Contacts of the helix formed by residues 1261 - 1273 (chain B) in PDB entry 1Z1J
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 VAL1261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1205B LEU* 6.3 2.0 - - + -
1209B TYR* 4.7 11.7 - - - +
1242B LEU* 6.3 1.1 - - + -
1244B GLN* 5.8 0.4 - - - +
1247B VAL* 3.5 44.2 - - + -
1250B LEU* 4.5 16.2 - - + +
1254B SER* 5.1 7.9 - - - -
1260B ALA* 1.3 74.8 - - - +
1262B LEU* 1.3 74.4 + - + +
1264B MET* 3.2 6.9 + - - +
1265B CYS* 2.8 38.4 + - - -
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Residues in contact with LEU1262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224B THR* 4.4 5.2 - - - +
1225B THR* 3.2 26.6 - - - +
1226B THR* 3.5 25.8 - - - +
1227B LEU* 4.4 11.9 - - + +
1244B GLN* 6.0 3.6 - - - +
1260B ALA* 4.2 2.2 - - + +
1261B VAL* 1.3 86.4 - - + +
1263B ASP* 1.3 61.1 + - - +
1265B CYS* 2.7 37.0 + - - +
1266B ALA 3.0 4.9 + - - -
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Residues in contact with ASP1263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220B LEU* 4.4 18.8 - - + +
1221B ASN* 5.6 0.7 - - - -
1222B ARG* 4.1 14.5 + - - +
1224B THR* 2.8 46.0 + - - +
1260B ALA* 3.6 23.6 - - + +
1261B VAL 3.5 0.4 - - - -
1262B LEU* 1.3 79.1 - - - +
1264B MET* 1.3 63.8 + - - +
1266B ALA* 2.9 17.8 + - - +
1267B ALA* 3.3 5.0 + - - +
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Residues in contact with MET1264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205B LEU* 5.1 8.1 - - + +
1208B LEU* 3.3 54.3 - - + -
1209B TYR* 4.3 10.3 - - + +
1212B VAL* 4.2 9.0 - - + -
1219B PHE* 4.4 16.8 - - + -
1220B LEU* 4.7 15.5 + - + +
1259B ILE* 3.7 30.1 - - + -
1260B ALA 3.5 15.8 + - - +
1261B VAL* 3.2 12.4 + - - +
1262B LEU 3.1 0.6 - - - -
1263B ASP* 1.3 77.6 - - - +
1265B CYS* 1.3 59.3 + - - +
1267B ALA* 2.8 27.1 + - - +
1268B LEU* 2.9 11.9 - - + +
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Residues in contact with CYS1265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205B LEU* 4.7 9.0 - - - -
1225B THR* 3.8 4.9 - - + -
1226B THR 5.6 0.7 - - - -
1230B PHE* 3.0 52.6 - - + -
1242B LEU* 4.8 6.7 - - - -
1261B VAL* 2.8 42.4 + - - -
1262B LEU* 2.7 21.8 + - - +
1264B MET* 1.3 71.6 - - - +
1266B ALA* 1.3 59.3 + - - -
1268B LEU* 3.0 25.5 + - - +
1269B LYS 3.5 1.4 + - - -
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Residues in contact with ALA1266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222B ARG* 3.2 28.9 - - + +
1223B PHE 3.3 27.6 - - - +
1225B THR* 3.5 17.9 - - + +
1262B LEU 3.0 4.0 + - - -
1263B ASP 2.9 13.7 + - - +
1265B CYS* 1.3 73.1 - - - +
1267B ALA* 1.3 64.9 + - - +
1268B LEU 3.1 0.9 + - - -
1269B LYS* 3.1 16.6 + - - +
1270B GLU 3.2 9.5 + - - -
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Residues in contact with ALA1267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208B LEU* 5.3 0.9 - - + -
1219B PHE* 3.0 48.1 - - + +
1221B ASN 4.7 0.2 - - - -
1222B ARG* 3.9 7.5 - - - +
1263B ASP 3.3 2.6 + - - +
1264B MET* 2.8 22.0 + - - +
1266B ALA* 1.3 77.8 - - - +
1268B LEU* 1.3 57.3 + - + +
1270B GLU* 3.7 5.4 + - - +
1271B LEU* 2.8 36.9 + - + +
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Residues in contact with LEU1268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1201B THR* 5.1 1.3 - - + -
1204B VAL* 4.9 13.0 - - + -
1205B LEU* 3.3 31.6 - - + -
1208B LEU* 3.9 15.3 - - + -
1230B PHE* 3.3 19.5 - - + -
1239B TYR* 5.0 14.1 - - + -
1264B MET 2.9 31.0 - - - +
1265B CYS* 3.0 17.9 - - - +
1267B ALA* 1.3 77.1 - - - +
1269B LYS* 1.3 60.5 + - - +
1271B LEU* 2.5 33.0 + - + +
1272B LEU* 2.9 23.4 + - + +
1287B LEU* 5.1 7.2 - - + -
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Residues in contact with LYS1269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222B ARG* 3.2 25.2 - - - +
1223B PHE* 5.1 2.8 + - - +
1225B THR* 3.8 29.8 + - - +
1229B ASP* 5.0 10.2 - - - +
1230B PHE* 4.6 11.8 - - + +
1233B VAL* 4.5 35.7 - - + -
1237B TYR* 5.0 0.8 - - - -
1265B CYS 3.5 2.4 + - - +
1266B ALA* 3.1 12.9 + - - +
1268B LEU* 1.3 80.4 - - - +
1270B GLU* 1.3 59.3 + - - +
1272B LEU* 4.0 1.7 - - - +
1273B GLN* 3.0 63.7 + - - +
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Residues in contact with GLU1270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218B TRP* 5.0 8.7 - - - +
1219B PHE* 5.3 7.3 - - - +
1221B ASN 4.4 5.1 - - - +
1222B ARG* 3.4 36.4 + - + +
1266B ALA 3.2 6.1 + - - +
1267B ALA* 3.9 7.1 - - - +
1269B LYS* 1.3 78.7 - - - +
1271B LEU* 1.3 58.7 + - - +
1272B LEU 3.4 0.4 - - - -
1273B GLN* 3.2 1.9 - - - +
1274B ASN* 3.0 35.4 - - + +
1275B GLY 2.9 25.6 + - - +
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Residues in contact with LEU1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208B LEU* 4.6 10.3 - - + -
1218B TRP* 5.3 4.7 - - + -
1219B PHE* 5.0 11.0 - - + -
1267B ALA* 2.8 29.5 + - + +
1268B LEU* 2.5 27.3 + - + +
1270B GLU* 1.3 74.0 - - - +
1272B LEU* 1.3 66.7 + - + +
1275B GLY* 2.8 38.1 - - - +
1276B MET* 3.9 25.9 - - + +
1281B ILE* 4.3 20.9 - - + -
1287B LEU* 4.2 23.6 - - + +
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Residues in contact with LEU1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234B ALA* 6.4 0.4 - - - -
1237B TYR* 3.5 56.3 + - + -
1239B TYR* 3.9 27.4 - - + +
1268B LEU* 2.9 19.1 + - + +
1269B LYS* 4.3 0.9 - - - +
1271B LEU* 1.3 90.8 - - + +
1273B GLN* 1.3 66.3 + - - +
1274B ASN 3.0 4.4 + - - -
1275B GLY* 3.8 4.4 + - - -
1287B LEU* 3.7 28.9 - - + -
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Residues in contact with GLN1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222B ARG* 2.9 32.8 - - - +
1233B VAL* 5.6 2.2 - - + +
1237B TYR* 2.9 25.2 + - + +
1269B LYS* 3.0 48.3 + - - +
1270B GLU* 3.2 2.4 - - - +
1272B LEU* 1.3 77.3 - - - +
1274B ASN* 1.3 76.3 + - - +
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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