Contacts of the helix formed by residues 1326 - 1337 (chain A) in PDB entry 1DJO
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 ASP1326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1276A GLN* 4.8 0.2 - - - -
1324A THR* 3.1 13.4 + - - +
1325A GLN* 1.3 76.4 - - - +
1327A SER* 1.3 64.4 + - - +
1328A LYS* 2.9 26.4 + - - +
1329A GLU* 3.0 19.8 + - + +
1330A LEU* 2.9 21.6 + - - +
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Residues in contact with SER1327 (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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1271A ARG* 3.2 22.2 + - - -
1276A GLN* 2.9 25.7 + - - -
1301A ASP* 3.3 33.3 + - - -
1302A TRP 5.1 1.1 - - - -
1303A VAL* 3.6 9.6 - - - +
1325A GLN 3.5 3.4 + - - -
1326A ASP* 1.3 73.0 + - - +
1328A LYS* 1.3 60.4 + - - +
1330A LEU* 3.1 7.6 + - - +
1331A GLN* 2.8 28.8 + - - +
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Residues in contact with LYS1328 (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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1291A ARG* 2.6 43.2 - - - +
1298A ASP* 3.6 9.2 + - - +
1301A ASP* 4.6 13.2 - - - +
1302A TRP 5.5 0.7 - - - -
1326A ASP* 2.9 12.9 + - - +
1327A SER* 1.3 79.2 - - - +
1329A GLU* 1.3 62.8 + - + +
1331A GLN* 3.3 8.8 + - - +
1332A ARG* 3.1 21.1 + - - +
1335A TRP* 6.2 0.2 - - - -
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Residues in contact with GLU1329 (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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1323A LYS* 5.0 4.7 + - - -
1324A THR* 3.8 20.1 - - + +
1326A ASP* 3.0 24.6 + - + +
1328A LYS* 1.3 75.8 - - + +
1330A LEU* 1.3 65.5 + - - +
1332A ARG* 2.9 40.6 + - - +
1333A ILE* 3.0 30.2 + - - +
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Residues in contact with LEU1330 (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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1276A GLN* 3.3 44.2 - - + +
1278A ILE* 5.1 7.6 - - + -
1303A VAL* 4.1 11.0 - - + -
1317A ALA* 5.8 1.3 - - - +
1320A ALA* 4.0 21.5 - - + -
1321A MET* 4.4 13.0 - - + -
1324A THR* 3.6 36.8 - - + +
1325A GLN 5.2 0.2 - - - -
1326A ASP 2.9 9.9 + - - +
1327A SER* 3.2 11.0 - - - +
1329A GLU* 1.3 77.6 - - - +
1331A GLN* 1.3 57.1 + - - +
1333A ILE* 3.2 5.0 + - - +
1334A PHE* 3.0 43.9 + - + -
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Residues in contact with GLN1331 (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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1291A ARG* 2.7 35.0 + - - +
1303A VAL* 3.7 6.3 - - + +
1304A VAL* 2.9 44.1 + - - +
1327A SER 2.8 13.1 + - - +
1328A LYS* 3.6 16.2 - - - +
1330A LEU* 1.3 74.9 - - - +
1332A ARG* 1.3 64.2 + - - +
1334A PHE* 3.2 2.5 + - - +
1335A TRP* 3.1 65.9 + - + +
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Residues in contact with ARG1332 (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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1206A ARG* 3.8 3.0 - - - +
1212A GLU* 2.7 42.6 + - - -
1323A LYS* 4.5 1.2 - - - +
1328A LYS 3.1 13.1 + - - +
1329A GLU* 2.9 42.8 + - - +
1331A GLN* 1.3 76.9 - - - +
1333A ILE* 1.3 82.7 + - - +
1335A TRP* 3.1 20.9 + - - +
1336A GLU* 3.1 51.1 + - + +
1337A TYR* 4.2 1.8 - - - -
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Residues in contact with ILE1333 (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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1213A PHE* 4.0 16.6 - - + -
1316A LEU* 3.9 27.8 - - + -
1320A ALA* 3.8 27.6 - - + -
1323A LYS* 4.3 4.3 - - - +
1324A THR* 4.0 20.6 - - + -
1329A GLU 3.0 21.0 + - - +
1330A LEU* 3.4 9.0 - - - +
1331A GLN 3.1 0.2 - - - -
1332A ARG* 1.3 104.3 - - - +
1334A PHE* 1.3 62.9 + - + +
1337A TYR* 3.1 39.4 + - + +
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Residues in contact with PHE1334 (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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1169A ARG* 5.2 0.7 + - - -
1278A ILE* 3.9 28.7 - - + -
1303A VAL* 4.2 8.3 - - + -
1304A VAL 3.5 17.5 - - - +
1305A ALA* 3.5 29.3 - - + +
1306A HIS* 3.7 20.6 + - - +
1308A LEU* 4.1 6.0 - - + +
1313A ALA* 3.4 44.2 - - + -
1316A LEU* 3.8 27.3 - - + +
1317A ALA* 3.9 11.9 - - - -
1320A ALA* 5.6 1.1 - - + -
1330A LEU* 3.0 30.9 + - + +
1331A GLN* 3.2 7.3 + - - +
1333A ILE* 1.3 77.2 - - + +
1335A TRP* 1.3 60.7 + - + +
1336A GLU 3.5 0.2 - - - -
1337A TYR* 4.1 8.9 - - - +
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Residues in contact with TRP1335 (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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1205A LYS* 3.1 22.5 + - - -
1289A VAL 5.6 0.2 + - - -
1291A ARG* 3.7 41.6 - - + +
1304A VAL* 4.5 7.9 - - - +
1306A HIS* 4.0 33.6 - + + -
1331A GLN* 3.1 44.7 + - + +
1332A ARG* 3.1 10.3 + - - +
1333A ILE 3.1 1.0 - - - -
1334A PHE* 1.3 81.5 - - - +
1336A GLU* 1.3 61.1 + - + +
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Residues in contact with GLU1336 (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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1205A LYS* 3.7 10.9 - - - +
1206A ARG* 3.0 65.4 + - + +
1332A ARG* 3.1 46.1 + - + +
1333A ILE 3.2 0.2 + - - -
1335A TRP* 1.3 84.1 - - + +
1337A TYR* 1.3 66.2 + - + +
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Residues in contact with TYR1337 (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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1108A TYR* 2.8 26.2 + - - +
1111A ASN* 5.6 0.2 + - - -
1112A LEU* 3.5 29.2 - - + -
1169A ARG* 2.8 49.4 + - - -
1205A LYS* 3.8 7.7 - - - +
1206A ARG* 3.4 49.1 - - + +
1207A HIS* 5.4 0.2 - - - -
1211A SER* 3.7 22.2 - - - -
1212A GLU* 2.7 48.4 + - - +
1213A PHE* 3.7 15.0 - + - -
1308A LEU* 4.9 0.5 - - - +
1316A LEU* 4.0 8.9 - - + +
1332A ARG* 4.2 8.3 - - - -
1333A ILE* 3.1 28.5 + - + +
1334A PHE 4.1 9.7 - - - +
1336A GLU* 1.3 84.5 + - + +
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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