Contacts of the helix formed by residues 1336 - 1355 (chain A) in PDB entry 3F2B
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 THR1336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1331A LYS* 6.0 0.7 - - - +
1334A GLN 4.7 5.4 - - - +
1335A ALA* 1.3 75.0 - - - +
1337A ALA* 1.3 65.5 + - - +
1338A LYS* 3.3 9.5 + - - +
1339A GLU* 2.7 55.8 + - - +
1340A LYS* 3.0 10.8 + - - +
12P G 4.8 11.7 - - - +
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Residues in contact with ALA1337 (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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1335A ALA 3.7 1.8 + - - -
1336A THR* 1.3 71.5 - - - +
1338A LYS* 1.3 68.8 + - + +
1340A LYS* 3.4 13.8 + - - +
1341A SER* 3.0 28.9 + - - -
12P G 5.4 4.9 + - + +
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Residues in contact with LYS1338 (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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1308A ASP* 4.1 21.0 - - - +
1336A THR* 2.8 8.8 + - - +
1337A ALA* 1.3 83.9 - - + +
1339A GLU* 1.3 66.2 + - - +
1340A LYS 3.2 1.3 - - - -
1341A SER* 3.4 9.8 + - - +
1342A LEU* 3.1 21.5 + - - +
11P G 3.8 52.8 - - - +
12P G 3.3 39.3 + - - +
13P C 5.5 2.8 - - - +
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Residues in contact with GLU1339 (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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1324A ARG* 5.5 4.7 - - - +
1328A ILE* 3.7 27.1 - - + +
1331A LYS* 3.1 42.1 + - - +
1335A ALA* 4.3 8.6 - - + -
1336A THR* 2.7 54.1 + - - +
1338A LYS* 1.3 79.3 - - + +
1340A LYS* 1.3 55.4 + - - +
1342A LEU* 3.3 8.4 + - + +
1343A LEU* 2.8 29.1 + - - +
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Residues in contact with LYS1340 (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* 5.4 0.4 - - + -
1332A GLY 5.0 2.9 - - - -
1333A ILE* 4.5 17.7 + - - +
1335A ALA* 3.3 37.8 + - + +
1336A THR 3.0 11.5 + - - +
1337A ALA* 3.6 14.1 - - - +
1339A GLU* 1.3 74.3 - - - +
1341A SER* 1.3 60.0 + - - +
1343A LEU* 3.6 13.7 - - + +
1344A THR* 2.9 33.2 + - - -
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Residues in contact with SER1341 (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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1308A ASP* 3.4 26.9 - - - -
1337A ALA 3.0 17.8 + - - -
1338A LYS* 3.9 9.7 - - - +
1339A GLU 3.3 0.4 - - - -
1340A LYS* 1.3 75.4 - - - +
1342A LEU* 1.3 62.6 + - - +
1344A THR* 3.5 6.8 + - - -
1345A VAL* 3.1 26.4 + - - +
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Residues in contact with LEU1342 (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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1308A ASP* 3.8 21.4 - - + +
1309A PHE* 3.6 32.3 - - - +
1310A ASP* 3.7 6.5 - - + +
1324A ARG* 3.4 35.9 - - - +
1328A ILE* 3.9 9.6 - - + -
1338A LYS 3.1 13.8 + - - +
1339A GLU* 3.6 10.3 - - + +
1341A SER* 1.3 78.2 - - - +
1343A LEU* 1.3 62.9 + - - +
1345A VAL* 3.0 4.2 + - + +
1346A LEU* 2.9 40.5 + - + +
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Residues in contact with LEU1343 (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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1161A ARG* 3.8 34.8 - - - +
1325A ILE* 3.7 33.2 - - + +
1328A ILE* 4.0 22.2 - - + +
1329A ASN* 3.7 22.4 - - - +
1339A GLU 2.8 19.7 + - - +
1340A LYS* 3.6 13.9 - - + +
1342A LEU* 1.3 71.7 - - - +
1344A THR* 1.3 65.2 + - - +
1346A LEU* 3.1 5.4 + - - +
1347A GLU* 2.9 30.8 + - + +
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Residues in contact with THR1344 (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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1153A ILE* 5.5 0.2 - - - +
1154A GLY* 6.3 0.9 - - - -
1301A TYR* 3.5 20.0 - - - +
1340A LYS 2.9 16.5 + - - -
1341A SER* 3.6 12.0 - - - +
1343A LEU* 1.3 79.3 - - - +
1345A VAL* 1.3 65.8 + - + +
1347A GLU* 3.3 20.9 + - - +
1348A VAL* 3.3 14.5 - - + +
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Residues in contact with VAL1345 (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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1301A TYR* 4.4 9.9 - - + +
1302A PHE* 4.0 9.0 - - + -
1306A ALA* 3.9 28.5 - - + -
1307A GLU 4.7 0.7 - - - +
1308A ASP* 3.1 30.7 - - + +
1309A PHE* 4.2 18.4 - - + -
1314A MET* 5.0 3.4 - - - -
1341A SER 3.1 17.5 - - - +
1342A LEU* 3.0 4.8 + - + +
1344A THR* 1.3 78.6 - - + +
1346A LEU* 1.3 67.2 + - + +
1348A VAL* 3.2 11.4 + - - +
1349A ALA* 3.1 19.6 + - - +
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Residues in contact with LEU1346 (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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1310A ASP* 4.3 11.9 - - + +
1313A ALA* 5.2 3.1 - - + -
1314A MET* 4.0 28.0 - - + -
1321A ILE* 3.5 18.0 - - + +
1324A ARG* 3.8 29.6 - - + -
1325A ILE* 3.8 23.6 - - + +
1328A ILE* 4.6 5.8 - - + -
1342A LEU* 2.9 49.1 + - + +
1343A LEU* 3.8 2.0 - - - +
1345A VAL* 1.3 75.2 - - + +
1347A GLU* 1.3 67.2 + - - +
1349A ALA* 3.1 3.2 + - - -
1350A LEU* 2.9 21.7 + - - +
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Residues in contact with GLU1347 (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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1146A ILE* 5.6 2.5 - - - +
1147A MET* 5.0 8.2 - - + +
1153A ILE* 4.1 20.4 - - + +
1161A ARG* 2.8 39.8 + - - +
1164A ARG* 2.6 35.7 + - - -
1325A ILE* 4.0 16.5 - - + +
1343A LEU* 2.9 22.9 + - + +
1344A THR* 3.5 16.3 + - - +
1345A VAL 3.2 0.2 - - - -
1346A LEU* 1.3 79.1 - - - +
1348A VAL* 1.3 60.2 + - - +
1350A LEU* 3.4 4.8 + - - +
1351A GLU* 3.2 21.1 + - - +
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Residues in contact with VAL1348 (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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1153A ILE* 3.7 22.0 - - + +
1154A GLY* 4.7 5.4 - - - +
1297A TYR* 5.3 1.3 - - + -
1298A TYR* 3.6 22.0 - - + -
1301A TYR* 3.6 38.8 - - + +
1302A PHE* 3.2 25.1 - - + -
1344A THR* 3.3 17.9 - - + +
1345A VAL 3.2 6.5 + - - +
1347A GLU* 1.3 76.5 - - - +
1349A ALA* 1.3 55.9 + - - +
1351A GLU* 3.8 1.9 - - - +
1352A MET* 2.9 25.8 + - - +
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Residues in contact with ALA1349 (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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1302A PHE* 3.9 10.8 - - + -
1314A MET* 4.1 18.6 - - + -
1321A ILE* 4.1 7.9 - - + -
1345A VAL 3.1 12.2 + - - +
1346A LEU* 3.1 13.6 + - - +
1348A VAL* 1.3 76.9 - - - +
1350A LEU* 1.3 58.6 + - - +
1352A MET* 3.3 5.2 + - - +
1353A CYS* 2.9 33.1 + - - -
1359A PHE* 3.9 20.8 - - + -
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Residues in contact with LEU1350 (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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1145A GLN 3.8 17.5 - - - +
1146A ILE* 4.1 19.5 - - - +
1147A MET* 4.2 26.0 - - + -
1318A SER* 3.3 43.7 - - - +
1321A ILE* 3.7 16.1 - - + +
1322A ARG* 4.0 20.6 - - + +
1325A ILE* 4.4 4.7 - - + -
1346A LEU 2.9 16.5 + - - +
1347A GLU* 3.8 4.5 - - - +
1349A ALA* 1.3 72.9 - - - +
1351A GLU* 1.3 61.6 + - - +
1353A CYS* 3.0 4.7 + - - +
1354A GLU* 2.9 29.2 + - + +
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Residues in contact with GLU1351 (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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1139A LEU* 3.9 14.3 - - + +
1141A VAL* 5.2 0.4 - - + -
1146A ILE* 3.8 38.4 - - + +
1151A GLY 4.9 0.2 - - - -
1153A ILE* 3.5 19.4 + - + +
1290A LYS* 2.8 37.7 + - - -
1298A TYR* 2.3 33.2 + - - +
1347A GLU 3.2 13.8 + - - +
1348A VAL* 3.8 3.4 - - - +
1350A LEU* 1.3 78.0 - - - +
1352A MET* 1.3 66.1 + - - +
1354A GLU* 3.3 1.6 + - - +
1355A ARG* 3.2 33.9 + - + +
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Residues in contact with MET1352 (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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1295A LEU* 4.7 1.8 - - + -
1298A TYR* 3.5 53.7 + - + -
1302A PHE* 3.9 1.6 - - - -
1348A VAL 2.9 17.1 + - - +
1349A ALA* 3.4 11.7 - - - +
1350A LEU 3.3 0.2 - - - -
1351A GLU* 1.3 77.0 - - - +
1353A CYS* 1.3 61.3 + - - +
1355A ARG* 3.2 7.1 + - - +
1357A PHE* 3.4 28.6 + - + -
1358A SER* 3.3 37.7 - - - +
1359A PHE* 3.4 34.8 - - + -
1379A LEU* 3.6 19.7 - - + -
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Residues in contact with CYS1353 (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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1314A MET 4.5 0.4 - - - -
1317A GLY* 4.3 6.1 - - - -
1318A SER* 4.1 26.5 - - - +
1321A ILE* 3.6 19.3 - - - -
1349A ALA 2.9 18.5 + - - +
1350A LEU 3.0 7.8 + - - +
1352A MET* 1.3 76.5 - - - +
1354A GLU* 1.3 60.0 + - - +
1356A GLY* 3.0 20.4 + - - -
1357A PHE 3.6 18.8 + - - +
1358A SER* 4.6 5.4 - - - -
1359A PHE* 4.2 20.4 - - - -
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Residues in contact with GLU1354 (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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1140A GLY 5.2 0.5 - - - +
1141A VAL* 3.5 22.9 - - + +
1145A GLN* 2.8 67.2 + - - +
1146A ILE* 4.1 7.9 - - + -
1318A SER* 2.4 27.5 + - - +
1322A ARG* 3.5 11.3 + - - -
1350A LEU* 2.9 20.0 + - + +
1351A GLU 3.3 4.5 + - - +
1353A CYS* 1.3 72.4 - - - +
1355A ARG* 1.3 59.5 + - - +
1356A GLY* 3.0 7.3 + - - -
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Residues in contact with ARG1355 (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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1138A PRO 4.7 1.4 + - - -
1139A LEU* 3.0 53.3 + - - +
1141A VAL* 3.9 13.9 - - + -
1290A LYS* 2.3 43.4 + - - +
1291A VAL* 4.1 10.1 + - - +
1294A PRO* 3.5 24.1 - - - +
1297A TYR* 4.8 0.2 - - - -
1298A TYR* 3.3 25.1 + - - +
1351A GLU* 3.2 21.0 + - + +
1352A MET* 3.6 6.7 - - - +
1353A CYS 3.1 1.0 - - - -
1354A GLU* 1.3 77.1 - - - +
1356A GLY* 1.3 58.5 + - - +
1357A PHE* 3.7 23.2 - - + -
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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