9 9.5 + - - +
1332A ARG* 2.5 31.5 + - - +
1334A SER* 1.3 71.7 - - - +
1336A ILE* 1.3 57.2 + - + +
1338A GLU* 3.9 2.6 - - - -
1339A ILE* 2.9 40.6 + - + +
1358A LEU* 6.1 2.2 - - + -
1359A GLY* 3.7 26.9 - - - +
1362A MET* 3.3 35.0 - - + -
1363A THR* 5.1 1.3 - - - +
1368A VAL* 5.5 0.9 - - + -
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Residues in contact with ILE1336 (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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1332A ARG* 4.0 15.5 - - - +
1333A TYR* 3.7 24.0 - - + +
1335A ILE* 1.3 76.4 - - + +
1337A ARG* 1.3 68.4 + - + +
1339A ILE* 4.2 1.3 - - + -
1340A ASN* 3.3 22.2 + - - +
1352A PRO* 6.2 1.3 - - + -
1355A ILE* 3.3 46.5 - - + +
1356A GLN* 3.8 24.5 - - + +
1359A GLY* 3.8 20.4 - - - +
202E SER* 4.5 15.0 - - - +
204E THR* 5.9 2.9 - - + -
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Residues in contact with ARG1337 (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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1142A ASN* 5.8 3.2 - - - +
1315A THR* 3.8 28.8 - - - +
1316A THR 5.4 2.0 + - - -
1333A TYR* 3.6 26.5 - - + +
1334A SER* 2.9 14.7 + - - +
1336A ILE* 1.3 86.4 - - + +
1338A GLU* 1.3 63.1 + - - +
1340A ASN* 3.8 2.9 + - - +
1341A TYR* 2.9 33.8 + - + +
149E LEU* 5.4 6.3 - - - -
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Residues in contact with GLU1338 (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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1125A ARG* 2.3 42.9 + - - +
1129A ILE* 3.5 17.5 - - + +
1316A THR 4.1 3.6 - - - +
1317A ASN* 3.0 33.2 + - - +
1318A HIS 4.4 2.3 + - - -
1319A VAL* 4.7 7.8 - - - +
1334A SER* 2.9 20.2 + - - +
1335A ILE* 4.1 3.4 - - - +
1337A ARG* 1.3 80.4 - - - +
1339A ILE* 1.3 65.7 + - - +
1341A TYR* 3.3 13.6 - - + +
1342A THR* 2.9 25.1 + - + +
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Residues in contact with ILE1339 (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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1097A ILE* 5.5 3.4 - - + -
1126A ILE* 4.4 25.4 - - + -
1129A ILE* 3.6 35.7 - - + -
1130A ILE* 5.0 7.2 - - + -
1335A ILE* 2.9 26.9 + - + +
1338A GLU* 1.3 75.6 - - - +
1340A ASN* 1.3 65.1 + - - +
1342A THR* 3.2 4.5 - - + +
1343A MET* 3.0 37.6 + - + +
1355A ILE* 3.6 37.5 - - + -
1358A LEU* 5.0 13.0 - - + -
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Residues in contact with ASN1340 (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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1336A ILE 3.3 20.9 + - - +
1337A ARG* 3.9 2.7 - - - +
1338A GLU 3.4 0.2 - - - -
1339A ILE* 1.3 79.7 - - - +
1341A TYR* 1.3 63.9 + - - +
1343A MET* 3.9 7.7 - - - +
1344A SER* 3.2 23.5 + - - -
1350A VAL 5.8 1.4 + - - -
1351A ASP 5.5 5.4 + - - +
1352A PRO* 5.5 14.7 - - + +
1355A ILE* 4.3 10.8 - - + +
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Residues in contact with TYR1341 (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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1121A LEU* 5.1 14.0 - - + +
1337A ARG* 2.9 27.0 + - + +
1338A GLU* 3.3 16.2 - - + +
1339A ILE 3.1 0.2 - - - -
1340A ASN* 1.3 75.0 - - - +
1342A THR* 1.3 81.3 + - - +
1344A SER* 2.8 25.2 + - - -
1345A ASN* 3.5 31.9 + - - -
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Residues in contact with THR1342 (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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1121A LEU* 3.3 28.0 + - - +
1122A GLY 4.6 3.3 + - - -
1125A ARG* 4.7 13.1 - - + +
1126A ILE* 4.1 24.2 - - + +
1129A ILE* 5.2 6.3 - - + -
1338A GLU* 2.9 18.4 + - - +
1339A ILE* 3.2 17.3 - - + +
1341A TYR* 1.3 86.1 - - - +
1343A MET* 1.3 61.1 + - - +
1345A ASN* 3.4 20.6 + - - +
1346A HIS* 3.6 17.2 - - - -
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Residues in contact with MET1343 (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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1097A ILE* 4.0 22.4 - - + +
1126A ILE* 4.4 17.7 - - + -
1339A ILE* 3.0 24.6 + - + +
1340A ASN* 3.9 5.6 - - - +
1342A THR* 1.3 78.3 - - + +
1344A SER* 1.3 59.8 + - - +
1345A ASN 3.4 0.9 - - - -
1346A HIS* 4.4 8.8 - - + +
1347A GLY 2.8 23.4 + - - +
1348A MET* 4.4 14.9 - - + +
1349A SER* 5.3 1.7 - - - -
1350A VAL* 3.5 35.7 - - + -
1355A ILE* 3.5 30.3 - - + -
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Residues in contact with SER1344 (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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1340A ASN* 3.2 17.0 + - - -
1341A TYR* 2.8 22.4 + - - -
1343A MET* 1.3 79.1 - - - +
1345A ASN* 1.3 67.5 + - - +
1347A GLY* 3.8 11.2 + - - -
1348A MET 5.0 5.1 - - - +
1349A SER* 6.2 0.9 - - - +
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Residues in contact with ASN1345 (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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1121A LEU* 3.3 32.9 - - + +
1341A TYR* 3.8 37.8 + - - -
1342A THR* 3.4 9.1 + - - +
1343A MET 3.4 0.6 - - - -
1344A SER* 1.3 82.8 + - - +
1346A HIS* 1.3 61.1 - - + +
1347A GLY* 3.0 9.5 + - - -
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Residues in contact with HIS1346 (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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1121A LEU* 2.2 38.7 + - + +
1122A GLY* 3.4 20.2 - - - -
1123A VAL* 4.7 4.0 - - + -
1126A ILE* 6.0 4.9 - - + -
1342A THR* 3.6 21.7 + - - +
1343A MET* 4.4 6.7 - - + +
1344A SER 3.6 0.2 - - - -
1345A ASN* 1.3 76.7 - - + +
1347A GLY* 1.3 59.9 + - - +
1348A MET* 5.1 10.8 - - + +
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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