Contacts of the helix formed by residues 1201 - 1214 (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 THR1201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1199B THR* 2.8 27.9 + - - +
1200B ILE* 1.3 74.0 - - - +
1202B LEU* 1.3 51.2 + - - +
1203B ASN 2.7 8.5 + - - +
1204B VAL* 2.8 5.6 + - - +
1205B LEU* 2.7 61.8 + - + +
1230B PHE* 4.9 8.3 - - + -
1234B ALA* 6.0 1.8 - - + -
1239B TYR* 3.3 27.2 - - + +
1240B GLU 3.3 20.2 + - - +
1241B PRO 5.0 1.6 - - - -
1242B LEU* 4.7 13.2 - - + -
1268B LEU* 5.1 0.9 - - + -
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Residues in contact with LEU1202 (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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1200B ILE* 2.3 31.0 + - + +
1201B THR* 1.3 68.2 - - - +
1203B ASN* 1.3 58.3 + - - +
1205B LEU* 3.9 13.5 - - + -
1206B ALA* 3.3 24.1 + - - +
1242B LEU* 6.2 3.5 - - + +
1246B HIS* 3.1 51.4 - - + +
1247B VAL* 5.8 0.9 - - + -
1249B ILE* 3.6 25.4 - - + -
1250B LEU* 4.0 22.2 - - + -
1293B PRO* 3.8 17.5 - - + +
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Residues in contact with ASN1203 (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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1109B GLY 3.0 23.3 + - - +
1111B THR* 4.8 1.4 - - - +
1129B ALA* 4.8 1.2 - - - +
1200B ILE* 3.1 24.8 + - + +
1201B THR 2.7 5.3 + - - -
1202B LEU* 1.3 78.2 - - - +
1204B VAL* 1.3 58.5 + - - +
1205B LEU 3.0 1.3 - - - -
1207B TRP* 2.9 29.8 + - - +
1288B GLU 4.0 2.0 - - - -
1289B ASP* 2.6 31.5 + - - +
1290B GLU* 4.6 1.0 - - - +
1291B PHE* 3.1 25.6 - - - +
1292B THR* 3.0 28.3 - - - +
1293B PRO* 4.1 1.7 - - - +
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Residues in contact with VAL1204 (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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1199B THR* 3.3 30.7 - - + -
1201B THR* 2.8 8.3 + - - +
1203B ASN* 1.3 77.0 - - - +
1205B LEU* 1.3 62.8 + - + +
1207B TRP* 3.3 13.0 - - + +
1208B LEU* 3.4 12.5 - - + +
1239B TYR* 4.5 10.1 - - + +
1268B LEU* 4.9 8.7 - - + -
1287B LEU* 3.4 44.0 - - + +
1288B GLU 2.9 23.6 - - - +
1289B ASP* 3.3 12.1 - - + -
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Residues in contact with LEU1205 (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* 2.7 39.2 + - + +
1202B LEU* 3.9 15.7 - - + +
1204B VAL* 1.3 74.3 - - - +
1206B ALA* 1.3 54.3 + - - +
1207B TRP 2.7 4.2 + - - -
1208B LEU* 2.7 42.5 + - + +
1209B TYR* 3.6 6.2 + - - -
1230B PHE* 4.3 7.6 - - + -
1242B LEU* 4.3 18.4 - - + -
1250B LEU* 5.4 11.2 - - + -
1261B VAL* 6.3 1.3 - - + -
1264B MET* 5.1 6.5 - - + +
1265B CYS* 4.7 9.9 - - - -
1268B LEU* 3.3 42.4 - - + -
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Residues in contact with ALA1206 (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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1202B LEU 3.3 18.3 + - - +
1203B ASN 3.4 4.2 + - - +
1205B LEU* 1.3 77.0 - - - +
1207B TRP* 1.3 59.8 + - - +
1208B LEU 3.3 0.2 - - - -
1209B TYR* 3.6 19.6 - - - +
1250B LEU* 4.6 6.0 - - + +
1253B LEU* 5.0 3.4 - - + -
1291B PHE 4.1 3.4 - - - +
1292B THR 4.2 0.2 - - - -
1293B PRO* 3.5 37.0 - - + -
1296B VAL* 3.1 26.7 - - - +
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Residues in contact with TRP1207 (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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1003B PHE* 4.2 11.0 - + - -
1203B ASN 2.9 17.1 + - - +
1204B VAL* 3.3 13.7 - - + +
1205B LEU 2.7 3.4 + - - -
1206B ALA* 1.3 73.3 - - - +
1208B LEU* 1.3 76.3 + - + +
1210B ALA* 3.2 6.6 + - - +
1211B ALA* 3.2 17.0 + - - +
1281B ILE* 3.3 59.7 - - + -
1282B LEU* 4.2 16.0 - - + +
1284B SER* 4.6 10.8 - - - -
1286B ILE 4.0 15.3 - - - -
1287B LEU* 4.0 13.9 - - + -
1288B GLU* 3.8 36.1 - - + +
1291B PHE* 3.5 36.3 - + + -
1296B VAL* 4.4 5.6 - - - -
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Residues in contact with LEU1208 (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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1204B VAL* 3.4 13.0 - - + +
1205B LEU* 2.7 20.0 + - - +
1207B TRP* 1.3 86.5 - - + +
1209B TYR* 1.3 54.8 + - - +
1211B ALA* 2.8 23.5 + - - +
1212B VAL* 2.9 18.2 + - - +
1219B PHE* 4.5 12.1 - - + -
1264B MET* 3.3 42.4 - - + -
1267B ALA* 5.3 2.0 - - + -
1268B LEU* 3.9 22.7 - - + -
1271B LEU* 4.6 10.3 - - + -
1281B ILE* 4.0 27.4 - - + -
1287B LEU* 5.4 4.0 - - + -
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Residues in contact with TYR1209 (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 3.6 4.7 + - - -
1206B ALA* 3.6 21.8 - - - +
1207B TRP 3.2 0.6 - - - -
1208B LEU* 1.3 79.7 - - - +
1210B ALA* 1.3 56.3 + - - +
1212B VAL* 3.6 7.7 - - - +
1213B ILE* 3.1 33.3 + - + +
1250B LEU* 4.3 15.7 + - + -
1253B LEU* 3.1 56.7 - - + +
1254B SER* 2.8 36.3 + - - -
1256B GLN 5.2 0.7 - - - -
1257B THR* 3.4 5.8 - - + -
1259B ILE* 3.3 36.7 + - + -
1260B ALA 4.1 7.5 + - - -
1261B VAL* 4.7 6.0 - - + +
1264B MET* 4.7 10.3 - - + -
1296B VAL* 4.7 1.8 - - + -
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Residues in contact with ALA1210 (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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1003B PHE* 3.5 31.9 - - + -
1206B ALA 3.9 0.4 + - - -
1207B TRP 3.2 8.9 + - - +
1208B LEU 3.2 0.4 - - - -
1209B TYR* 1.3 76.5 - - - +
1211B ALA* 1.3 63.9 + - - +
1212B VAL 3.3 0.7 - - - -
1213B ILE* 3.9 8.5 - - - -
1214B ASN* 3.1 28.4 + - - -
1282B LEU* 4.3 4.1 - - - +
1296B VAL* 3.3 26.5 - - + -
1300B CYS* 3.8 5.4 - - - -
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Residues in contact with ALA1211 (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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1207B TRP 3.2 6.5 + - - +
1208B LEU* 2.8 21.9 + - - +
1210B ALA* 1.3 78.4 - - - +
1212B VAL* 1.3 61.1 + - - +
1214B ASN* 3.2 17.8 + - - +
1216B ASP* 3.2 17.5 + - - +
1219B PHE* 4.0 9.9 - - + -
1281B ILE* 3.6 31.0 - - + -
1282B LEU* 3.7 15.5 - - + +
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Residues in contact with VAL1212 (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 2.9 16.0 + - - +
1209B TYR 3.6 8.1 - - - +
1211B ALA* 1.3 77.1 - - - +
1213B ILE* 1.3 55.7 + - - +
1215B GLY* 2.6 37.4 + - - +
1216B ASP 4.4 1.3 - - - -
1217B ARG* 3.8 34.8 + - + +
1219B PHE* 4.2 13.7 - - + -
1220B LEU* 4.9 7.0 - - + -
1257B THR* 3.7 25.6 - - + -
1259B ILE* 4.0 24.7 - - + -
1264B MET* 4.2 8.5 - - + -
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Residues in contact with ILE1213 (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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1209B TYR* 3.1 21.3 + - + +
1210B ALA* 4.0 3.6 - - - +
1211B ALA 3.4 0.2 - - - -
1212B VAL* 1.3 78.4 - - + +
1214B ASN* 1.3 69.7 + - - +
1215B GLY 3.2 3.8 + - - -
1217B ARG* 5.8 0.4 - - - +
1256B GLN* 4.8 26.5 - - + +
1257B THR* 4.9 4.5 - - + -
1296B VAL* 5.4 3.4 - - + -
1300B CYS* 4.1 30.3 - - + +
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Residues in contact with ASN1214 (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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1001B SER* 2.4 40.7 - - - +
1002B GLY* 3.2 18.1 + - - +
1003B PHE* 3.8 2.7 + - - +
1210B ALA* 3.1 20.3 + - - +
1211B ALA 3.2 5.0 + - - +
1212B VAL 2.9 1.4 + - - -
1213B ILE* 1.3 90.8 + - - +
1215B GLY* 1.3 51.2 + - - +
1216B ASP* 2.7 22.4 + - - +
1282B LEU* 4.3 14.2 - - + +
1300B CYS* 4.6 9.9 - - - -
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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