Contacts of the helix formed by residues 1289 - 1307 (chain A) in PDB entry 4C2A
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 SER1289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1286A SER 4.4 1.5 + - - -
1287A ARG 4.1 0.4 + - - -
1288A LEU* 1.3 77.7 - - - +
1290A GLU* 1.3 59.1 + - - +
1291A ALA* 3.7 7.6 + - - +
1292A GLU* 2.9 39.8 + - - +
1293A PHE* 2.9 27.0 + - - +
1349A TYR* 3.6 4.7 - - - -
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Residues in contact with GLU1290 (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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1289A SER* 1.3 74.9 - - - +
1291A ALA* 1.3 61.4 + - - +
1293A PHE* 3.3 3.3 + - - +
1294A GLU* 3.1 33.6 + - + +
1349A TYR* 3.7 46.1 - - + +
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Residues in contact with ALA1291 (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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1289A SER* 3.3 6.6 + - - +
1290A GLU* 1.3 79.0 - - - +
1292A GLU* 1.3 63.3 + - + +
1294A GLU* 3.3 18.7 + - - +
1295A VAL* 3.3 17.2 + - - +
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Residues in contact with GLU1292 (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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1287A ARG 4.0 5.2 - - - +
1288A LEU* 3.6 14.5 - - + +
1289A SER* 2.9 39.6 + - - +
1291A ALA* 1.3 75.5 - - + +
1293A PHE* 1.3 65.3 + - - +
1295A VAL* 3.1 8.0 + - + +
1296A LEU* 3.0 18.0 + - - +
1442A SER* 5.7 4.5 - - - -
1443A VAL* 3.7 37.9 - - + +
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Residues in contact with PHE1293 (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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1282A LEU* 4.3 13.9 - - + -
1283A ASP 3.6 25.8 - - - -
1284A GLY* 4.7 2.9 - - - -
1285A SER 6.1 0.2 - - - -
1288A LEU* 4.5 8.5 - - + +
1289A SER 2.9 17.9 + - - +
1290A GLU 3.5 3.1 - - - +
1292A GLU* 1.3 77.1 - - - +
1294A GLU* 1.3 59.6 + - - +
1296A LEU* 3.2 21.3 + - + +
1297A LYS* 2.9 42.8 + - + +
1320A GLU* 4.2 10.3 - - + -
1347A VAL* 3.5 39.5 - - + -
1348A LYS 3.8 11.9 - - - -
1349A TYR* 3.5 36.1 - + + -
1350A ALA 5.4 0.2 - - - -
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Residues in contact with GLU1294 (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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1290A GLU* 3.1 26.3 + - + +
1291A ALA* 3.4 11.7 - - - +
1292A GLU 3.2 0.2 - - - -
1293A PHE* 1.3 80.1 - - - +
1295A VAL* 1.3 56.4 + - + +
1297A LYS* 2.9 36.1 + - - +
1298A ALA* 2.9 29.3 + - - +
1345A SER 4.3 3.5 - - - +
1349A TYR* 5.7 1.6 - - - +
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Residues in contact with VAL1295 (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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1291A ALA 3.4 14.8 - - - +
1292A GLU* 3.1 10.0 + - + +
1294A GLU* 1.3 74.5 - - + +
1296A LEU* 1.3 64.7 + - - +
1298A ALA* 3.4 7.0 + - + +
1299A PHE* 3.0 22.5 + - - +
1443A VAL* 3.4 42.6 - - + +
1444A ASP* 4.9 8.7 - - - +
1446A LEU* 4.3 3.6 - - + -
1447A GLU* 6.6 0.2 - - + -
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Residues in contact with LEU1296 (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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1282A LEU* 4.3 26.9 - - + -
1283A ASP* 4.3 9.0 - - + +
1288A LEU* 3.8 24.7 - - + -
1292A GLU 3.0 12.0 + - - +
1293A PHE* 3.4 22.2 - - + +
1295A VAL* 1.3 77.6 - - - +
1297A LYS* 1.3 61.7 + - - +
1299A PHE* 3.2 7.9 + - + +
1300A VAL* 3.1 22.1 + - - +
1384A LEU* 4.0 35.2 - - + -
1416A ILE* 4.2 8.7 - - + -
1443A VAL* 4.9 1.6 - - + -
1446A LEU* 3.8 23.5 - - + +
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Residues in contact with LYS1297 (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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1282A LEU* 4.3 13.0 - - + -
1293A PHE* 2.9 35.1 + - + +
1294A GLU* 2.9 40.0 + - - +
1295A VAL 3.3 0.2 - - - -
1296A LEU* 1.3 73.6 - - - +
1298A ALA* 1.3 65.3 + - - +
1300A VAL* 3.2 9.9 + - - +
1301A VAL* 3.0 28.0 + - - +
1344A ALA 3.5 24.4 - - - +
1345A SER* 2.7 26.2 + - - +
1346A GLN* 3.9 3.2 - - - +
1347A VAL* 2.9 33.1 + - + +
1349A TYR 5.5 0.4 - - - +
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Residues in contact with ALA1298 (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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1294A GLU 2.9 18.3 + - - +
1295A VAL* 3.7 7.9 - - + +
1296A LEU 3.3 0.2 - - - -
1297A LYS* 1.3 75.8 - - - +
1299A PHE* 1.3 57.4 + - - +
1301A VAL* 3.5 7.8 + - - +
1302A ASP* 2.9 39.3 + - - +
1345A SER* 6.4 0.4 - - - -
2470A CA 4.2 0.7 - - - -
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Residues in contact with PHE1299 (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 VAL 3.0 14.0 + - - +
1296A LEU* 3.3 16.2 - - + +
1298A ALA* 1.3 74.9 - - - +
1300A VAL* 1.3 69.0 + - + +
1302A ASP* 3.3 10.2 + - - +
1303A MET* 3.0 54.9 + - - +
1382A LEU* 4.4 6.1 - - + -
1384A LEU* 3.9 23.1 - - + -
1414A VAL* 5.8 0.2 - - + -
1446A LEU* 3.6 57.0 - - + -
1447A GLU* 4.6 0.9 - - - +
1450A ARG* 3.8 26.5 - - + +
1453A ILE* 4.2 16.6 - - + -
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Residues in contact with VAL1300 (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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1280A PHE* 3.9 41.2 - - + -
1282A LEU* 3.6 32.8 - - + -
1296A LEU 3.1 14.3 + - - +
1297A LYS* 3.2 8.9 + - - +
1299A PHE* 1.3 83.2 - - + +
1301A VAL* 1.3 65.9 + - - +
1303A MET* 3.3 3.8 + - - +
1304A MET* 3.0 38.5 + - - +
1318A VAL* 4.6 4.9 - - + -
1344A ALA* 4.3 12.6 - - + +
1384A LEU* 4.3 2.2 - - + -
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Residues in contact with VAL1301 (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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1297A LYS 3.0 14.5 + - - +
1298A ALA* 3.7 9.0 - - - +
1300A VAL* 1.3 74.5 - - - +
1302A ASP* 1.3 66.3 + - - +
1304A MET* 3.2 10.1 + - - +
1305A GLU* 3.0 41.2 + - - +
1341A ARG* 3.7 37.0 - - + +
1344A ALA* 4.2 7.2 - - + -
1345A SER* 3.9 22.4 - - - +
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Residues in contact with ASP1302 (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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1268A HIS* 3.2 27.9 + - + -
1298A ALA* 2.9 24.1 + - - +
1299A PHE* 3.4 11.6 - - - +
1300A VAL 3.2 0.2 - - - -
1301A VAL* 1.3 77.1 - - - +
1303A MET* 1.3 58.2 + - - +
1305A GLU* 3.1 8.2 + - - +
1306A GLN* 2.9 28.2 + - - +
1447A GLU* 5.5 1.2 - - - +
1450A ARG* 3.4 35.5 + - - +
2468A CAC 5.6 1.8 - - - +
2470A CA 2.4 27.5 - - - -
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Residues in contact with MET1303 (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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1278A LEU* 4.3 1.1 - - + -
1280A PHE* 3.9 14.1 - - + -
1299A PHE* 3.0 47.5 + - + +
1300A VAL 3.3 7.8 + - - +
1302A ASP* 1.3 76.5 - - - +
1304A MET* 1.3 56.7 + - - +
1306A GLN* 3.8 6.9 - - - +
1307A LEU* 2.9 44.1 + - + +
1382A LEU* 3.7 21.5 - - + -
1450A ARG* 4.0 10.3 - - + -
1453A ILE* 4.2 9.6 - - + -
1454A VAL* 3.9 24.2 - - + -
1457A LEU* 3.7 30.3 - - + -
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Residues in contact with MET1304 (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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1280A PHE* 3.9 19.1 - - + -
1300A VAL* 3.0 25.0 + - - +
1301A VAL* 3.2 12.1 + - - +
1303A MET* 1.3 76.0 - - - +
1305A GLU* 1.3 60.2 + - - +
1308A ARG 3.3 2.4 + - - -
1309A VAL* 3.0 49.7 + - + +
1316A VAL* 4.2 15.7 - - + -
1318A VAL* 4.9 4.9 - - - -
1329A ILE* 4.9 1.3 - - + -
1340A LEU* 3.8 39.9 - - + +
1341A ARG* 3.8 17.2 - - + +
1344A ALA* 3.9 24.5 - - - -
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Residues in contact with GLU1305 (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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1266A PRO* 3.5 26.1 - - - +
1268A HIS* 2.6 37.1 + - + +
1271A TYR* 3.2 16.9 - - + -
1301A VAL* 3.0 31.6 + - - +
1302A ASP* 3.1 10.7 + - - +
1304A MET* 1.3 75.3 - - - +
1306A GLN* 1.3 65.5 + - - +
1308A ARG* 3.1 17.6 + - - +
1341A ARG* 3.6 29.4 + - - +
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Residues in contact with GLN1306 (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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1268A HIS* 3.6 25.0 - - + +
1269A ASP 4.6 0.4 - - - +
1270A PHE* 3.0 44.7 + - - +
1271A TYR* 3.3 14.3 - - - +
1272A CYS* 3.0 26.2 + - - -
1302A ASP 2.9 11.9 + - - +
1303A MET 3.4 4.7 + - - +
1305A GLU* 1.3 76.2 - - - +
1307A LEU* 1.3 58.9 + - - +
1308A ARG 3.2 2.5 + - - -
1450A ARG* 2.9 30.5 + - - +
1451A ASP* 3.5 18.4 + - - +
1454A VAL* 3.4 28.6 - - + +
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Residues in contact with LEU1307 (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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1272A CYS* 3.4 38.1 - - - +
1273A SER* 4.5 2.1 - - - -
1274A ARG* 5.0 5.5 + - + -
1276A LEU* 4.3 15.0 - - + -
1278A LEU* 3.5 31.4 - - + -
1303A MET* 2.9 29.2 + - + +
1306A GLN* 1.3 74.9 - - - +
1308A ARG* 1.3 70.6 + - - +
1309A VAL* 3.3 13.1 + - + -
1314A VAL* 3.6 18.8 - - + +
1454A VAL* 4.2 15.5 - - + -
1457A LEU* 4.0 19.7 - - + -
1458A CYS* 4.4 1.6 - - - -
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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