Contacts of the helix formed by residues 1218 - 1230 (chain B) in PDB entry 3KHR
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 GLY1218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214B LYS* 2.8 20.4 + - - -
1215B GLY 5.0 0.4 + - - -
1216B MET 3.7 0.8 - - - -
1217B ILE* 1.3 80.4 - - - +
1219B GLU* 1.3 65.6 + - - -
1220B ALA 3.4 3.1 + - - -
1221B LYS 3.5 0.6 + - - -
1222B ALA* 3.0 24.8 + - - +
1911J C 3.6 14.6 - - - -
1912J A 5.8 3.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
1210B PHE* 5.3 2.2 - - + -
1214B LYS* 3.8 41.2 - - + +
1218B GLY* 1.3 70.9 - - - -
1220B ALA* 1.3 59.2 + - - +
1222B ALA* 3.4 2.6 + - - +
1223B LYS* 3.0 63.3 + - + +
1911J C 3.1 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219B GLU* 1.3 74.9 - - - +
1221B LYS* 1.3 62.6 + - + +
1223B LYS* 3.6 7.4 + - - +
1224B TYR* 3.2 23.4 + - - +
1910J C 3.4 53.8 - - - +
1911J C 2.9 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185B GLY* 3.1 28.5 - - - +
1186B ILE* 4.2 13.2 - - + -
1190B THR* 4.0 19.8 + - + +
1217B ILE* 3.7 30.6 + - + +
1218B GLY 3.5 2.2 + - - -
1219B GLU 3.4 0.2 - - - -
1220B ALA* 1.3 79.0 - - + +
1222B ALA* 1.3 60.5 + - - +
1224B TYR* 3.7 9.8 - - + +
1225B LEU* 3.0 35.0 + - - +
1812H A 4.5 12.9 + - - -
1813H G 4.1 17.3 - - - -
1910J C 5.9 7.0 - - - +
1911J C 4.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210B PHE* 3.8 20.2 - - + -
1213B LEU* 4.0 21.8 - - + -
1214B LYS* 4.0 12.8 - - - -
1217B ILE* 3.6 9.3 - - + +
1218B GLY 3.0 18.8 + - - +
1219B GLU 3.6 3.8 - - - +
1221B LYS* 1.3 75.6 - - - +
1223B LYS* 1.3 63.9 + - - +
1224B TYR 3.3 0.2 + - - -
1225B LEU* 3.4 1.3 + - - +
1226B ILE* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210B PHE* 4.0 23.6 - - + -
1219B GLU* 3.0 51.3 + - - +
1220B ALA* 3.9 6.7 - - - +
1222B ALA* 1.3 75.6 - - - +
1224B TYR* 1.3 57.6 + - - +
1226B ILE* 4.0 2.9 - - - +
1227B SER* 2.9 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149B VAL* 3.4 22.6 - - + +
1183B VAL* 4.0 7.1 - - + +
1184B PRO* 2.7 33.2 + - - +
1185B GLY* 5.0 5.2 - - - -
1186B ILE* 5.0 5.2 - - + -
1220B ALA 3.2 16.6 + - - +
1221B LYS* 3.7 11.0 - - + +
1223B LYS* 1.3 77.5 - - - +
1225B LEU* 1.3 77.2 + - + +
1227B SER* 3.3 6.1 + - - -
1228B LEU* 2.9 46.2 + - + +
1233B TYR* 3.8 32.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180B ILE* 4.1 11.4 - - + -
1183B VAL* 4.1 7.6 - - + -
1186B ILE* 3.8 30.7 - - + -
1194B LEU* 4.0 24.2 - - + -
1202B LEU* 3.8 21.7 - - + +
1205B THR* 4.0 20.0 - - + -
1213B LEU* 5.3 1.3 - - + -
1217B ILE* 3.9 25.4 - - + -
1221B LYS 3.0 15.6 + - - +
1222B ALA* 4.0 2.9 - - - +
1224B TYR* 1.3 86.1 - - + +
1226B ILE* 1.3 58.1 + - - +
1228B LEU* 3.2 4.1 + - + +
1229B ALA* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205B THR* 3.9 26.5 - - - +
1206B LEU* 4.2 5.6 - - + -
1208B ILE 5.5 1.8 - - - +
1210B PHE* 3.1 41.1 - - + -
1213B LEU* 4.0 15.5 - - + -
1222B ALA 3.0 18.1 + - - +
1223B LYS* 4.0 4.0 - - - +
1225B LEU* 1.3 75.2 - - - +
1227B SER* 1.3 58.1 + - - +
1229B ALA* 3.1 2.8 + - - +
1230B ARG* 2.9 70.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223B LYS 2.9 21.1 + - - -
1224B TYR* 3.5 6.3 - - - -
1226B ILE* 1.3 79.6 - - - +
1228B LEU* 1.3 59.4 + - - +
1230B ARG* 3.5 5.8 + - - +
1231B ASP 3.4 1.9 + - - -
1232B GLU* 3.0 37.6 + - - +
1233B TYR* 3.3 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147B ASN* 4.5 0.9 - - - +
1149B VAL* 3.6 34.1 - - + -
1150B PHE* 4.0 22.9 - - + -
1175B ILE* 3.6 10.6 - - - +
1183B VAL* 3.9 12.6 - - + -
1202B LEU* 4.1 16.8 - - + -
1224B TYR* 2.9 55.5 + - + +
1225B LEU* 3.6 3.8 - - - +
1227B SER* 1.3 76.8 - - - +
1229B ALA* 1.3 57.1 + - - +
1231B ASP* 2.9 21.1 + - - -
1233B TYR* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 5.6 1.7 - - - +
207A SER* 4.4 2.9 + - - -
1175B ILE* 3.5 28.6 - - + +
1202B LEU* 3.4 21.0 - - + +
1205B THR* 3.4 19.5 - - - +
1206B LEU* 3.7 23.8 - - + +
1225B LEU 2.8 20.9 + - - +
1226B ILE 3.6 3.8 - - - +
1228B LEU* 1.3 73.0 - - - +
1230B ARG* 1.3 59.5 + - - +
1231B ASP 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 6.0 6.3 - - - +
206A LEU* 5.3 16.6 - - + +
1172B LYS* 5.0 1.3 + - - -
1206B LEU* 3.6 20.5 - - + +
1226B ILE* 2.9 45.2 + - - +
1227B SER* 3.9 6.5 - - - +
1228B LEU 3.2 0.4 - - - -
1229B ALA* 1.3 74.4 - - - +
1231B ASP* 1.3 71.8 + - - +
1232B GLU* 3.5 33.5 + - + +
----------------------------------------------------------
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