Contacts of the helix formed by residues 1108 - 1129 (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 SER1108 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107D PRO* 1.3 77.6 - - - +
1109D LEU* 1.3 64.6 + - - +
1110D SER* 3.7 9.6 + - - -
1111D LYS* 3.1 30.4 + - - +
1112D MET* 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108D SER* 1.3 73.4 - - - +
1110D SER* 1.3 63.0 + - - +
1112D MET* 3.3 6.2 + - + +
1113D ILE* 2.9 46.2 + - + +
1238D PRO* 3.7 41.6 - - + +
1240D MET* 4.3 28.3 - - + -
1241D LEU* 4.3 12.1 - - + -
1269D GLU* 5.2 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108D SER* 3.2 9.1 + - - -
1109D LEU* 1.3 79.1 - - - +
1111D LYS* 1.3 63.7 + - - +
1113D ILE* 3.4 5.7 + - - +
1114D GLN* 3.2 22.0 + - - +
1269D GLU* 5.3 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107D PRO* 3.7 17.3 - - + -
1108D SER* 3.1 27.2 + - - +
1110D SER* 1.3 79.9 - - - +
1112D MET* 1.3 62.6 + - - +
1114D GLN* 3.2 16.9 + - - +
1115D MET* 3.2 22.2 + - + +
1147D PHE* 5.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107D PRO* 3.4 33.4 - - + +
1108D SER 3.0 13.2 + - - +
1109D LEU* 3.9 7.2 - - - +
1111D LYS* 1.3 72.7 - - - +
1113D ILE* 1.3 62.5 + - - +
1115D MET* 3.4 5.8 + - - +
1116D ALA* 2.9 30.1 + - - +
1202D LEU* 5.5 0.3 - - - +
1205D ILE* 3.4 29.6 - - + +
1206D ALA* 3.1 43.5 - - + +
1238D PRO* 5.0 12.3 - - + -
1241D LEU* 3.4 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109D LEU* 2.9 28.6 + - + +
1110D SER* 3.8 5.8 - - - +
1112D MET* 1.3 76.7 - - - +
1114D GLN* 1.3 58.7 + - - +
1116D ALA* 3.6 4.7 - - + +
1117D GLY 2.9 25.5 + - - -
1240D MET* 3.6 38.8 - - + -
1241D LEU* 3.9 15.0 - - + -
1244D LEU* 5.7 1.1 - - + -
1266D ILE* 4.0 28.3 - - + -
1269D GLU* 3.8 37.9 - - + +
1270D MET* 3.5 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110D SER 3.2 12.3 + - - +
1111D LYS* 3.2 12.5 + - - +
1113D ILE* 1.3 77.0 - - - +
1115D MET* 1.3 62.8 + - + +
1117D GLY 3.5 0.2 + - - -
1118D GLU* 2.9 57.6 + - - +
1147D PHE 6.1 0.4 - - - +
1269D GLU 4.8 1.5 + - - +
1270D MET* 3.4 28.1 - - - +
1271D GLU* 3.0 58.1 + - + +
1274D PHE* 4.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087D LEU* 4.0 21.3 - - + -
1090D TYR* 3.7 32.8 - - + +
1091D LEU* 4.7 3.6 - - + -
1107D PRO* 5.4 6.7 - - + -
1111D LYS* 3.2 16.9 + - + +
1112D MET* 3.7 7.0 - - - +
1113D ILE 3.3 0.2 - - - -
1114D GLN* 1.3 78.6 - - + +
1116D ALA* 1.3 62.7 + - - +
1118D GLU* 3.2 10.1 + - - +
1119D ILE* 2.9 31.5 + - + +
1143D VAL* 5.5 2.5 - - + -
1147D PHE* 4.9 9.9 - - + +
1149D VAL* 3.4 23.1 - - + +
1205D ILE* 4.2 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112D MET 2.9 18.5 + - - +
1113D ILE* 3.6 11.7 - - + +
1115D MET* 1.3 76.2 - - - +
1117D GLY* 1.3 57.2 + - - +
1119D ILE* 3.4 4.2 + - - -
1120D ALA* 2.9 30.9 + - - +
1198D PHE* 3.5 14.3 - - + -
1202D LEU* 3.6 28.9 - - + -
1205D ILE* 5.1 1.3 - - + +
1241D LEU* 5.2 2.0 - - + -
1244D LEU* 5.5 3.4 - - + -
1266D ILE* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113D ILE 2.9 16.5 + - - -
1116D ALA* 1.3 76.7 - - - +
1118D GLU* 1.3 56.2 + - - +
1120D ALA* 3.7 4.1 - - - +
1121D ASP* 2.9 30.7 + - - +
1263D ILE* 4.5 4.1 - - - +
1266D ILE* 3.8 13.2 - - - +
1270D MET* 3.7 21.5 - - - -
1274D PHE* 4.1 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061D HIS* 3.3 42.9 + - + +
1114D GLN* 2.9 50.2 + - - +
1115D MET* 3.7 4.4 + - - +
1117D GLY* 1.3 74.6 - - - +
1119D ILE* 1.3 65.2 + - - +
1121D ASP* 3.4 1.0 + - - -
1122D GLY* 3.1 18.5 + - - -
1147D PHE 4.2 1.2 - - - +
1148D THR* 3.7 22.7 + - - +
1149D VAL* 2.9 42.9 + - - +
1150D LYS* 5.6 0.2 - - - -
1270D MET* 4.2 2.9 - - + -
1274D PHE* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087D LEU* 4.1 23.3 - - + -
1115D MET* 2.9 25.3 + - + +
1116D ALA* 3.8 5.4 - - - +
1118D GLU* 1.3 76.7 - - - +
1120D ALA* 1.3 57.0 + - - +
1122D GLY 3.3 1.0 + - - -
1123D MET* 3.0 28.6 + - + +
1136D LEU* 4.1 24.9 - - + -
1141D CYS* 4.5 9.2 - - - -
1149D VAL* 3.8 19.3 - - + -
1150D LYS* 5.7 0.4 - - - +
1151D ILE* 3.6 10.7 - - + +
1198D PHE* 3.7 21.1 - - + -
1201D VAL* 3.9 23.6 - - + -
1205D ILE* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116D ALA 2.9 19.2 + - - +
1117D GLY* 3.7 6.7 - - - +
1119D ILE* 1.3 74.7 - - - +
1121D ASP* 1.3 59.8 + - - +
1123D MET* 3.2 2.9 + - - +
1124D ALA* 2.8 29.3 + - - +
1198D PHE* 3.7 18.4 - - + -
1259D PHE* 3.7 17.7 - - + +
1262D ILE* 4.4 9.9 - - + -
1263D ILE* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059D CYS* 4.0 3.6 - - - -
1061D HIS* 2.8 29.3 + - - +
1117D GLY 2.9 17.9 + - - +
1118D GLU 3.7 0.7 - - - +
1119D ILE 3.3 0.2 - - - -
1120D ALA* 1.3 73.1 - - - +
1122D GLY* 1.3 65.8 + - - +
1124D ALA* 3.2 2.6 + - - +
1125D TYR* 3.0 22.9 + - - +
1263D ILE* 3.6 10.1 - - + +
1274D PHE* 4.0 7.9 - - + -
1278D SER* 3.5 8.0 - - - -
1279D PHE* 2.8 26.1 + - - +
1280D TYR* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059D CYS* 4.6 1.3 - - - -
1061D HIS* 3.8 19.8 - - - +
1062D VAL* 4.3 10.5 - - - +
1118D GLU 3.1 10.7 + - - -
1119D ILE 3.7 0.2 - - - -
1121D ASP* 1.3 76.9 - - - +
1123D MET* 1.3 59.7 + - - +
1125D TYR* 3.2 8.5 + - - +
1126D LEU* 3.1 19.9 + - - +
1151D ILE* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119D ILE* 3.0 20.3 + - + +
1120D ALA 3.6 1.6 - - - +
1122D GLY* 1.3 73.3 - - - +
1124D ALA* 1.3 65.4 + - - +
1126D LEU* 3.2 9.6 + - + +
1127D ASN* 3.0 30.2 + - - +
1133D HIS* 3.7 22.2 - - + -
1136D LEU* 3.9 25.8 - - + -
1151D ILE* 3.5 17.9 - - + -
1194D ASP* 3.2 41.1 - - + +
1259D PHE* 3.5 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120D ALA 2.8 19.9 + - - +
1121D ASP 3.2 6.5 + - - +
1123D MET* 1.3 72.8 - - - +
1125D TYR* 1.3 57.8 + - - +
1127D ASN* 3.5 3.7 + - - +
1128D ALA* 2.9 31.9 + - - +
1259D PHE* 3.9 14.5 - - + +
1260D LEU* 4.1 12.6 - - + +
1263D ILE* 4.0 17.0 - - + -
1279D PHE* 3.9 19.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056D GLU* 3.6 9.4 + - - -
1057D PHE* 3.6 30.4 - + + -
1058D ASN* 2.9 36.4 + - - +
1059D CYS* 3.6 30.7 - - + -
1062D VAL* 4.4 6.5 - - + -
1121D ASP 3.0 11.8 + - - +
1122D GLY 3.4 8.1 - - - +
1123D MET 3.2 0.2 - - - -
1124D ALA* 1.3 76.6 - - - +
1126D LEU* 1.3 70.8 + - + +
1128D ALA* 3.4 3.4 + - - +
1129D ASN* 3.1 52.2 + - - +
1279D PHE* 3.8 29.8 - + + -
1284D GLU* 3.5 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057D PHE* 3.6 43.5 - - + -
1062D VAL* 5.4 2.7 - - + -
1122D GLY 3.1 10.6 + - - +
1123D MET* 3.2 15.0 + - + +
1125D TYR* 1.3 87.6 - - + +
1127D ASN* 1.3 63.6 + - - +
1129D ASN* 3.1 13.4 + - + +
1130D LYS 3.2 0.3 + - - -
1131D PHE* 3.1 33.2 + - + +
1133D HIS* 4.2 20.4 - - + +
1151D ILE* 5.8 0.7 - - + -
1154D PHE* 3.9 29.8 - - + -
1157D THR* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123D MET* 3.0 14.0 + - - +
1124D ALA* 4.1 4.0 - - - +
1126D LEU* 1.3 77.5 - - - +
1128D ALA* 1.3 57.1 + - - +
1130D LYS* 3.0 28.2 + - - +
1131D PHE 2.7 30.8 + - - +
1132D VAL* 4.1 3.2 - - - +
1160D ILE* 5.1 4.7 - - + +
1191D THR* 2.5 38.6 + - - +
1194D ASP* 3.7 15.2 + - - +
1259D PHE* 3.3 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124D ALA 2.9 18.9 + - - +
1125D TYR 3.6 5.2 - - - +
1126D LEU 3.2 0.2 - - - -
1127D ASN* 1.3 76.8 - - - +
1129D ASN* 1.3 61.3 + - - +
1130D LYS* 3.1 12.7 + - - +
1260D LEU* 6.4 0.9 - - + -
1279D PHE* 3.6 25.8 - - + -
1284D GLU* 5.2 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056D GLU* 3.8 23.3 + - - +
1057D PHE* 5.2 2.5 - - + -
1125D TYR* 3.1 49.2 + - - +
1126D LEU* 3.1 10.0 + - - +
1128D ALA* 1.3 76.3 + - - +
1130D LYS* 1.3 69.4 + - - +
1131D PHE* 3.5 19.1 - - + -
1159D ASP* 5.1 0.3 - - - +
1284D GLU* 3.4 16.4 + - - +
----------------------------------------------------------
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