Contacts of the helix formed by residues 1078 - 1099 (chain A) in PDB entry 2OJ9
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 SER1078 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076A PRO 3.5 2.8 + - - -
1077A PRO* 1.3 77.2 - - - +
1079A LEU* 1.3 67.0 + - - +
1080A SER* 3.6 8.0 + - - -
1081A LYS* 3.0 27.5 + - - +
1082A MET* 2.9 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1079 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078A SER* 1.3 73.1 - - - +
1080A SER* 1.3 57.8 + - - +
1082A MET* 3.2 9.7 + - - +
1083A ILE* 2.9 42.0 + - + +
1208A PRO* 3.7 40.8 - - + -
1210A MET* 3.9 34.1 - - + -
1211A LEU* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1080 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078A SER* 3.1 8.6 + - - -
1079A LEU* 1.3 80.1 - - - +
1081A LYS* 1.3 66.2 + - - +
1083A ILE* 3.5 11.4 + - - +
1084A GLN* 3.2 21.7 + - - +
1239A GLU* 5.0 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1081 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077A PRO* 3.8 18.8 - - + -
1078A SER* 3.0 23.9 + - - +
1080A SER* 1.3 81.8 + - - +
1082A MET* 1.3 64.7 + - - +
1084A GLN* 3.3 8.5 + - + +
1085A MET* 3.1 29.6 + - + +
1241A GLU* 4.2 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1082 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077A PRO* 3.3 42.8 - - + +
1078A SER 2.9 6.3 + - - +
1079A LEU* 3.6 23.6 - - + +
1081A LYS* 1.3 76.8 - - - +
1083A ILE* 1.3 61.3 + - - +
1085A MET* 3.4 4.7 + - - +
1086A ALA* 2.9 29.0 + - - +
1172A LEU* 5.4 0.5 - - - +
1175A ILE* 3.6 29.0 - - + +
1176A ALA* 4.3 13.5 - - - -
1208A PRO* 4.1 17.0 - - + -
1211A LEU* 3.7 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1083 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079A LEU* 2.9 39.3 + - + +
1080A SER* 3.7 8.1 - - - +
1081A LYS 3.3 0.2 - - - -
1082A MET* 1.3 74.4 - - - +
1084A GLN* 1.3 61.0 + - - +
1086A ALA* 3.3 6.5 + - - +
1087A GLY* 2.8 28.2 + - - -
1210A MET* 3.6 31.9 - - + -
1211A LEU* 4.6 6.1 - - + -
1236A ILE* 3.9 25.3 - - + +
1239A GLU* 3.5 40.2 - - + +
1240A MET* 3.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1084 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080A SER 3.2 14.5 + - - +
1081A LYS* 3.5 14.6 - - + +
1082A MET 3.2 0.2 - - - -
1083A ILE* 1.3 76.8 - - - +
1085A MET* 1.3 63.1 + - + +
1087A GLY 3.3 1.4 + - - -
1088A GLU* 2.9 59.2 + - - +
1239A GLU 4.2 1.7 - - - +
1240A MET* 3.4 24.9 - - - +
1241A GLU* 2.9 61.1 + - + +
1244A PHE* 5.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1085 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A LEU* 4.2 20.0 - - - -
1060A TYR* 4.5 20.9 - - + +
1061A LEU* 4.8 3.8 - - + -
1064A LEU* 5.5 0.2 - - + -
1077A PRO* 3.6 34.8 - - + -
1081A LYS* 3.1 16.9 + - + +
1082A MET* 3.7 6.3 - - - +
1083A ILE 3.4 0.2 - - - -
1084A GLN* 1.3 76.1 - - + +
1086A ALA* 1.3 59.7 + - - +
1088A GLU* 3.2 10.9 + - - +
1089A ILE* 2.9 37.2 + - + +
1117A PHE 5.4 2.5 - - - +
1119A VAL* 3.7 18.6 - - + -
1175A ILE* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1086 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082A MET 2.9 18.1 + - - +
1083A ILE* 3.6 7.9 - - - +
1084A GLN 3.3 0.2 - - - -
1085A MET* 1.3 76.3 - - - +
1087A GLY* 1.3 57.4 + - - +
1089A ILE* 4.6 3.6 - - - +
1090A ALA* 2.8 31.7 + - - +
1168A PHE* 3.5 15.5 - - + -
1172A LEU* 3.6 28.5 - - + -
1175A ILE* 4.8 1.3 - - + +
1211A LEU* 5.6 3.4 - - + -
1214A LEU* 5.3 4.5 - - + -
1236A ILE* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1087 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083A ILE 2.8 20.5 + - - -
1084A GLN 3.7 1.3 - - - -
1086A ALA* 1.3 72.7 - - - +
1088A GLU* 1.3 57.4 + - - +
1090A ALA* 3.5 3.9 + - - +
1091A ASP* 2.9 30.1 + - - +
1233A ILE* 4.3 5.2 - - - +
1236A ILE* 3.7 17.0 - - - +
1240A MET* 3.7 15.7 - - - -
1244A PHE* 4.0 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031A HIS* 3.3 36.2 + - + +
1084A GLN* 2.9 53.5 + - - +
1085A MET* 3.7 7.9 - - - +
1087A GLY* 1.3 72.7 - - - +
1089A ILE* 1.3 66.8 + - - +
1091A ASP* 3.3 1.4 + - - -
1092A GLY* 3.1 18.9 + - - -
1117A PHE 4.3 1.7 - - - +
1118A THR* 3.8 20.0 + - - +
1119A VAL* 2.9 45.2 + - - +
1240A MET* 4.2 3.4 - - + -
1244A PHE* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A LEU* 4.0 11.2 - - + -
1085A MET* 2.9 25.5 + - + +
1086A ALA* 3.8 4.9 - - - +
1088A GLU* 1.3 76.3 - - - +
1090A ALA* 1.3 62.3 + - - +
1092A GLY 3.3 1.2 + - - -
1093A MET* 3.0 23.6 + - + +
1106A LEU* 4.3 13.0 - - + -
1111A CYS* 4.2 6.7 - - - -
1119A VAL* 3.4 31.2 - - + -
1121A ILE* 3.6 22.0 - - + +
1168A PHE* 3.7 22.4 - - + -
1171A VAL* 4.0 24.7 - - + -
1175A ILE* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086A ALA 2.8 18.9 + - - +
1087A GLY* 3.9 1.6 - - - +
1089A ILE* 1.3 78.0 - - - +
1091A ASP* 1.3 57.2 + - - +
1094A ALA* 2.8 31.5 + - - +
1168A PHE* 4.0 15.7 - - + -
1229A PHE* 3.7 21.7 - - + +
1232A ILE* 4.1 10.8 - - + -
1233A ILE* 3.6 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029A CYS* 4.3 2.4 - - - -
1031A HIS* 2.8 26.1 + - - +
1087A GLY 2.9 18.3 + - - +
1088A GLU 3.6 4.7 - - - +
1090A ALA* 1.3 75.6 - - - +
1092A GLY* 1.3 64.6 + - - +
1094A ALA* 3.4 1.2 + - - +
1095A TYR* 3.0 23.2 + - - +
1233A ILE* 3.5 8.0 - - + +
1244A PHE* 3.9 7.4 - - + -
1248A SER* 3.3 8.2 - - - -
1249A PHE* 2.7 27.5 + - - +
1250A TYR* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029A CYS* 4.2 3.1 - - - -
1031A HIS* 3.7 28.6 - - - +
1032A VAL* 3.8 7.5 - - - +
1088A GLU 3.1 11.3 + - - -
1089A ILE 3.8 2.5 - - - -
1091A ASP* 1.3 76.0 - - - +
1093A MET* 1.3 56.8 + - - +
1095A TYR* 3.4 4.2 + - - +
1096A LEU* 3.1 30.7 + - - +
1121A ILE* 4.0 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089A ILE* 3.0 20.2 + - + +
1090A ALA 3.7 0.2 - - - +
1092A GLY* 1.3 76.0 - - - +
1094A ALA* 1.3 59.3 + - - +
1095A TYR 3.1 0.4 - - - -
1096A LEU* 3.2 17.3 + - + +
1097A ASN* 2.8 39.1 + - - +
1103A HIS* 3.7 14.8 - - + +
1106A LEU* 3.8 21.8 - - + -
1121A ILE* 3.8 25.1 - - + -
1164A ASP* 3.2 42.2 - - + +
1229A PHE* 3.5 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1094 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090A ALA 2.8 22.3 + - - +
1091A ASP 3.8 4.3 - - - +
1093A MET* 1.3 73.1 - - - +
1095A TYR* 1.3 58.0 + - - +
1097A ASN* 3.9 3.4 - - - +
1098A ALA* 2.9 31.0 + - - +
1229A PHE* 3.7 17.9 - - + +
1230A LEU* 4.1 17.3 - - + +
1233A ILE* 4.0 14.4 - - + -
1249A PHE* 3.5 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1095 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A GLU 3.8 5.7 + - - -
1027A PHE* 3.6 25.9 - + + -
1028A ASN* 2.9 44.0 + - - +
1029A CYS* 3.6 29.8 - - + -
1032A VAL* 4.4 1.1 - - + -
1091A ASP 3.0 13.5 + - - +
1092A GLY 3.4 9.6 - - - +
1093A MET 3.1 0.2 - - - -
1094A ALA* 1.3 75.7 - - - +
1096A LEU* 1.3 75.5 + - + +
1098A ALA* 3.4 1.7 + - - +
1099A ASN* 2.9 52.0 + - - +
1249A PHE* 3.6 32.9 - + + -
1254A GLU* 3.9 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1096 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A PHE* 3.5 50.7 - - + -
1032A VAL* 4.3 8.7 - - + -
1092A GLY 3.1 16.9 + - - +
1093A MET* 3.2 20.2 + - + +
1095A TYR* 1.3 87.3 - - + +
1097A ASN* 1.3 61.6 + - - +
1099A ASN* 3.0 11.1 + - - +
1101A PHE* 2.9 38.3 + - + +
1103A HIS* 4.6 10.8 - - + +
1121A ILE* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1097 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093A MET* 2.8 21.4 + - - +
1094A ALA* 4.1 4.7 - - - +
1096A LEU* 1.3 72.8 - - - +
1098A ALA* 1.3 62.6 + - - +
1100A LYS* 3.0 17.5 + - - +
1101A PHE 3.0 19.7 - - - +
1161A THR* 2.2 39.9 + - - +
1164A ASP* 3.5 14.6 - - - +
1229A PHE* 3.0 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1098 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A ALA 2.9 19.9 + - - +
1095A TYR 3.6 4.3 - - - +
1096A LEU 3.2 0.2 - - - -
1097A ASN* 1.3 77.0 - - - +
1099A ASN* 1.3 61.6 + - - +
1100A LYS* 3.2 14.3 + - - +
1230A LEU* 6.4 1.3 - - + -
1249A PHE* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1099 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A GLU 6.0 1.1 - - - -
1027A PHE* 5.9 0.2 - - + -
1095A TYR* 2.9 51.5 + - + +
1096A LEU* 3.0 2.8 + - - -
1098A ALA* 1.3 82.2 + - - +
1100A LYS* 1.3 65.9 + - - +
1101A PHE* 3.0 39.5 - - + -
1249A PHE* 5.2 1.7 - - - -
1254A GLU* 5.1 2.0 + - - +
----------------------------------------------------------
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