Contacts of the helix formed by residues 1322 - 1339 (chain H) in PDB entry 5TJ4
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 VAL1322 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1239B LYS* 6.4 0.2 - - - -
1259H VAL* 5.4 1.6 - - + -
1314H LEU* 3.1 19.5 + - - +
1316H ASN* 4.1 18.4 - - + +
1321H LEU* 1.3 78.0 - - - +
1323H GLU* 1.3 67.9 + - - +
1324H ALA* 4.1 19.5 - - + +
1325H ARG* 3.3 50.3 + - + +
1326H ALA 3.7 2.8 + - - -
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Residues in contact with GLU1323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238B GLY* 6.0 0.6 - - - -
1239B LYS* 5.0 14.7 - - + +
1244B GLU* 3.4 27.4 - - + -
1296H LEU* 4.0 24.1 - - + +
1321H LEU* 3.7 14.3 + - + +
1322H VAL* 1.3 70.5 - - - +
1324H ALA* 1.3 58.6 + - - +
1326H ALA* 3.1 6.1 + - - +
1327H LYS* 2.9 27.5 + - - +
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Residues in contact with ALA1324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243B SER 5.4 1.1 - - - +
1244B GLU* 3.4 28.0 + - - +
1245B ASP* 4.2 8.0 - - - +
1259H VAL* 3.9 25.3 - - + +
1322H VAL* 3.3 13.8 - - + +
1323H GLU* 1.3 78.9 - - - +
1325H ARG* 1.3 55.4 + - - +
1327H LYS* 3.6 2.1 + - - +
1328H ALA* 3.0 28.8 + - - +
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Residues in contact with ARG1325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259H VAL* 3.4 24.2 + - + +
1260H LEU* 5.3 5.3 - - + +
1262H ASP 4.0 16.4 + - - -
1263H LEU* 4.3 20.2 - - + +
1264H THR 5.9 0.2 - - - +
1267H LYS* 5.9 1.8 - - - +
1313H SER* 2.7 35.4 + - - +
1314H LEU* 3.6 19.5 - - + -
1315H PHE 2.9 26.5 + - - -
1316H ASN* 3.9 11.3 - - - +
1322H VAL* 3.3 33.3 + - + +
1323H GLU 3.2 0.4 - - - -
1324H ALA* 1.3 74.2 - - - +
1326H ALA* 1.3 66.2 + - - +
1328H ALA* 3.3 4.8 + - - +
1329H ILE* 3.0 27.1 + - + +
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Residues in contact with ALA1326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292H VAL* 3.7 18.1 - - + +
1295H VAL* 5.9 0.2 - - + -
1296H LEU* 4.1 26.0 - - + +
1314H LEU* 3.5 22.9 - - + +
1321H LEU* 5.2 3.8 - - + -
1322H VAL 3.7 4.3 + - - +
1323H GLU* 3.1 9.2 + - - +
1325H ARG* 1.3 77.3 - - - +
1327H LYS* 1.3 64.1 + - - +
1329H ILE* 3.2 4.1 + - - +
1330H LEU* 2.9 29.8 + - - +
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Residues in contact with LYS1327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244B GLU* 3.7 17.0 - - + +
1245B ASP* 5.5 4.0 - - + -
1244H GLU* 4.8 13.5 - - + +
1296H LEU* 4.5 5.5 - - + +
1323H GLU 2.9 15.6 + - - +
1324H ALA 3.7 5.4 - - - +
1326H ALA* 1.3 75.4 - - - +
1328H ALA* 1.3 56.3 + - - +
1330H LEU* 3.1 13.9 + - - +
1331H ASP* 2.9 40.1 + - - +
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Residues in contact with ALA1328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256H MET* 3.4 43.4 - - + +
1259H VAL* 4.6 3.8 - - + -
1260H LEU* 4.5 18.2 - - + -
1324H ALA 3.0 19.2 + - - +
1325H ARG* 3.5 7.9 - - - +
1327H LYS* 1.3 76.1 - - - +
1329H ILE* 1.3 63.6 + - - +
1331H ASP* 3.2 2.9 + - - -
1332H PHE* 3.0 20.0 + - - +
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Residues in contact with ILE1329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260H LEU* 4.5 17.3 - - + -
1271H VAL* 4.0 28.9 - - + -
1275H LEU* 4.2 20.4 - - + -
1292H VAL* 4.3 18.6 - - + -
1310H LEU* 4.3 14.4 - - + -
1314H LEU* 4.1 17.0 - - + -
1325H ARG* 3.0 20.2 + - + +
1326H ALA 3.6 6.1 - - - +
1328H ALA* 1.3 76.1 - - - +
1330H LEU* 1.3 59.9 + - - +
1332H PHE* 3.3 6.0 + - + +
1333H LEU* 2.9 44.6 + - + +
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Residues in contact with LEU1330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243H SER* 3.7 23.8 + - - +
1244H GLU* 4.4 9.2 - - + +
1289H GLU* 3.8 24.5 - - + +
1292H VAL* 3.7 22.0 - - + -
1293H SER* 3.6 27.4 - - - +
1296H LEU* 3.7 27.8 - - + -
1326H ALA 2.9 21.6 + - - +
1327H LYS* 3.5 7.9 - - - +
1329H ILE* 1.3 75.5 - - - +
1331H ASP* 1.3 53.6 + - - +
1333H LEU* 3.2 6.1 + - + +
1334H ASP* 2.7 34.8 + - - +
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Residues in contact with ASP1331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243H SER* 4.5 1.6 + - - -
1244H GLU* 4.0 23.7 - - - +
1252H LYS* 5.4 6.6 - - - +
1256H MET* 3.5 32.9 - - - +
1327H LYS* 2.9 25.1 + - - +
1328H ALA* 3.2 3.7 + - - +
1330H LEU* 1.3 72.8 - - - +
1332H PHE* 1.3 64.3 + - - +
1334H ASP* 3.5 7.4 + - - +
1335H ALA* 3.0 23.7 + - - +
1394H VAL* 5.1 0.5 - - - +
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Residues in contact with PHE1332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256H MET* 3.3 12.0 - - + +
1275H LEU* 3.7 43.1 - - + -
1279H LEU* 5.1 1.6 - - + -
1328H ALA 3.0 13.5 + - - +
1329H ILE* 3.5 10.1 - - + +
1330H LEU 3.3 0.2 - - - -
1331H ASP* 1.3 76.9 - - - +
1333H LEU* 1.3 63.3 + - + +
1335H ALA* 3.2 9.3 + - - +
1336H LEU* 2.8 48.0 + - + +
1394H VAL* 4.9 1.1 - - + -
1395H VAL* 3.6 46.1 - - + +
1398H ILE* 3.6 32.3 - - + -
1399H LEU* 4.0 16.2 - - + -
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Residues in contact with LEU1333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275H LEU* 4.1 8.7 - - + -
1278H CYS* 4.1 7.9 - - - -
1285H ARG* 3.0 49.7 + - + +
1288H LEU* 3.4 34.3 - - + +
1289H GLU* 4.1 21.5 - - + -
1329H ILE* 2.9 34.9 + - + +
1330H LEU* 3.7 8.7 - - + +
1332H PHE* 1.3 89.2 - - + +
1334H ASP* 1.3 61.1 + - - +
1336H LEU* 3.3 4.3 + - + +
1337H LEU 3.0 18.4 + - - -
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Residues in contact with ASP1334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241H LEU* 5.4 2.5 - - + -
1242H GLY* 5.0 12.8 - - - -
1243H SER* 4.5 10.5 - - - +
1285H ARG* 4.7 0.7 - - - +
1330H LEU 2.7 22.4 + - - +
1331H ASP* 3.6 9.6 - - - +
1332H PHE 3.3 0.2 - - - -
1333H LEU* 1.3 72.5 - - - +
1335H ALA* 1.3 57.8 + - - +
1337H LEU* 2.8 41.0 - - + +
1338H GLU* 3.9 4.2 + - - +
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Residues in contact with ALA1335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331H ASP 3.0 14.0 + - - +
1332H PHE 3.2 8.0 + - - +
1334H ASP* 1.3 74.1 - - - +
1336H LEU* 1.3 64.7 + - - +
1338H GLU* 2.9 26.0 + - - +
1339H LEU* 3.7 2.1 + - - +
1391H ALA* 3.4 27.1 - - - +
1394H VAL* 4.0 24.2 - - + -
1395H VAL* 4.1 5.4 - - + -
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Residues in contact with LEU1336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278H CYS* 3.8 29.2 - - + -
1279H LEU* 3.6 22.0 - - + -
1285H ARG* 4.0 15.5 - - + -
1332H PHE* 2.8 38.4 + - + +
1333H LEU* 3.3 7.8 + - + +
1335H ALA* 1.3 73.6 - - - +
1337H LEU* 1.3 61.3 + - - +
1339H LEU* 3.3 10.5 + - + +
1343H GLN* 3.3 48.5 + - + +
1395H VAL* 3.8 20.6 - - + +
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Residues in contact with LEU1337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241H LEU* 3.6 43.1 - - + -
1242H GLY 4.8 1.3 - - - +
1282H GLU* 5.0 7.6 - - - +
1285H ARG* 3.9 34.0 - - - +
1333H LEU 3.0 7.9 + - - -
1334H ASP* 2.8 24.9 - - + +
1335H ALA 3.1 1.2 + - - -
1336H LEU* 1.3 76.8 - - - +
1338H GLU* 1.3 95.7 - - - +
1339H LEU 3.2 8.8 - - - +
1343H GLN* 5.2 0.2 - - - +
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Residues in contact with GLU1338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229H ARG* 2.4 35.9 + - - -
1334H ASP 4.0 7.0 - - - +
1335H ALA* 2.9 16.4 + - - +
1337H LEU* 1.3 97.5 - - - +
1339H LEU* 1.3 57.8 + - + +
1340H SER* 5.0 0.2 - - - -
1387H ARG* 4.7 14.5 - - - +
1388H ILE* 3.8 16.6 - - + +
1391H ALA* 3.6 20.9 - - + -
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Residues in contact with LEU1339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335H ALA 4.0 6.3 - - - +
1336H LEU* 3.3 15.4 - - + +
1337H LEU 3.1 10.5 - - - +
1338H GLU* 1.3 78.1 - - - +
1340H SER* 1.3 57.8 + - - +
1342H GLU* 3.9 13.9 - - + +
1343H GLN* 2.8 35.4 + - + -
1346H VAL* 4.6 5.6 - - + -
1388H ILE* 3.9 13.0 - - + +
1391H ALA* 3.7 10.1 - - + -
1392H LEU* 3.5 50.3 - - + +
1395H VAL* 3.7 32.1 - - + -
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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