Contacts of the helix formed by residues 1339 - 1357 (chain A) in PDB entry 4ABL
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 HIS1339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1337A LYS 4.1 9.6 - - - -
1338A GLN* 1.3 76.4 - - - +
1340A PRO* 1.3 73.6 - - + +
1341A ASP* 3.3 18.3 + - - +
1342A LYS* 3.1 26.3 + - + +
1343A VAL* 3.0 21.4 + - - +
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Residues in contact with PRO1340 (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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1333A THR* 3.9 19.1 - - + -
1338A GLN 3.6 6.3 - - - +
1339A HIS* 1.3 85.5 - - + +
1341A ASP* 1.3 56.5 + - - +
1343A VAL* 3.3 1.6 + - - +
1344A ALA* 2.9 31.0 + - - +
1375A VAL* 3.8 37.9 - - + -
1378A VAL* 3.8 17.7 - - + +
1379A PHE* 4.5 2.3 - - - -
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Residues in contact with ASP1341 (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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1339A HIS* 3.3 22.5 + - - +
1340A PRO* 1.3 77.2 - - - +
1342A LYS* 1.3 74.9 + - - +
1344A ALA* 3.5 2.3 + - - +
1345A GLU* 3.1 23.4 + - - +
1378A VAL* 3.7 19.4 - - + +
1382A ASN* 4.4 3.7 + - - +
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Residues in contact with LYS1342 (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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1338A GLN* 5.8 3.4 - - - +
1339A HIS* 3.1 29.3 + - + +
1341A ASP* 1.3 89.7 + - - +
1343A VAL* 1.3 62.2 + - + +
1345A GLU* 3.4 6.2 + - - +
1346A ALA* 3.0 29.8 + - - +
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Residues in contact with VAL1343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307A VAL* 4.1 10.7 - - + +
1330A ALA 4.0 10.1 - - - -
1331A ILE 3.2 29.8 - - - +
1333A THR* 3.7 15.0 - - + -
1338A GLN* 3.7 25.4 - - + +
1339A HIS 3.0 16.5 + - - +
1340A PRO 3.6 7.0 - - - +
1342A LYS* 1.3 76.8 - - + +
1344A ALA* 1.3 63.4 + - - +
1346A ALA* 3.2 6.5 + - - +
1347A ILE* 2.9 43.4 + - + +
1379A PHE* 4.1 7.0 - - + -
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Residues in contact with ALA1344 (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 PRO 2.9 17.7 + - - +
1341A ASP 3.8 4.0 - - - +
1343A VAL* 1.3 76.1 - - - +
1345A GLU* 1.3 63.4 + - - +
1347A ILE* 3.4 0.5 + - - +
1348A ILE* 3.1 30.3 + - + +
1378A VAL* 4.5 4.9 - - + -
1379A PHE* 3.8 46.2 - - + -
1382A ASN* 4.1 14.1 - - + +
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Residues in contact with GLU1345 (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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1341A ASP 3.1 15.7 + - - +
1342A LYS* 3.7 7.2 - - - +
1344A ALA* 1.3 79.6 - - - +
1346A ALA* 1.3 56.8 + - - +
1349A ASP* 2.9 48.4 + - - +
1382A ASN* 2.8 20.0 + - - +
1385A LYS* 2.7 33.0 + - - -
1386A ARG* 3.1 22.7 + - - +
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Residues in contact with ALA1346 (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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1307A VAL* 3.8 13.2 - - + -
1308A LYS* 3.7 31.7 - - + +
1342A LYS 3.0 17.5 + - - +
1343A VAL* 3.2 4.5 + - - +
1345A GLU* 1.3 74.6 - - - +
1347A ILE* 1.3 65.1 + - - +
1349A ASP* 3.4 7.0 + - - +
1350A ALA* 3.0 24.1 + - - +
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Residues in contact with ILE1347 (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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1229A PHE* 4.3 23.6 - - + -
1307A VAL* 3.7 14.6 - - + -
1311A VAL* 3.9 19.0 - - + +
1328A LEU* 3.9 29.6 - - + -
1329A PRO 4.2 9.0 - - - +
1331A ILE* 4.3 4.0 - - + +
1343A VAL* 2.9 26.8 + - + +
1344A ALA 3.9 3.4 - - - +
1346A ALA* 1.3 75.5 - - - +
1348A ILE* 1.3 64.6 + - - +
1350A ALA* 3.2 5.0 + - - +
1351A ILE* 3.2 27.2 + - + +
1368A VAL* 4.4 4.7 - - + -
1379A PHE* 3.8 29.2 - - + -
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Residues in contact with ILE1348 (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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1209A TYR* 3.7 7.4 - - + +
1222A MET* 6.0 1.3 - - - -
1224A ILE* 3.9 18.8 - - + -
1229A PHE* 3.8 33.9 - - + -
1344A ALA* 3.1 19.0 + - + +
1347A ILE* 1.3 75.7 - - + +
1349A ASP* 1.3 66.7 + - - +
1351A ILE* 3.2 7.6 + - - +
1352A GLU* 2.9 20.6 + - - +
1379A PHE* 4.8 4.0 - - + +
1382A ASN* 3.6 28.9 - - + +
1383A MET* 4.2 13.7 - - + +
1386A ARG* 3.5 31.4 - - - +
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Residues in contact with ASP1349 (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 LYS* 4.1 22.8 + - + +
1345A GLU* 2.9 37.0 + - - +
1346A ALA* 3.7 6.1 - - - +
1347A ILE 3.3 0.2 - - - -
1348A ILE* 1.3 76.4 - - - +
1350A ALA* 1.3 62.1 + - - +
1352A GLU* 3.3 7.1 + - - +
1353A ASP* 3.0 29.1 + - - +
1386A ARG* 2.8 28.3 + - - +
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Residues in contact with ALA1350 (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 LYS* 3.7 25.0 - - + +
1311A VAL* 3.6 28.0 - - + -
1312A SER* 3.8 11.5 + - - +
1315A LEU* 3.9 3.2 - - - +
1346A ALA 3.0 14.4 + - - +
1347A ILE 3.5 9.2 - - - +
1348A ILE 3.2 0.2 - - - -
1349A ASP* 1.3 75.7 - - - +
1351A ILE* 1.3 61.4 + - - +
1353A ASP* 3.4 3.0 + - - +
1354A PHE* 3.1 24.3 + - - +
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Residues in contact with ILE1351 (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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1224A ILE* 4.0 26.0 - - + -
1227A ILE* 4.0 30.1 - - + -
1229A PHE* 3.4 39.5 - - + -
1311A VAL* 4.5 5.4 - - + -
1315A LEU* 4.1 18.8 - - + -
1347A ILE* 3.2 18.8 + - + +
1348A ILE* 3.2 7.0 + - - +
1350A ALA* 1.3 73.5 - - - +
1352A GLU* 1.3 66.0 + - - +
1354A PHE* 3.3 2.3 + - - +
1355A VAL* 3.0 22.7 + - + +
1366A VAL* 3.9 19.1 - - + -
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Residues in contact with GLU1352 (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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1208A PHE* 4.0 28.0 - - + -
1209A TYR* 2.6 46.2 + - + +
1224A ILE* 4.1 10.2 - - + +
1348A ILE 2.9 8.8 + - - +
1349A ASP* 3.6 11.2 - - - +
1351A ILE* 1.3 78.5 - - - +
1353A ASP* 1.3 65.3 + - - +
1355A VAL* 3.3 2.4 + - - +
1356A GLN* 2.8 32.7 + - + +
1386A ARG* 3.9 6.5 + - - -
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Residues in contact with ASP1353 (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 LYS* 2.6 35.4 + - - -
1312A SER* 5.5 2.9 - - - +
1349A ASP* 3.0 20.5 + - - +
1350A ALA* 3.8 4.9 - - - +
1351A ILE 3.3 0.2 - - - -
1352A GLU* 1.3 86.8 - - - +
1354A PHE* 1.3 57.5 + - - +
1356A GLN* 3.2 14.8 + - - +
1357A LYS* 3.0 55.2 + - - +
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Residues in contact with PHE1354 (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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1227A ILE* 3.9 18.6 - - + -
1312A SER* 5.4 3.1 - - - +
1315A LEU* 3.7 46.4 - - + -
1316A GLN* 4.4 4.9 - - + -
1319A GLU* 3.3 36.3 - - + -
1350A ALA 3.1 16.8 + - - +
1351A ILE 3.3 3.3 + - - +
1353A ASP* 1.3 76.9 - - - +
1355A VAL* 1.3 63.7 + - - +
1357A LYS* 3.5 4.3 + - - -
1358A GLY 3.5 1.9 + - - -
1359A SER* 3.1 55.8 + - - -
1360A ALA* 3.4 25.6 - - + -
1363A VAL* 4.3 4.3 - - + -
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Residues in contact with VAL1355 (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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1208A PHE* 3.8 19.6 - - + -
1224A ILE* 3.5 23.1 - - + +
1225A GLY* 3.7 24.5 - - - +
1226A SER* 4.7 2.7 - - - +
1227A ILE* 3.8 24.5 - - + -
1351A ILE 3.0 19.3 + - - +
1352A GLU* 3.7 5.2 - - - +
1354A PHE* 1.3 73.9 - - - +
1356A GLN* 1.3 65.2 - - - +
1358A GLY* 2.9 16.5 + - - -
1360A ALA* 4.3 12.3 - - + +
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Residues in contact with GLN1356 (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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1208A PHE* 3.6 33.8 - - + -
1352A GLU* 2.8 24.1 + - + +
1353A ASP* 3.7 17.8 + - - +
1355A VAL* 1.3 73.1 - - - +
1357A LYS* 1.3 83.9 + - - +
1358A GLY 3.3 1.2 + - - -
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Residues in contact with LYS1357 (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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1353A ASP* 3.0 44.3 + - - +
1354A PHE* 3.9 2.7 - - - +
1355A VAL 3.2 0.4 - - - -
1356A GLN* 1.3 91.6 - - - +
1358A GLY* 1.3 60.6 + - - +
1359A SER* 3.5 17.6 + - - +
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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