Contacts of the helix formed by residues 1322 - 1339 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259C VAL* 5.4 1.3 - - + -
1314C LEU 3.1 19.7 + - - +
1316C ASN* 4.1 18.2 - - + +
1320C VAL* 6.3 0.2 - - + -
1321C LEU* 1.3 80.5 - - - +
1323C GLU* 1.3 65.8 + - - +
1324C ALA* 4.1 20.2 - - + +
1325C ARG* 3.3 49.5 + - + +
1326C ALA 3.7 3.1 + - - -
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Residues in contact with GLU1323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1296C LEU* 3.8 18.7 - - + +
1321C LEU* 3.6 25.4 + - + +
1322C VAL* 1.3 71.3 - - - +
1324C ALA* 1.3 63.7 + - - +
1326C ALA* 3.0 15.6 + - - +
1327C LYS* 3.1 13.5 + - - +
121E LEU* 5.0 5.8 - - - +
142E LYS* 3.4 34.7 - - + +
144E LYS* 3.1 39.4 + - - +
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Residues in contact with ALA1324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259C VAL* 3.9 24.8 - - + +
1322C VAL* 4.1 13.2 - - + +
1323C GLU* 1.3 79.7 - - - +
1325C ARG* 1.3 55.8 + - - +
1327C LYS* 4.1 1.4 - - - +
1328C ALA* 3.1 28.1 + - - +
141E ALA* 3.9 18.3 - - + +
142E LYS* 4.4 11.5 - - + +
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Residues in contact with ARG1325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259C VAL* 3.4 24.8 + - + +
1260C LEU* 5.4 3.4 - - + -
1262C ASP 4.0 12.5 + - - -
1263C LEU* 3.6 31.5 - - + +
1267C LYS* 4.0 4.8 - - - +
1313C SER 2.7 35.4 + - - -
1314C LEU* 3.6 20.9 - - + -
1315C PHE 2.9 26.3 + - - -
1316C ASN* 3.9 11.5 - - - +
1322C VAL* 3.3 32.4 + - + +
1323C GLU 3.2 0.6 - - - -
1324C ALA* 1.3 72.2 - - - +
1326C ALA* 1.3 67.8 + - - +
1328C ALA* 3.3 4.4 + - - +
1329C ILE* 3.0 27.1 + - + +
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Residues in contact with ALA1326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292C VAL* 3.7 15.9 - - + +
1296C LEU* 4.1 26.5 - - + +
1314C LEU* 3.6 23.8 - - + +
1321C LEU* 5.2 4.3 - - + -
1322C VAL 3.7 5.2 + - - +
1323C GLU* 3.0 9.0 + - - +
1325C ARG* 1.3 78.5 - - - +
1327C LYS* 1.3 57.0 + - - +
1329C ILE* 3.1 6.3 + - - +
1330C LEU* 2.9 32.6 + - - +
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Residues in contact with LYS1327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243C SER 4.4 15.0 + - - -
1244C GLU* 5.3 5.1 + - - -
1245C ASP* 5.4 5.7 - - - +
1246C SER 6.0 1.2 - - - +
1247C ARG* 2.4 38.2 - - - +
1252C LYS* 5.1 1.4 - - - +
1296C LEU* 4.5 3.7 - - + +
1323C GLU 3.1 12.5 + - - +
1324C ALA 4.1 0.4 - - - +
1326C ALA* 1.3 72.2 - - - +
1328C ALA* 1.3 56.5 + - - +
1330C LEU* 3.1 18.9 + - + +
1331C ASP* 2.7 60.0 + - - +
140E LYS* 3.4 16.5 + - - +
141E ALA 3.3 27.6 - - - +
143E GLY* 4.2 17.2 - - - +
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Residues in contact with ALA1328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256C MET* 3.4 43.0 - - + +
1259C VAL* 4.7 4.0 - - + -
1260C LEU* 4.5 17.9 - - + -
1324C ALA 3.1 20.7 + - - +
1325C ARG* 3.5 8.1 - - - +
1327C LYS* 1.3 76.0 - - - +
1329C ILE* 1.3 64.6 + - - +
1331C ASP* 3.3 2.0 + - - -
1332C PHE* 3.0 19.6 + - - +
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Residues in contact with ILE1329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260C LEU* 4.6 17.3 - - + -
1271C VAL* 3.9 27.8 - - + -
1275C LEU* 4.2 21.3 - - + -
1292C VAL* 4.4 18.8 - - + -
1310C LEU* 4.3 14.8 - - + -
1314C LEU* 4.1 16.8 - - + -
1325C ARG* 3.0 20.6 + - + +
1326C ALA 3.1 6.3 + - - +
1328C ALA* 1.3 75.3 - - - +
1330C LEU* 1.3 58.1 + - - +
1332C PHE* 3.3 6.8 + - + +
1333C LEU* 2.9 44.9 + - + +
1398C ILE* 6.5 0.2 - - + -
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Residues in contact with LEU1330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289C GLU* 3.8 24.5 - - + +
1292C VAL* 3.3 25.6 - - + +
1293C SER* 3.6 24.7 - - - +
1296C LEU* 3.7 30.7 - - + -
1326C ALA 2.9 18.7 + - - +
1327C LYS* 3.1 15.5 + - + +
1329C ILE* 1.3 76.2 - - - +
1331C ASP* 1.3 53.3 + - - +
1333C LEU* 3.2 6.2 + - + +
1334C ASP* 2.7 42.8 + - - +
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Residues in contact with ASP1331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244C GLU* 5.8 0.3 - - - +
1247C ARG* 3.3 27.2 + - - -
1252C LYS* 3.7 23.1 + - + +
1256C MET* 3.5 29.2 - - - +
1327C LYS* 2.7 50.3 + - - +
1328C ALA* 3.5 2.1 - - - +
1330C LEU* 1.3 71.7 - - - +
1332C PHE* 1.3 63.4 + - - +
1334C ASP* 3.7 9.1 - - - +
1335C ALA* 3.0 23.9 + - - +
1394C VAL* 5.1 0.3 - - - +
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Residues in contact with PHE1332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256C MET* 3.4 11.5 - - + +
1275C LEU* 3.7 44.2 - - + -
1279C LEU* 5.1 1.8 - - + -
1328C ALA 3.0 12.9 + - - +
1329C ILE* 3.5 11.0 - - + +
1331C ASP* 1.3 75.7 - - - +
1333C LEU* 1.3 65.5 + - + +
1335C ALA* 3.2 7.4 + - - +
1336C LEU* 2.8 47.3 + - + +
1394C VAL* 4.9 0.9 - - + -
1395C VAL* 3.7 46.5 - - + +
1398C ILE* 3.6 33.2 - - + -
1399C LEU* 4.1 15.7 - - + -
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Residues in contact with LEU1333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275C LEU* 4.1 11.4 - - + -
1278C CYS* 4.1 13.7 - - - -
1285C ARG* 3.0 49.3 + - + +
1288C LEU* 4.2 9.6 - - + +
1289C GLU* 4.1 34.1 - - + +
1292C VAL* 5.1 0.2 - - + -
1329C ILE* 2.9 38.2 + - + +
1330C LEU* 3.2 7.6 + - + +
1332C PHE* 1.3 90.9 - - + +
1334C ASP* 1.3 65.0 + - - +
1336C LEU* 3.3 5.5 + - + +
1337C LEU 3.0 14.0 + - - -
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Residues in contact with ASP1334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243C SER 5.7 1.0 - - - +
1244C GLU* 3.2 25.6 - - - +
1252C LYS* 5.8 3.8 + - - +
1285C ARG* 4.7 1.0 + - - +
1289C GLU* 2.6 31.7 - - - +
1330C LEU* 2.7 22.4 + - - +
1331C ASP* 3.7 11.3 - - - +
1332C PHE 3.3 0.2 - - - -
1333C LEU* 1.3 71.0 - - - +
1335C ALA* 1.3 62.1 + - - +
1337C LEU* 3.4 22.2 - - - +
1338C GLU* 3.8 12.1 + - - +
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Residues in contact with ALA1335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249C MET* 6.4 1.3 - - - -
1331C ASP 3.0 14.1 + - - +
1332C PHE 3.4 7.9 - - - +
1334C ASP* 1.3 74.9 - - - +
1336C LEU* 1.3 66.2 + - - +
1338C GLU* 2.9 25.2 + - - +
1339C LEU* 3.8 2.1 + - - +
1391C ALA* 3.4 26.2 - - + +
1394C VAL* 4.0 23.8 - - + -
1395C VAL* 4.1 5.4 - - + -
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Residues in contact with LEU1336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278C CYS* 3.8 28.9 - - + -
1279C LEU* 3.6 21.8 - - + -
1285C ARG* 4.0 15.5 - - + -
1332C PHE* 2.8 38.9 + - + +
1333C LEU* 3.3 8.3 + - + +
1335C ALA* 1.3 71.7 - - - +
1337C LEU* 1.3 61.0 + - - +
1339C LEU* 3.3 10.4 + - + +
1343C GLN* 3.3 49.1 + - + +
1395C VAL* 3.8 21.1 - - + +
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Residues in contact with LEU1337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282C GLU* 3.5 19.1 - - - +
1285C ARG* 3.3 34.0 - - - +
1289C GLU* 6.1 0.2 - - - +
1333C LEU 3.0 12.7 + - - +
1334C ASP* 3.4 15.9 - - - +
1335C ALA 3.0 0.6 + - - -
1336C LEU* 1.3 77.4 - - - +
1338C GLU* 1.3 68.1 + - - +
1339C LEU 3.2 8.8 + - - +
1343C GLN* 5.2 0.2 - - - +
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Residues in contact with GLU1338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229C ARG* 4.3 14.6 + - - -
1334C ASP 3.9 11.6 - - - +
1335C ALA* 2.9 16.4 + - - +
1337C LEU* 1.3 84.7 - - - +
1339C LEU* 1.3 62.1 + - + +
1340C SER* 3.8 2.8 + - - -
1387C ARG* 2.7 59.4 + - + +
1388C ILE* 4.6 14.8 - - + +
1391C ALA* 3.6 20.2 - - + -
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Residues in contact with LEU1339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ALA 4.7 1.6 - - - +
1335C ALA 4.0 9.2 - - - +
1336C LEU* 3.6 13.2 - - + +
1337C LEU 3.2 11.4 - - - +
1338C GLU* 1.3 77.3 - - - +
1340C SER* 1.3 59.4 + - - +
1342C GLU* 3.3 25.6 - - + +
1343C GLN* 2.8 33.4 + - + -
1346C VAL* 4.7 4.3 - - + -
1388C ILE* 3.9 6.5 - - + +
1391C ALA* 3.7 10.5 - - + -
1392C LEU* 3.5 47.6 - - + +
1395C VAL* 3.7 31.0 - - + -
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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