Contacts of the helix formed by residues 1190 - 1207 (chain G) in PDB entry 3F5P
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 THR1190 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132G VAL* 4.0 15.7 - - - +
1164G ASP 3.8 20.4 - - - +
1165G PTR 3.8 9.0 - - + -
1182G GLU* 4.8 5.1 + - + +
1188G VAL* 4.6 10.9 + - + -
1189G PHE* 1.3 81.6 - - - +
1191G THR* 1.3 65.2 + - - +
1192G TYR* 3.1 38.9 + - + +
1193G SER* 2.6 25.2 + - - -
1194G ASP 3.2 4.2 + - - -
1253G PRO* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127G ASN* 2.7 45.5 - - + +
1130G LYS* 6.1 1.3 - - - +
1131G PHE 4.8 0.4 - - - +
1132G VAL* 4.2 3.2 - - - +
1160G ILE* 4.2 21.3 - - + +
1164G ASP* 5.4 0.6 + - + -
1190G THR* 1.3 74.1 - - - +
1192G TYR* 1.3 80.0 + - - +
1194G ASP* 3.1 8.8 + - - +
1195G VAL* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190G THR* 2.9 27.5 - - + +
1191G THR* 1.3 87.7 + - - +
1193G SER* 1.3 62.0 + - - +
1195G VAL* 3.1 10.5 + - + +
1196G TRP 3.0 14.0 + - - -
1253G PRO* 3.4 46.7 - - + +
1254G LYS* 4.3 24.5 - - + +
1256G ARG* 2.9 23.7 + - + +
1257G PRO 5.5 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132G VAL* 4.6 0.2 - - - +
1180G SER* 3.5 25.8 + - - -
1182G GLU* 4.1 2.9 + - - -
1183G SER* 3.6 12.6 - - - -
1188G VAL 4.6 1.1 - - - -
1189G PHE* 3.6 14.6 - - - +
1190G THR* 2.6 36.4 + - - -
1192G TYR* 1.3 76.0 - - - +
1194G ASP* 1.3 68.3 + - - +
1196G TRP* 3.3 4.5 + - - +
1197G SER* 3.1 23.6 + - - -
1256G ARG* 3.7 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123G MET* 3.2 29.5 - - + +
1127G ASN* 3.7 6.1 + - - -
1132G VAL* 3.7 14.6 - - - +
1133G HIS* 2.7 26.2 + - - +
1134G ARG* 2.9 28.3 + - - -
1135G ASP 4.6 0.2 + - - -
1136G LEU* 4.1 5.8 - - - +
1190G THR 3.2 5.0 + - - -
1191G THR* 3.1 12.4 + - - +
1193G SER* 1.3 76.0 + - - +
1195G VAL* 1.3 61.9 + - - +
1197G SER* 3.2 7.7 + - - +
1198G PHE* 2.8 27.4 + - - +
1259G PHE* 3.7 6.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127G ASN* 5.3 0.2 - - - +
1191G THR* 3.0 21.0 + - - +
1192G TYR* 3.1 11.6 + - + +
1194G ASP* 1.3 75.2 - - - +
1196G TRP* 1.3 64.1 + - - +
1198G PHE* 3.1 4.6 - - - +
1199G GLY 3.0 16.8 + - - -
1248G CYS* 3.5 31.5 - - + +
1256G ARG* 4.1 8.5 - - + -
1257G PRO* 3.5 30.1 - - + +
1258G SER* 4.7 1.3 - - - -
1259G PHE* 3.7 34.5 - - + +
1262G ILE* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177G ARG 5.2 1.0 + - - -
1178G TRP 3.5 18.4 + - - -
1179G MET 3.1 18.2 + - - -
1180G SER* 3.7 9.6 - - - -
1181G PRO* 3.6 31.2 - - + -
1192G TYR 3.0 5.3 + - - -
1193G SER 3.3 9.4 - - - +
1195G VAL* 1.3 75.5 - - - +
1197G SER* 1.3 61.1 + - - +
1199G GLY* 2.8 19.9 + - - -
1200G VAL* 3.1 18.6 + - + +
1213G TYR* 4.0 15.1 + - - -
1225G VAL* 3.6 24.5 - - + -
1229G GLY 4.6 3.6 - - - -
1230G LEU* 4.5 10.8 - - + -
1248G CYS 3.4 11.8 + - - -
1249G TRP* 3.4 58.4 + + + -
1250G GLN 4.5 0.4 - - - -
1251G TYR* 5.3 1.6 - + - -
1256G ARG* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1197 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134G ARG 4.8 8.7 + - - -
1135G ASP 5.5 0.2 - - - -
1136G LEU* 3.5 31.1 + - - -
1178G TRP* 2.8 27.4 + - - +
1180G SER 5.4 0.2 + - - -
1193G SER 3.1 10.4 + - - -
1194G ASP* 3.2 11.1 + - - -
1196G TRP* 1.3 78.2 - - - +
1198G PHE* 1.3 65.3 + - - +
1200G VAL* 2.8 18.3 + - - +
1201G VAL* 2.9 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1198 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116G ALA* 3.5 31.4 - - + -
1119G ILE* 3.6 29.4 - - + -
1120G ALA* 3.8 15.0 - - + -
1136G LEU* 3.7 6.6 - - + +
1194G ASP 2.8 13.7 + - - +
1195G VAL 3.1 11.0 + - - +
1197G SER* 1.3 74.5 - - - +
1199G GLY* 1.3 62.7 + - - +
1201G VAL* 3.1 11.9 + - + +
1202G LEU* 3.0 53.0 + - + +
1244G LEU* 4.6 0.9 - - + -
1248G CYS* 3.9 9.9 - - - -
1259G PHE* 3.6 19.7 - + + -
1262G ILE* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1199 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195G VAL 3.0 6.3 + - - -
1196G TRP 2.8 10.3 + - - -
1198G PHE* 1.3 76.9 - - - +
1200G VAL* 1.3 62.3 + - - +
1202G LEU* 3.4 9.6 + - - +
1203G TRP* 3.1 16.6 + - - +
1245G MET* 3.9 4.9 - - - +
1248G CYS* 3.8 18.8 - - - -
1249G TRP* 3.4 24.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1200 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177G ARG 4.0 11.4 - - - +
1178G TRP* 3.4 31.9 - - + +
1196G TRP* 3.6 33.9 - - + +
1197G SER* 2.8 12.3 + - - +
1199G GLY* 1.3 77.6 - - - +
1201G VAL* 1.3 54.7 + - - +
1203G TRP* 3.2 4.4 - - - +
1204G GLU* 2.8 25.5 + - + +
1212G PRO* 3.9 24.5 - - + -
1213G TYR* 5.1 2.0 - - - +
1231G LEU* 4.6 8.5 - - + -
1249G TRP* 4.0 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087G LEU* 4.7 4.3 - - + -
1119G ILE* 3.7 32.5 - - + -
1136G LEU* 3.7 21.8 - - + +
1137G ALA* 4.3 10.1 - - - -
1138G ALA* 4.1 19.3 - - + +
1141G CYS* 5.0 1.1 - - - -
1178G TRP* 5.1 0.4 - - + -
1197G SER 3.0 16.8 - - - +
1198G PHE* 3.1 16.1 + - + +
1200G VAL* 1.3 71.6 - - - +
1202G LEU* 1.3 61.0 + - + +
1204G GLU* 3.3 9.5 + - - +
1205G ILE* 2.9 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1202 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112G MET 5.3 0.2 - - - +
1116G ALA* 3.4 33.9 - - + -
1198G PHE* 3.0 35.0 + - + +
1199G GLY* 3.4 9.6 - - - +
1201G VAL* 1.3 74.6 - - + +
1203G TRP* 1.3 54.5 + - - +
1205G ILE* 3.0 15.7 + - + +
1206G ALA* 2.8 33.8 + - - +
1241G LEU* 4.0 19.4 - - + +
1244G LEU* 3.6 35.9 - - + -
1245G MET* 3.7 23.0 - - + +
1248G CYS* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199G GLY 3.1 9.6 + - - +
1200G VAL* 3.2 14.8 - - - +
1202G LEU* 1.3 79.4 - - - +
1204G GLU* 1.3 68.0 + - - +
1206G ALA* 3.0 12.9 + - - +
1207G THR* 3.0 42.9 + - + +
1210G GLU* 3.7 28.0 - - + -
1211G GLN 3.9 13.9 - - - -
1212G PRO* 3.7 29.4 - - + -
1213G TYR 4.8 0.7 - - - -
1214G GLN 5.9 0.2 - - - -
1231G LEU* 3.6 34.2 - - + +
1232G ASP 3.3 23.5 + - - -
1234G PRO* 3.7 18.3 - - + +
1242G PHE* 5.2 0.7 - + - -
1245G MET* 3.6 17.1 - - - +
1249G TRP* 3.9 11.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088G LYS* 4.0 15.1 + - - +
1091G LEU* 3.8 4.0 - - + +
1138G ALA* 3.0 46.7 + - + +
1139G ARG 5.0 0.2 + - - -
1178G TRP* 3.1 35.7 + - + +
1200G VAL 2.8 19.6 + - - +
1201G VAL* 3.4 11.4 - - - +
1202G LEU 3.3 0.2 - - - -
1203G TRP* 1.3 77.8 - - + +
1205G ILE* 1.3 62.9 + - - +
1207G THR* 3.1 8.0 + - - -
1208G LEU 3.0 4.3 + - - -
1209G ALA* 2.8 33.9 + - - +
1210G GLU 4.4 13.2 - - - +
1212G PRO* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087G LEU* 4.4 11.4 - - + -
1091G LEU* 3.7 28.2 - - + +
1107G PRO* 3.9 12.7 - - + +
1112G MET* 3.4 35.2 - - + +
1115G MET* 4.1 33.7 - - + -
1116G ALA 4.8 2.0 - - - +
1119G ILE* 4.5 4.7 - - + -
1201G VAL* 2.9 37.2 + - + +
1202G LEU* 3.0 23.3 + - + +
1204G GLU* 1.3 76.5 - - - +
1206G ALA* 1.3 62.1 + - - +
1207G THR 3.3 0.5 + - - -
1208G LEU* 3.3 9.9 + - - +
1241G LEU* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1206 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104G LEU 5.6 0.5 - - - +
1106G PRO* 3.5 21.8 - - - +
1112G MET* 2.9 20.6 - - + +
1202G LEU 2.8 12.5 + - - +
1203G TRP 3.0 9.8 + - - +
1205G ILE* 1.3 77.9 - - - +
1207G THR* 1.3 57.8 + - - +
1208G LEU* 3.4 1.2 + - - +
1234G PRO* 3.9 19.3 - - + +
1235G ASP 5.0 3.5 - - - +
1237G CYS* 4.0 11.3 - - + +
1245G MET* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095G ARG* 3.7 13.3 + - - -
1104G LEU* 5.6 3.5 - - - +
1203G TRP* 3.0 44.3 + - + +
1204G GLU* 3.2 5.9 + - - -
1206G ALA* 1.3 74.9 - - - +
1208G LEU* 1.3 72.1 + - - +
1210G GLU* 3.4 35.5 + - + +
1234G PRO* 3.7 30.3 - - + -
----------------------------------------------------------
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