Contacts of the helix formed by residues 1190 - 1207 (chain D) in PDB entry 2ZM3
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132D VAL* 3.3 16.3 - - - +
1164D ASP 3.6 19.3 - - - +
1165D PTR 3.7 11.9 - - + -
1182D GLU* 5.1 1.7 + - - +
1188D VAL* 4.3 12.3 - - + -
1189D PHE* 1.3 80.6 - - - +
1191D THR* 1.3 66.7 + - - +
1192D TYR* 3.0 41.6 + - + +
1193D SER* 2.9 21.3 + - - -
1194D ASP* 3.3 5.4 + - - -
1253D PRO* 5.2 0.9 - - - +
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Residues in contact with THR1191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127D ASN* 2.5 44.8 + - - +
1132D VAL* 3.6 5.3 - - - +
1160D ILE* 5.0 5.6 - - - +
1164D ASP 4.9 1.8 + - - -
1190D THR* 1.3 75.3 - - - +
1192D TYR* 1.3 90.6 + - + +
1194D ASP* 3.2 7.3 + - - +
1195D VAL* 3.1 24.6 + - + +
1258D SER* 5.8 5.4 - - - -
1259D PHE* 4.3 6.1 + - - -
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Residues in contact with TYR1192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182D GLU* 4.7 0.2 - - - +
1190D THR* 2.9 27.7 + - + +
1191D THR* 1.3 95.0 - - + +
1193D SER* 1.3 55.2 + - - +
1195D VAL* 3.2 9.6 + - + +
1196D TRP 3.1 16.8 + - - -
1253D PRO* 3.3 44.4 - - + +
1254D LYS* 4.1 35.1 - - + +
1256D ARG* 3.0 27.8 + - + +
1257D PRO 5.3 5.6 - - - -
1258D SER* 6.1 3.8 - - - -
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Residues in contact with SER1193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178D TRP 5.0 0.2 - - - +
1180D SER* 3.5 24.3 + - - -
1182D GLU* 3.9 5.1 + - - -
1183D SER* 3.7 10.3 - - - -
1188D VAL 4.5 0.7 - - - -
1189D PHE* 3.4 15.4 - - - +
1190D THR* 2.9 33.3 + - - -
1192D TYR* 1.3 75.6 - - - +
1194D ASP* 1.3 66.9 + - - +
1195D VAL 3.3 0.2 - - - -
1196D TRP* 3.5 4.0 + - - +
1197D SER* 3.2 24.9 + - - -
1256D ARG* 3.9 8.5 - - - +
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Residues in contact with ASP1194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123D MET* 3.2 20.0 - - + +
1127D ASN* 3.7 12.0 + - - -
1132D VAL* 3.7 3.0 - - - +
1133D HIS* 2.9 23.8 + - - +
1134D ARG* 3.0 26.4 + - - +
1135D ASP 4.9 0.2 + - - -
1136D LEU* 3.7 5.7 - - - +
1189D PHE* 6.1 0.2 - - - +
1190D THR 3.3 9.5 + - - +
1191D THR* 3.2 11.2 + - - +
1192D TYR 3.2 0.4 - - - -
1193D SER* 1.3 78.5 + - - +
1195D VAL* 1.3 58.5 + - - +
1197D SER* 3.4 7.2 + - - -
1198D PHE* 3.0 26.9 + - - +
1259D PHE* 3.5 18.8 - - + -
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Residues in contact with VAL1195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191D THR* 3.1 18.1 + - + +
1192D TYR* 3.2 13.0 + - + +
1194D ASP* 1.3 74.0 - - - +
1196D TRP* 1.3 64.4 + - - +
1198D PHE* 3.2 5.9 - - + +
1199D GLY 3.1 16.3 + - - -
1248D CYS* 3.4 29.3 - - + +
1256D ARG* 4.3 4.7 - - + -
1257D PRO* 3.3 37.2 - - + +
1258D SER* 4.6 1.8 - - - -
1259D PHE* 3.7 31.6 - - + +
1262D ILE* 4.8 4.5 - - + -
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Residues in contact with TRP1196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177D ARG 5.3 1.0 + - - -
1178D TRP 3.6 10.8 + - - -
1179D MET 3.4 11.3 + - - -
1180D SER* 3.5 26.5 - - - -
1181D PRO* 3.6 20.2 - - + -
1192D TYR 3.1 5.9 + - - -
1193D SER 3.5 8.3 - - - +
1194D ASP 3.3 0.2 - - - -
1195D VAL* 1.3 76.9 - - - +
1197D SER* 1.3 60.0 + - - +
1199D GLY 2.9 16.6 + - - -
1200D VAL* 3.3 18.5 + - + +
1213D TYR* 4.2 14.3 + - - -
1225D VAL* 3.8 22.4 - - + -
1229D GLY 4.7 3.1 - - - -
1230D LEU* 4.1 13.0 - - + -
1248D CYS 3.5 12.7 + - - -
1249D TRP* 3.3 68.7 + + + -
1250D GLN 4.2 1.6 - - - -
1251D TYR* 5.2 1.1 - + - -
1256D ARG* 3.6 31.9 - - - +
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Residues in contact with SER1197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134D ARG 5.3 5.1 + - - -
1136D LEU* 3.6 32.1 + - - -
1178D TRP* 2.8 27.6 + - - +
1179D MET* 5.0 0.3 - - - -
1193D SER 3.2 12.3 + - - -
1194D ASP* 3.7 10.0 + - - -
1195D VAL 3.3 0.2 - - - -
1196D TRP* 1.3 77.6 - - - +
1198D PHE* 1.3 63.3 + - - +
1200D VAL* 2.9 17.7 + - - +
1201D VAL* 3.1 17.9 + - - +
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Residues in contact with PHE1198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116D ALA* 3.5 29.6 - - + -
1119D ILE* 3.7 22.2 - - + -
1120D ALA* 3.7 22.2 - - + -
1136D LEU* 3.7 9.1 - - + +
1194D ASP 3.0 14.5 + - - +
1195D VAL* 3.2 9.9 - - + +
1197D SER* 1.3 76.7 - - - +
1199D GLY* 1.3 63.5 + - - +
1201D VAL* 3.2 8.7 + - + +
1202D LEU* 3.0 53.1 + - + +
1244D LEU* 4.9 0.4 - - + -
1248D CYS* 3.9 14.4 - - - -
1259D PHE* 3.6 24.7 - + + -
1262D ILE* 3.8 26.9 - - + -
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Residues in contact with GLY1199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195D VAL 3.1 6.7 + - - -
1196D TRP 2.9 10.5 + - - -
1198D PHE* 1.3 75.3 - - - +
1200D VAL* 1.3 56.1 + - - +
1202D LEU* 3.3 12.4 - - - +
1203D TRP* 3.1 20.1 + - - +
1245D MET* 3.8 4.4 - - - +
1248D CYS* 3.8 18.2 - - - -
1249D TRP* 3.3 25.0 - - - -
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Residues in contact with VAL1200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177D ARG 4.0 13.7 - - - +
1178D TRP* 3.6 27.6 - - + +
1196D TRP* 3.6 30.1 - - + +
1197D SER* 2.9 9.3 + - - +
1199D GLY* 1.3 76.3 - - - +
1201D VAL* 1.3 60.2 + - - +
1203D TRP* 3.3 4.2 + - + +
1204D GLU* 2.8 26.1 + - - +
1212D PRO* 3.9 24.9 - - + -
1213D TYR* 5.3 2.7 - - - +
1231D LEU* 4.5 8.5 - - + -
1249D TRP* 3.8 18.4 - - + +
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Residues in contact with VAL1201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D LEU* 5.7 1.8 - - + -
1119D ILE* 3.9 28.5 - - + -
1136D LEU* 3.9 16.2 - - + -
1137D ALA* 3.8 28.0 - - - -
1138D ALA* 4.2 8.1 - - + +
1141D CYS* 5.6 0.9 - - - -
1178D TRP* 4.8 0.4 - - - +
1197D SER 3.1 15.5 + - - +
1198D PHE* 3.2 17.0 + - + +
1200D VAL* 1.3 72.6 - - - +
1202D LEU* 1.3 68.6 + - + +
1203D TRP 3.1 0.2 - - - -
1204D GLU* 2.9 13.3 + - + +
1205D ILE* 2.8 39.9 + - + +
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Residues in contact with LEU1202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116D ALA* 3.6 32.3 - - + -
1198D PHE* 3.0 34.4 + - + +
1199D GLY* 3.3 11.7 - - - +
1201D VAL* 1.3 82.9 - - + +
1203D TRP* 1.3 57.1 + - - +
1205D ILE* 3.2 14.1 + - + +
1206D ALA* 3.0 23.2 + - - +
1241D LEU* 3.9 18.4 - - + +
1244D LEU* 3.8 34.3 - - + -
1245D MET* 3.5 31.5 - - + +
1248D CYS* 4.7 0.4 - - - -
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Residues in contact with TRP1203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199D GLY 3.1 11.2 + - - +
1200D VAL 3.4 9.2 - - - +
1202D LEU* 1.3 79.1 - - - +
1204D GLU* 1.3 65.9 + - - +
1206D ALA* 3.3 1.0 + - - +
1207D THR* 3.0 44.6 + - + +
1210D GLU* 3.6 37.5 - - + -
1211D GLN 3.9 7.9 - - - -
1212D PRO* 3.5 36.3 - - + -
1213D TYR 4.6 1.1 - - - -
1214D GLN 5.8 0.2 - - - -
1231D LEU* 3.6 40.5 - - + +
1232D ASP 3.2 25.6 + - - -
1234D PRO* 3.7 20.6 - - + +
1242D PHE* 5.7 0.2 - + - -
1245D MET* 3.5 20.8 - - - +
1249D TRP* 4.1 1.6 - + + -
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Residues in contact with GLU1204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D LYS* 4.5 12.1 + - - +
1091D LEU* 4.0 2.6 - - + +
1138D ALA* 3.0 40.7 + - + +
1139D ARG 5.0 0.3 + - - -
1178D TRP* 2.9 46.4 + - + -
1200D VAL 2.8 14.2 + - - +
1201D VAL* 2.9 14.2 + - - +
1203D TRP* 1.3 81.5 - - + +
1205D ILE* 1.3 57.5 + - - +
1207D THR* 3.3 6.5 + - - -
1208D LEU 2.9 8.8 + - - -
1209D ALA* 2.7 35.4 + - - +
1210D GLU 4.4 14.4 - - - +
1212D PRO* 4.6 2.2 - - + -
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Residues in contact with ILE1205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087D LEU* 4.6 8.5 - - + -
1091D LEU* 4.0 26.0 - - + -
1107D PRO* 3.7 16.3 - - + +
1112D MET* 3.4 37.5 - - + +
1115D MET* 4.2 27.6 - - + -
1116D ALA 5.1 0.9 - - - +
1119D ILE* 4.4 13.2 - - + -
1138D ALA* 6.1 0.2 - - + -
1201D VAL* 2.8 39.4 + - + +
1202D LEU* 3.6 17.5 - - + +
1204D GLU* 1.3 72.8 - - - +
1206D ALA* 1.3 61.6 + - - +
1208D LEU* 3.4 9.2 + - - +
1241D LEU* 5.5 0.4 - - + -
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Residues in contact with ALA1206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107D PRO* 5.7 1.2 - - - +
1112D MET* 3.1 19.5 - - + +
1202D LEU 3.0 14.8 + - - +
1203D TRP 3.7 5.4 - - - +
1204D GLU 3.3 0.2 - - - -
1205D ILE* 1.3 76.9 - - - +
1207D THR* 1.3 60.5 + - - +
1208D LEU* 3.4 2.0 - - - +
1234D PRO* 3.7 26.1 - - + +
1236D ASN 5.9 1.2 - - - -
1237D CYS* 4.1 13.4 + - + +
1238D PRO* 5.8 0.4 - - + -
1245D MET* 4.0 11.0 - - + -
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Residues in contact with THR1207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095D ARG* 4.5 4.0 + - - -
1203D TRP* 3.0 49.6 + - + +
1204D GLU* 3.3 5.5 + - - -
1206D ALA* 1.3 76.1 - - - +
1208D LEU* 1.3 70.2 + - - +
1210D GLU* 3.3 44.0 + - - +
1234D PRO* 3.7 23.3 - - + -
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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