Contacts of the helix formed by residues 1210 - 1221 (chain B) in PDB entry 1Y8Z
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 GLY1210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201B TRP* 3.7 7.5 + - - -
1207B THR 3.0 11.0 + - - -
1208B TRP 3.1 2.8 + - - -
1209B LYS* 1.3 80.1 - - - +
1211B PHE* 1.3 63.9 + - - +
1212B TYR 3.3 2.2 - - - -
1213B GLN* 3.2 22.9 + - - +
1214B MET 3.2 15.6 + - - -
1293B LEU* 3.7 17.0 - - - +
1295B LYS* 4.6 2.7 - - - -
1322B TRP* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201B TRP* 3.7 13.2 - + + -
1204B ARG 4.0 10.5 - - - -
1205B THR* 4.0 13.0 - - + -
1206B THR 3.4 42.0 - - - -
1207B THR* 3.4 11.4 + - + -
1209B LYS 3.5 1.6 - - - -
1210B GLY* 1.3 74.9 - - - +
1212B TYR* 1.3 105.8 + + - +
1214B MET 3.1 0.7 + - - -
1215B PHE* 2.9 41.1 + + - -
1231B MET* 3.5 24.5 - - + +
1234B LEU* 4.0 11.9 - - + -
1239B ALA* 4.8 7.4 - - + -
1243B ILE* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1207B THR* 4.0 23.7 + - + -
1210B GLY 3.3 0.6 - - - -
1211B PHE* 1.3 113.0 - + - +
1213B GLN* 1.3 68.4 + - - +
1215B PHE* 3.3 6.2 + + - +
1216B ASP* 2.9 28.1 + - - +
1239B ALA* 4.1 3.3 + - - +
1242B ALA* 3.5 26.3 - - - +
1243B ILE* 3.9 12.4 - - + +
1246B LYS* 3.4 37.8 + - + -
1248B ILE* 3.8 24.6 - - + +
1D C 5.4 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1207B THR 4.6 0.7 - - - +
1210B GLY* 3.2 26.2 - - - +
1211B PHE 3.2 0.2 - - - -
1212B TYR* 1.3 79.3 + - - +
1214B MET* 1.3 61.6 + - - +
1216B ASP* 3.4 7.6 + - - +
1217B PHE* 2.8 30.3 + - - +
1293B LEU* 4.3 4.0 - - + -
1295B LYS* 3.3 26.5 + - - +
1322B TRP* 3.4 40.9 - - + -
1348B PHE* 4.1 14.4 - - + -
1350B GLU* 4.8 8.4 + - + -
1353B MET* 5.0 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199B ASN* 4.3 2.9 - - + +
1201B TRP* 3.6 37.7 - - + -
1210B GLY 3.2 7.0 + - - +
1211B PHE 3.1 8.6 + - - +
1213B GLN* 1.3 73.5 - - - +
1215B PHE* 1.3 66.0 + - - +
1217B PHE* 3.2 7.4 + - - +
1218B HIS* 3.0 23.6 + - - +
1222B LEU* 4.1 13.9 - - + -
1229B THR* 3.8 23.3 - - + +
1231B MET* 3.6 21.1 - - + -
1291B TYR* 3.6 56.3 - - + -
1293B LEU* 4.1 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211B PHE* 2.9 43.2 + + - -
1212B TYR* 3.5 7.6 - - - +
1214B MET* 1.3 76.4 - - - +
1216B ASP* 1.3 62.5 + - - +
1218B HIS* 3.3 6.4 + - - +
1219B GLU* 3.0 23.8 + - - +
1231B MET* 3.5 24.5 - - + -
1234B LEU* 4.1 4.0 - - + -
1243B ILE* 4.0 17.9 - - + -
1248B ILE* 3.6 47.1 - - + -
1249B PRO 4.2 1.8 - - - -
1250B TYR* 4.2 7.2 - - + -
1269B ALA* 3.7 20.9 - - + -
1271B ILE* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212B TYR 2.9 16.4 + - - +
1213B GLN* 3.5 9.4 - - - +
1215B PHE* 1.3 76.5 - - - +
1217B PHE* 1.3 62.8 + - - +
1219B GLU* 3.1 13.3 + - - +
1220B LYS* 3.0 60.2 + - - +
1353B MET* 3.1 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213B GLN 2.8 21.1 + - - +
1214B MET* 3.7 7.0 - - + +
1216B ASP* 1.3 73.0 + - - +
1218B HIS* 1.3 57.6 + - - +
1221B PHE* 3.0 45.6 + + + +
1222B LEU* 3.2 40.9 + - + +
1291B TYR* 3.5 34.8 - + - -
1348B PHE* 3.7 23.8 - + + -
1353B MET* 3.6 35.4 - - + -
1356B THR* 4.2 6.1 - - + -
1357B PHE* 3.9 16.2 - - + -
1360B ILE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214B MET 3.0 13.7 + - - +
1215B PHE* 3.6 10.3 + - - +
1217B PHE* 1.3 78.1 - - - +
1219B GLU* 1.3 63.8 + - - +
1222B LEU* 3.5 19.0 + - + +
1223B LYS* 2.7 51.8 + - + +
1227B LYS 3.9 11.2 + - - -
1228B SER* 4.5 0.6 - - - -
1229B THR* 2.9 43.2 + - + +
1267B GLN 2.9 29.7 + - - -
1268B PRO* 3.8 13.4 - - + +
1269B ALA* 3.8 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215B PHE 3.0 13.7 + - - +
1216B ASP* 3.1 16.3 + - - +
1218B HIS* 1.3 81.7 + - - +
1220B LYS* 1.3 67.9 + - + +
1223B LYS* 4.6 8.5 - - + +
1224B PRO* 3.3 20.8 - - - +
1249B PRO* 5.7 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216B ASP* 3.0 46.6 + - - +
1219B GLU* 1.3 88.4 - - + +
1221B PHE* 1.3 87.5 + - + +
1224B PRO* 4.0 10.0 - - - +
1353B MET* 4.8 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1217B PHE* 3.0 38.0 + + + +
1219B GLU 3.6 0.6 - - - -
1220B LYS* 1.3 102.8 - - + +
1222B LEU* 1.3 65.0 + - - +
1223B LYS 3.6 0.9 - - - -
1224B PRO* 3.5 4.1 - - - +
1225B ALA* 3.3 23.9 + - - +
1353B MET* 3.6 23.1 - - + -
1354B GLU* 3.5 41.5 - - + -
1357B PHE* 3.8 40.9 - + + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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