Contacts of the helix formed by residues 1330 - 1345 (chain J) in PDB entry 5IJO
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 LEU1330 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1323J SER 2.7 29.4 - - - +
1324J LEU* 3.6 9.1 + - - +
1325J ARG* 4.0 1.3 - - - -
1329J ASN* 1.3 74.1 - - - +
1331J HIS* 1.3 65.6 + - - +
1332J PHE 3.3 1.1 - - - -
1333J THR* 3.5 19.8 + - - -
1334J GLU* 3.8 9.5 + - - +
1367J LEU* 6.5 1.3 - - + -
1389J ASP* 4.6 7.1 - - + +
1392J SER* 5.1 6.9 - - - -
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Residues in contact with HIS1331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280J ASP* 4.4 22.4 - - + -
1325J ARG* 4.1 7.2 - - + +
1329J ASN* 3.3 8.1 + - - +
1330J LEU* 1.3 75.0 - - - +
1332J PHE* 1.3 64.2 + - - +
1333J THR 3.3 0.5 + - - -
1334J GLU* 3.3 5.5 + - - +
1335J ALA* 3.1 22.4 + - + +
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Residues in contact with PHE1332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319J THR* 4.4 14.1 - - - +
1322J VAL* 5.6 0.4 - - + -
1323J SER* 3.6 20.8 + - - -
1325J ARG* 5.3 3.0 - - + +
1330J LEU* 3.3 0.4 - - - +
1331J HIS* 1.3 79.1 - - + +
1333J THR* 1.3 65.1 + - - +
1335J ALA* 4.3 7.4 - - - -
1336J THR* 2.8 27.4 + - - -
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Residues in contact with THR1333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320J LEU* 4.5 13.6 - - - +
1323J SER* 2.9 25.4 - - - -
1330J LEU* 3.5 17.2 + - - -
1331J HIS 3.2 1.2 - - - -
1332J PHE* 1.3 79.1 - - - +
1334J GLU* 1.3 61.6 + - - +
1336J THR* 3.9 1.9 - - - -
1337J LEU* 3.2 21.8 + - - +
1367J LEU* 5.5 10.1 - - - -
1396J VAL* 5.0 11.8 - - - +
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Residues in contact with GLU1334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1330J LEU 3.8 6.5 + - - +
1331J HIS* 3.3 7.7 + - - +
1332J PHE 3.3 0.4 - - - -
1333J THR* 1.3 78.7 - - - +
1335J ALA* 1.3 57.5 + - - +
1337J LEU* 3.3 4.4 + - - +
1338J HIS* 2.9 31.3 + - - +
1392J SER* 5.3 8.3 - - - +
1395J GLY 5.6 1.6 - - - -
1396J VAL* 4.5 22.2 - - + +
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Residues in contact with ALA1335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1280J ASP 5.8 1.1 - - - +
1283J CYS* 4.9 18.2 - - + -
1284J VAL* 5.6 6.3 - - + +
1287J LEU* 5.3 3.5 - - - +
1331J HIS 3.1 16.8 + - - +
1332J PHE* 3.3 8.0 + - - +
1334J GLU* 1.3 77.2 - - - +
1336J THR* 1.3 62.9 + - - +
1338J HIS* 3.3 6.0 + - - +
1339J LEU* 3.0 22.7 + - - +
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Residues in contact with THR1336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1316J LEU* 3.6 33.1 - - - +
1319J THR* 4.5 7.6 - - - -
1320J LEU* 4.3 15.0 - - - -
1332J PHE 2.8 17.2 + - - -
1333J THR 3.9 2.0 - - - -
1335J ALA* 1.3 75.8 - - - +
1337J LEU* 1.3 58.9 + - - +
1339J LEU* 3.1 8.7 + - - +
1340J LEU* 2.9 27.4 + - - +
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Residues in contact with LEU1337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320J LEU* 5.8 1.0 - - - +
1333J THR 3.2 15.5 + - - +
1334J GLU* 3.8 4.9 - - - +
1336J THR* 1.3 78.4 - - - +
1338J HIS* 1.3 51.8 + - - +
1340J LEU* 3.0 9.4 + - - +
1341J LEU* 2.6 36.5 + - - +
1396J VAL* 5.1 3.8 - - + +
1400J SER* 3.6 28.3 - - - -
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Residues in contact with HIS1338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287J LEU* 5.5 7.4 - - + -
1334J GLU 2.9 17.7 + - - +
1335J ALA* 3.8 6.1 - - - +
1337J LEU* 1.3 76.1 - - - +
1339J LEU* 1.3 58.7 + - - +
1341J LEU* 3.1 9.5 + - + +
1342J THR* 2.9 28.8 + - - -
1400J SER* 6.1 0.4 - - - +
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Residues in contact with LEU1339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287J LEU* 4.7 19.0 - - + +
1316J LEU* 5.4 6.7 - - + -
1335J ALA 3.0 13.5 + - - +
1336J THR* 3.1 10.5 + - - +
1338J HIS* 1.3 75.6 - - - +
1340J LEU* 1.3 63.2 + - - +
1342J THR* 3.3 7.1 + - - +
1343J LEU* 3.2 19.2 + - - +
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Residues in contact with LEU1340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313J LEU* 6.1 5.4 - - + -
1316J LEU* 5.4 9.1 - - + +
1336J THR 2.9 12.7 + - - +
1337J LEU* 3.4 11.7 - - - +
1339J LEU* 1.3 76.3 - - - +
1341J LEU* 1.3 52.8 + - - +
1343J LEU* 3.1 8.8 + - - +
1344J ALA* 2.6 36.4 + - + +
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Residues in contact with LEU1341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337J LEU 2.6 17.9 + - - +
1338J HIS* 3.1 15.0 + - - +
1340J LEU* 1.3 70.6 - - - +
1342J THR* 1.3 66.9 + - - +
1344J ALA* 3.0 18.4 + - - +
1345J ARG* 3.2 10.4 + - - +
1399J LEU 5.5 2.9 - - - +
1400J SER* 5.4 10.8 - - - -
1402J SER* 5.7 4.9 - - - -
1403J LEU* 5.4 13.2 - - + +
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Residues in contact with THR1342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287J LEU* 5.3 4.7 - - - -
1290J ALA* 5.2 14.6 - - - -
1291J LYS* 5.3 12.6 - - - -
1294J CYS* 5.6 4.9 - - - +
1338J HIS 2.9 12.3 + - - -
1339J LEU* 3.8 9.0 - - - -
1340J LEU 3.3 0.4 - - - -
1341J LEU* 1.3 77.6 - - - +
1343J LEU* 1.3 62.0 + - - +
1345J ARG* 3.2 18.7 + - - +
1346J THR 4.2 0.9 + - - -
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Residues in contact with LEU1343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339J LEU 3.2 10.1 + - - +
1340J LEU* 3.1 12.7 + - - +
1342J THR* 1.3 78.0 - - - +
1344J ALA* 1.3 58.4 + - - +
1346J THR* 2.8 31.1 + - - +
1349J GLY* 4.6 8.7 - - - -
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Residues in contact with ALA1344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1340J LEU 2.6 17.5 + - - +
1341J LEU* 3.0 15.2 + - - +
1343J LEU* 1.3 70.3 - - - +
1345J ARG* 1.3 66.9 + - - +
1346J THR 2.9 11.4 - - - +
1347J GLN* 4.5 0.3 - - - -
1349J GLY 5.2 0.4 - - - -
1350J ALA* 3.7 19.8 - - + +
1403J LEU* 4.8 14.4 - - + +
1406J GLN* 3.6 25.7 - - + +
1407J LEU 5.7 0.2 - - - +
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Residues in contact with ARG1345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294J CYS* 6.2 3.6 - - + -
1341J LEU 3.2 8.7 + - - +
1342J THR* 3.3 14.4 - - - +
1343J LEU 3.0 0.6 - - - -
1344J ALA* 1.3 77.4 - - - +
1346J THR* 1.3 62.4 + - - +
1347J GLN* 3.1 5.2 + - - +
1406J GLN* 4.7 7.0 - - - +
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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
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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