Contacts of the helix formed by residues 1131 - 1151 (chain C) in PDB entry 4DDG
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 THR1131 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 5.8 2.5 - - - +
96A ALA 3.5 13.1 + - - -
98A THR* 3.5 32.1 - - + +
101A LYS* 3.9 23.2 - - - +
1129C GLY 3.7 2.9 + - - +
1130C PHE* 1.3 70.0 - - - +
1132C GLU* 1.3 63.1 + - - +
1133C PHE* 3.5 13.2 - - + -
1134C THR* 2.7 25.7 + - - -
1135C ILE* 3.4 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122C LYS* 3.7 27.4 + - - +
1123C GLU* 5.2 5.9 - - - +
1126C VAL* 3.8 40.5 - - + +
1130C PHE 3.3 3.4 + - - -
1131C THR* 1.3 71.0 - - - +
1133C PHE* 1.3 61.1 + - - +
1134C THR 3.1 0.3 + - - -
1135C ILE* 3.2 3.7 + - - +
1136C GLU* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.9 2.7 - - - -
8A LYS* 3.5 36.2 - - + -
9A GLU* 3.6 36.8 - - + -
12A ASP* 3.6 38.6 - - + -
98A THR* 3.9 23.6 - - + -
1131C THR* 3.5 11.1 - - + -
1132C GLU* 1.3 80.2 - - - +
1134C THR* 1.3 87.0 + - + +
1136C GLU* 3.6 12.9 - - - +
1137C ASP* 3.2 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.3 34.5 - - - +
96A ALA* 3.0 27.4 + - - +
98A THR* 4.0 9.4 - - + -
1131C THR* 2.7 15.4 + - - +
1133C PHE* 1.3 105.2 - - + +
1135C ILE* 1.3 72.9 + - - +
1136C GLU 3.1 5.6 + - - -
1137C ASP* 3.3 12.7 - - - +
1138C PHE* 3.1 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 4.2 6.7 - - + -
1122C LYS* 4.2 11.9 - - + +
1125C LEU* 3.9 28.0 - - + -
1126C VAL* 3.7 27.8 - - + +
1130C PHE* 4.1 18.8 - - + -
1131C THR 3.4 8.1 - - - +
1132C GLU* 3.2 10.1 + - + +
1134C THR* 1.3 90.3 + - - +
1136C GLU* 1.3 62.7 + - - +
1137C ASP 3.3 0.7 - - - -
1138C PHE* 3.4 11.6 + - - +
1139C HIS* 2.9 29.8 + - - +
1174C TYR* 4.3 4.4 - - + -
1177C LEU* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.6 23.2 + - - -
1122C LYS* 3.5 28.3 + - - +
1132C GLU* 2.9 25.8 + - - +
1133C PHE* 3.6 14.3 - - - +
1134C THR 3.1 0.2 - - - -
1135C ILE* 1.3 80.1 - - - +
1137C ASP* 1.3 59.0 + - - +
1139C HIS* 3.5 5.7 + - - +
1140C ASN* 2.9 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 6.2 2.7 - - + -
5A ARG* 3.9 23.7 + - - +
8A LYS* 3.2 34.4 + - - +
1133C PHE 3.2 7.2 - - - +
1134C THR 3.3 15.3 - - - +
1136C GLU* 1.3 72.2 - - - +
1138C PHE* 1.3 62.6 + - + +
1140C ASN* 3.1 11.9 + - - +
1141C THR* 2.9 29.6 + - - -
1170C TYR* 3.9 23.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.6 9.6 - - - -
61A PRO* 3.5 28.3 - - + -
62A PHE* 4.4 0.9 - + - -
95A PRO* 3.8 12.8 - - + -
96A ALA* 4.7 2.0 - - - -
1134C THR 3.1 30.5 - - - -
1135C ILE* 3.4 12.5 + - - +
1136C GLU 3.4 0.2 - - - -
1137C ASP* 1.3 72.5 - - - +
1139C HIS* 1.3 66.0 + - - +
1141C THR* 3.2 5.2 + - - +
1142C PHE* 2.9 22.9 + - - +
1170C TYR* 3.5 52.2 - + - +
1173C VAL* 3.7 35.9 - - + -
1174C TYR* 3.9 26.8 - - + +
1177C LEU* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118C SER 3.2 24.9 - - - -
1119C ALA* 3.9 8.2 + - - +
1122C LYS* 3.5 42.5 - - + +
1135C ILE 2.9 18.3 + - - +
1136C GLU 3.6 4.0 - - - +
1138C PHE* 1.3 76.6 - - - +
1140C ASN* 1.3 66.7 + - - +
1142C PHE* 3.3 4.4 + - - +
1143C MET* 2.9 61.5 + - + +
1174C TYR* 3.1 33.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122C LYS* 5.4 1.0 + - - -
1136C GLU* 2.9 33.2 + - - +
1137C ASP* 3.2 13.5 + - - +
1139C HIS* 1.3 85.5 - - - +
1141C THR* 1.3 57.9 + - - +
1143C MET* 3.4 5.5 + - - +
1144C ASP* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137C ASP 2.9 12.8 + - - -
1138C PHE 3.2 6.3 + - - -
1140C ASN* 1.3 74.8 - - - +
1142C PHE* 1.3 63.6 + - - +
1144C ASP* 3.3 6.9 + - - +
1145C LEU* 2.9 37.4 + - + +
1167C THR* 3.3 37.6 - - + +
1170C TYR* 3.8 24.3 - - + +
1171C LEU 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097C GLY* 6.3 1.8 - - - -
1101C LEU* 5.2 5.4 - - + -
1114C PHE* 3.8 30.1 - + - -
1118C SER* 3.5 29.4 - - - -
1138C PHE 2.9 12.8 + - - +
1139C HIS* 3.4 8.1 - - - +
1141C THR* 1.3 78.4 - - - +
1143C MET* 1.3 61.7 + - - +
1145C LEU* 3.0 10.6 + - + +
1146C ILE* 2.9 34.9 + - + +
1171C LEU* 3.6 29.8 - - + -
1174C TYR* 3.4 37.2 - + + -
1175C LEU* 4.4 18.4 - - + -
1178C LEU* 4.4 5.6 - - + -
1227C LEU* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115C LYS* 4.1 27.7 - - + +
1118C SER* 3.5 25.4 - - - +
1119C ALA* 4.0 22.2 - - + -
1139C HIS* 2.9 57.0 + - + +
1140C ASN* 4.0 5.2 - - - +
1142C PHE* 1.3 74.9 - - + +
1144C ASP* 1.3 57.6 + - - +
1146C ILE* 3.2 11.9 + - + +
1147C GLU* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140C ASN* 2.9 21.9 + - - +
1141C THR* 3.6 7.6 - - - +
1143C MET* 1.3 75.8 - - - +
1145C LEU* 1.3 63.9 + - + +
1147C GLU* 3.0 22.6 + - - +
1148C GLN* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101C LEU* 3.9 20.6 - - + +
1141C THR* 2.9 37.4 + - + +
1142C PHE* 3.3 7.4 - - - +
1144C ASP* 1.3 80.2 - - + +
1146C ILE* 1.3 59.9 + - - +
1147C GLU 3.5 0.2 + - - -
1148C GLN* 3.4 31.7 + - - +
1149C VAL* 3.6 17.8 + - - +
1158C LEU* 4.9 5.0 - - + +
1161C SER* 4.1 10.1 - - - -
1162C PHE* 4.5 16.8 - - + -
1167C THR* 4.1 21.8 - - + +
1168C SER* 5.6 0.9 - - - +
1171C LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101C LEU* 4.3 6.7 - - + -
1104C LEU* 5.4 0.7 - - + -
1111C LEU* 4.1 19.5 - - + -
1114C PHE* 3.8 31.4 - - + -
1115C LYS* 4.2 22.0 - - + +
1118C SER* 3.2 31.0 - - - +
1142C PHE* 2.9 23.0 + - + +
1143C MET* 3.5 17.9 - - + +
1144C ASP 3.2 0.2 - - - -
1145C LEU* 1.3 77.0 - - - +
1147C GLU* 1.3 58.2 + - - +
1149C VAL* 3.1 11.2 - - + +
1150C GLU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143C MET 2.9 12.1 + - - +
1144C ASP* 3.0 34.4 + - - +
1146C ILE* 1.3 75.7 - - - +
1148C GLN* 1.3 63.0 + - + +
1149C VAL 3.1 1.3 - - - -
1150C GLU* 3.1 34.4 + - + +
1151C LYS 4.1 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144C ASP* 2.9 23.6 + - - +
1145C LEU* 3.4 29.0 - - - +
1146C ILE 3.4 0.4 - - - -
1147C GLU* 1.3 77.8 - - + +
1149C VAL* 1.3 56.4 + - - +
1151C LYS 3.3 12.8 - - - +
1153C THR* 3.2 29.5 - - + +
1157C ASP* 4.1 3.1 - - - +
1158C LEU* 3.8 17.2 + - + -
1161C SER* 2.5 34.5 + - - -
1167C THR* 5.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101C LEU* 3.4 38.8 - - + +
1104C LEU* 4.4 4.2 - - + +
1105C LEU* 3.5 36.9 - - + +
1111C LEU* 3.2 25.9 - - + +
1145C LEU 3.6 7.5 + - - +
1146C ILE* 3.1 28.0 + - + +
1147C GLU 3.1 0.4 - - - -
1148C GLN* 1.3 78.9 - - - +
1150C GLU* 1.3 67.7 + - - +
1151C LYS 3.6 1.6 - - - -
1152C GLN* 3.9 9.9 + - - +
1153C THR* 5.2 0.2 - - - -
1158C LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111C LEU* 3.4 27.3 - - + +
1115C LYS* 3.0 40.5 + - - +
1146C ILE 2.9 11.5 + - - +
1147C GLU* 3.1 32.6 + - + +
1149C VAL* 1.3 80.7 - - - +
1151C LYS* 1.3 61.4 + - + +
1152C GLN* 3.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147C GLU 4.1 3.5 + - - +
1148C GLN 3.3 11.4 - - - +
1149C VAL 3.9 0.2 - - - -
1150C GLU* 1.3 78.5 - - + +
1152C GLN* 1.3 70.9 + - - +
1153C THR* 3.2 4.0 + - - -
----------------------------------------------------------
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