Contacts of the helix formed by residues 1307 - 1319 (chain A) in PDB entry 5JH5
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 THR1307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283A ASP* 2.1 41.6 + - - +
1304A LYS 6.0 0.4 - - - +
1305A GLN 5.0 3.8 - - - +
1306A VAL* 1.3 81.7 - - - +
1308A LYS* 1.3 65.0 + - - +
1309A GLU* 3.9 12.0 + - - -
1310A GLY* 2.9 16.3 + - - -
1311A CYS* 3.2 15.4 + - - -
1330A LYS* 4.0 1.1 - - - +
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Residues in contact with LYS1308 (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 THR* 1.3 71.9 - - - +
1309A GLU* 1.3 59.9 + - - +
1311A CYS* 3.4 10.6 + - - +
1312A GLU* 3.1 43.8 + - - +
1326A GLN* 3.6 25.8 - - - +
1329A GLU* 4.5 27.4 + - - +
1330A LYS* 4.2 11.7 - - + +
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Residues in contact with GLU1309 (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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1283A ASP* 4.8 0.5 - - - +
1307A THR* 3.0 10.2 + - - +
1308A LYS* 1.3 76.1 - - - +
1310A GLY* 1.3 71.6 + - - +
1312A GLU* 3.2 17.1 + - + +
1313A GLN* 3.0 36.7 + - - +
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Residues in contact with GLY1310 (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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1283A ASP* 3.4 23.1 - - - -
1286A LEU* 3.1 16.9 - - - +
1307A THR* 2.9 12.3 + - - -
1309A GLU* 1.3 82.2 + - - +
1311A CYS* 1.3 60.5 + - - +
1313A GLN* 3.3 10.8 + - - +
1314A PHE 3.1 15.8 + - - -
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Residues in contact with CYS1311 (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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1286A LEU* 3.9 13.0 - - - -
1300A LEU* 4.8 2.5 - - - -
1306A VAL* 4.3 11.0 - - - -
1307A THR 3.2 17.6 + - - -
1308A LYS* 3.5 4.5 - - - +
1309A GLU 3.1 0.6 - - - -
1310A GLY* 1.3 73.2 - - - +
1312A GLU* 1.3 57.4 + - - +
1313A GLN 3.1 1.3 - - - -
1314A PHE* 2.7 21.3 + - - +
1315A ILE* 2.9 15.7 + - - +
1326A GLN* 2.8 25.1 - - - +
1330A LYS* 4.1 34.5 - - - -
1332A LEU* 4.0 13.9 - - + +
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Residues in contact with GLU1312 (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* 3.1 40.3 + - - +
1309A GLU* 3.2 17.3 + - - +
1311A CYS* 1.3 78.6 - - - +
1313A GLN* 1.3 55.7 + - - +
1315A ILE* 3.4 16.1 + - + +
1316A ALA* 3.0 28.1 + - - +
1326A GLN* 3.6 10.1 + - - +
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Residues in contact with GLN1313 (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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1309A GLU* 3.0 29.9 + - - +
1310A GLY* 3.5 12.3 - - - +
1311A CYS 3.1 0.2 - - - -
1312A GLU* 1.3 74.1 - - - +
1314A PHE* 1.3 61.7 + - - +
1316A ALA* 4.2 6.3 - - + -
1317A GLU* 2.5 59.3 + - + +
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Residues in contact with PHE1314 (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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1286A LEU* 3.3 40.8 - - + -
1289A PHE* 3.6 11.2 - - + -
1290A LYS* 3.3 37.6 - - + +
1295A ILE* 4.8 0.7 - - + -
1298A ILE* 4.0 24.0 - - + -
1310A GLY 3.1 11.4 + - - +
1311A CYS* 2.7 16.5 + - - +
1313A GLN* 1.3 69.9 - - - +
1315A ILE* 1.3 66.1 + - - +
1317A GLU* 3.9 2.8 - - - -
1318A MSE 3.0 42.3 + - + +
1324A PHE* 3.8 34.1 - + + -
1332A LEU* 4.0 17.0 - - + -
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Residues in contact with ILE1315 (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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1311A CYS 2.9 12.7 + - - +
1312A GLU* 3.7 15.7 - - + +
1314A PHE* 1.3 74.9 - - + +
1316A ALA* 1.3 56.7 + - - +
1318A MSE 3.9 0.6 - - - +
1319A SER* 3.0 35.8 + - - -
1322A VAL 4.9 0.2 - - - +
1323A GLN* 4.5 3.6 - - - +
1324A PHE* 3.0 44.1 + - + +
1325A GLY* 4.1 1.6 - - - -
1326A GLN* 3.6 43.3 - - + +
1332A LEU* 4.0 11.7 - - + -
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Residues in contact with ALA1316 (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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1312A GLU 3.0 18.0 + - - +
1313A GLN* 3.8 7.9 - - + +
1314A PHE 3.1 0.4 - - - -
1315A ILE* 1.3 73.4 - - - +
1317A GLU* 1.3 60.9 + - + +
1318A MSE 3.0 8.2 + - - -
1319A SER* 2.9 23.1 + - - -
1320A VAL* 4.5 2.9 + - - +
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Residues in contact with GLU1317 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1290A LYS* 2.3 53.5 + - + +
1313A GLN* 2.5 53.3 + - + +
1314A PHE* 5.8 0.2 - - - -
1316A ALA* 1.3 75.1 - - + +
1318A MSE 1.3 58.6 + - - +
1320A VAL* 5.2 3.8 + - - +
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Residues in contact with MSE1318 (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 PHE 4.0 3.8 - - - +
1290A LYS* 3.7 51.1 - - + +
1292A CYS 3.8 18.4 - - - +
1295A ILE* 4.6 3.4 - - + -
1314A PHE* 3.0 25.0 + - + +
1315A ILE 4.2 0.7 - - - +
1316A ALA 3.0 1.0 - - - -
1317A GLU* 1.3 77.5 - - - +
1319A SER* 1.3 53.5 + - - +
1320A VAL* 3.0 9.2 + - - -
1321A SER* 3.2 7.3 + - - -
1322A VAL* 2.8 44.5 + - + +
1324A PHE* 3.6 38.8 - - + -
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Residues in contact with SER1319 (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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1315A ILE* 3.0 18.2 + - - -
1316A ALA* 2.9 22.3 + - - -
1318A MSE 1.3 73.7 - - - +
1320A VAL* 1.3 66.7 + - - +
1322A VAL 2.8 15.9 + - - +
1323A GLN* 3.8 23.3 + - - +
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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