Contacts of the helix formed by residues 1288 - 1302 (chain A) in PDB entry 5IRC
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 ASN1288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1287A GLY* 1.3 68.5 - - - -
1289A LYS* 1.3 61.6 + - - +
1290A SER* 3.3 9.9 + - - -
1291A GLU* 3.1 31.5 + - + +
1292A MET* 2.8 30.3 + - - +
1316A THR* 3.9 16.7 + - - +
90F ASP* 3.1 38.5 + - - +
93F GLU* 2.8 39.3 + - - +
94F ASN* 3.8 6.9 - - - +
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Residues in contact with LYS1289 (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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1287A GLY 3.2 3.3 + - - +
1288A ASN* 1.3 70.6 + - - +
1290A SER* 1.3 62.2 + - - +
1292A MET* 3.3 19.9 + - + +
1293A GLU* 3.0 45.8 + - + +
67F ASP* 5.2 4.6 + - - -
94F ASN* 2.9 21.7 + - - +
97F GLU* 3.9 20.3 + - + +
98F LYS* 3.9 39.6 - - + +
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Residues in contact with SER1290 (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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1288A ASN* 3.3 9.1 + - - -
1289A LYS* 1.3 78.8 - - - +
1291A GLU* 1.3 63.5 + - - +
1293A GLU* 3.3 7.8 + - - +
1294A SER* 3.0 25.8 + - - -
93F GLU* 3.8 18.6 + - - -
97F GLU* 3.9 31.3 + - - +
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Residues in contact with GLU1291 (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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1288A ASN* 3.1 30.9 + - + +
1290A SER* 1.3 80.3 + - - +
1292A MET* 1.3 61.6 + - - +
1294A SER* 3.2 10.3 + - - -
1295A LEU* 2.9 28.9 + - - +
1312A PHE* 3.7 22.2 - - + -
1316A THR* 3.7 21.9 - - + +
93F GLU* 4.7 7.6 - - - +
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Residues in contact with MET1292 (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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1287A GLY* 3.6 28.7 - - - +
1288A ASN 2.8 21.6 + - - +
1289A LYS* 3.5 15.0 - - + +
1291A GLU* 1.3 76.3 - - - +
1293A GLU* 1.3 63.0 + - + +
1295A LEU* 3.3 5.2 + - - +
1296A GLN* 3.1 28.3 + - - +
1316A THR* 3.4 33.8 - - - +
1319A GLY* 3.5 30.1 - - - +
1320A ALA* 3.9 7.9 - - - +
1323A SER* 4.0 11.0 - - - +
64F GLU* 3.9 14.1 - - + +
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Residues in contact with GLU1293 (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 LYS* 3.0 42.0 + - + +
1290A SER* 3.7 7.8 - - - +
1292A MET* 1.3 77.5 - - + +
1294A SER* 1.3 58.4 + - - +
1296A GLN* 3.3 19.2 + - - +
1297A ARG* 2.9 41.5 + - + +
97F GLU* 4.0 13.9 - - - +
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Residues in contact with SER1294 (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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1290A SER 3.0 14.3 + - - -
1291A GLU* 3.2 21.3 + - - -
1293A GLU* 1.3 76.8 - - - +
1295A LEU* 1.3 56.3 + - - +
1297A ARG* 3.2 6.6 + - - +
1298A GLN* 2.9 55.3 + - - +
1312A PHE* 4.2 2.2 - - - -
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Residues in contact with LEU1295 (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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1264A PHE* 4.6 13.2 - - + -
1268A CYS* 5.2 0.9 - - - -
1291A GLU 2.9 12.9 + - - +
1292A MET 3.5 8.7 - - - +
1294A SER* 1.3 76.8 - - - +
1296A GLN* 1.3 57.0 + - - +
1298A GLN* 3.3 2.4 + - - +
1299A PHE* 2.9 26.2 + - - +
1305A LEU* 3.4 25.6 - - + -
1307A LEU* 3.5 17.7 - - + -
1312A PHE* 3.6 22.6 - - + -
1316A THR* 4.1 8.7 - - + +
1317A VAL* 3.9 33.4 - - + -
1320A ALA* 3.7 23.8 - - + -
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Residues in contact with GLN1296 (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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1247A PHE* 3.5 44.3 - - + -
1264A PHE* 4.6 1.6 - - + -
1292A MET* 3.1 16.1 + - - +
1293A GLU* 3.3 21.3 + - - +
1295A LEU* 1.3 77.8 - - - +
1297A ARG* 1.3 74.3 + - - +
1299A PHE* 3.2 1.5 + - - +
1300A ASP* 2.9 25.8 + - - +
1320A ALA* 4.4 12.5 + - + +
1323A SER* 3.7 22.5 + - - -
1327A GLU* 3.0 33.9 + - - +
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Residues in contact with ARG1297 (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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1239A ALA* 3.4 30.3 + - - +
1240A GLY 5.5 0.4 - - - -
1241A SER* 4.3 28.9 - - - +
1244A SER* 4.5 0.4 - - - -
1247A PHE* 3.7 25.1 - - - +
1293A GLU* 2.9 32.6 + - + +
1294A SER* 3.8 5.6 - - - +
1296A GLN* 1.3 94.6 + - - +
1298A GLN* 1.3 64.7 + - + +
1300A ASP* 3.0 34.4 + - - +
1301A GLN* 3.1 29.0 + - - +
1327A GLU* 5.1 1.0 + - - -
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Residues in contact with GLN1298 (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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1294A SER* 2.9 37.4 + - - +
1295A LEU* 3.8 4.5 - - - +
1297A ARG* 1.3 77.7 - - + +
1299A PHE* 1.3 58.3 + - - +
1301A GLN* 3.3 12.5 + - - +
1302A ASP* 3.0 27.7 + - - +
1305A LEU* 4.3 16.6 - - + +
1310A LYS* 3.3 31.4 - - - +
1312A PHE* 3.3 20.3 - - - -
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Residues in contact with PHE1299 (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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1246A TYR* 3.6 32.3 - + - -
1247A PHE* 3.9 12.6 - + - -
1263A ILE* 4.3 5.2 - - + -
1264A PHE* 3.6 52.3 - + + -
1267A ARG* 4.1 11.0 - - + -
1295A LEU 2.9 18.0 + - - +
1296A GLN 3.6 4.0 - - - +
1298A GLN* 1.3 74.5 - - - +
1300A ASP* 1.3 67.3 + - - +
1302A ASP 3.0 29.3 + - - -
1303A HIS* 3.1 54.8 + + + -
1305A LEU* 4.0 18.5 - - + +
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Residues in contact with ASP1300 (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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1244A SER* 2.8 34.0 + - - -
1245A ASN 4.5 1.0 + - - -
1246A TYR* 3.8 9.5 + - - +
1247A PHE* 3.7 9.3 - - - -
1296A GLN 2.9 11.2 + - - +
1297A ARG* 3.0 45.5 + - - +
1299A PHE* 1.3 78.7 - - - +
1301A GLN* 1.3 61.6 + - + +
1303A HIS* 3.8 17.3 + - - -
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Residues in contact with GLN1301 (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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1297A ARG* 3.1 16.4 + - - +
1298A GLN* 3.6 14.1 - - - +
1299A PHE 3.1 0.4 - - - -
1300A ASP* 1.3 81.5 - - + +
1302A ASP* 1.3 61.4 + - + +
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Residues in contact with ASP1302 (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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1298A GLN 3.0 8.7 + - - +
1299A PHE* 3.0 10.0 + - - +
1301A GLN* 1.3 82.1 - - + +
1303A HIS* 1.3 59.1 + - - +
1304A ASN* 2.9 35.0 + - - +
1305A LEU* 3.0 38.9 + - + +
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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