Contacts of the helix formed by residues 1131 - 1151 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129A GLY 3.6 2.7 + - - +
1130A PHE* 1.3 70.2 - - - +
1132A GLU* 1.3 62.0 + - - +
1133A PHE* 3.5 13.5 - - + -
1134A THR* 2.8 29.8 + - - -
1135A ILE* 3.4 8.5 - - - +
12B ASP* 5.5 4.3 - - - +
96B ALA 4.0 4.0 + - - -
98B THR* 3.2 33.9 - - + +
101B LYS* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122A LYS* 3.7 26.6 + - - +
1123A GLU* 5.2 5.9 - - - +
1126A VAL* 3.8 39.6 - - + +
1130A PHE 3.3 3.4 + - - -
1131A THR* 1.3 72.5 - - - +
1133A PHE* 1.3 58.4 - - - +
1134A THR 3.1 0.3 + - - -
1135A ILE* 3.2 5.2 + - - +
1136A GLU* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131A THR* 4.5 9.4 - - + -
1132A GLU* 1.3 78.9 - - - +
1134A THR* 1.3 83.0 + - + +
1136A GLU* 3.6 15.7 - - - +
1137A ASP* 3.2 20.3 - - - +
5B ARG* 5.2 2.5 - - - -
8B LYS* 3.6 30.4 - - + -
9B GLU* 3.5 37.5 - - + -
12B ASP* 3.2 45.3 - - + -
98B THR* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131A THR* 2.8 16.2 + - - +
1133A PHE* 1.3 105.0 - - + +
1135A ILE* 1.3 73.2 + - - +
1136A GLU 3.1 4.9 + - - -
1137A ASP* 3.3 13.1 - - - +
1138A PHE* 3.1 21.4 - - - -
5B ARG* 3.7 25.8 - - - +
9B GLU* 5.3 0.2 - - - +
96B ALA* 3.0 28.9 + - - +
98B THR* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122A LYS* 4.2 11.7 - - + +
1125A LEU* 3.9 27.6 - - + -
1126A VAL* 3.7 28.7 - - + +
1130A PHE* 4.1 18.4 - - + -
1131A THR 3.4 9.2 - - - +
1132A GLU* 3.2 9.8 + - + +
1134A THR* 1.3 90.8 + - - +
1136A GLU* 1.3 61.0 - - - +
1137A ASP 3.3 0.4 - - - -
1138A PHE* 3.4 11.3 + - - +
1139A HIS* 2.9 29.6 + - - +
1174A TYR* 4.3 4.4 - - + -
1177A LEU* 3.9 24.2 - - + -
96B ALA* 4.4 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122A LYS* 3.5 28.5 + - - +
1132A GLU* 2.9 26.6 + - - +
1133A PHE* 3.6 16.7 - - - +
1134A THR 3.1 0.2 - - - -
1135A ILE* 1.3 79.7 - - - +
1137A ASP* 1.3 58.5 + - - +
1139A HIS* 3.5 5.7 + - - +
1140A ASN* 2.9 46.0 + - - +
8B LYS* 4.0 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133A PHE 3.2 8.1 - - - +
1134A THR 3.3 15.0 - - - +
1136A GLU* 1.3 73.2 - - - +
1138A PHE* 1.3 62.1 + - + +
1140A ASN* 3.1 12.5 + - - +
1141A THR* 2.9 29.6 + - - -
1170A TYR* 3.9 23.3 + - + -
5B ARG* 3.9 18.5 + - - +
8B LYS* 3.1 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134A THR 3.1 30.7 - - - -
1135A ILE* 3.4 11.6 + - - +
1136A GLU 3.4 0.2 - - - -
1137A ASP* 1.3 74.0 - - - +
1139A HIS* 1.3 66.3 + - - +
1141A THR* 3.2 5.0 + - - +
1142A PHE* 2.9 23.2 + - - +
1170A TYR* 3.5 52.9 - + - +
1173A VAL* 3.7 35.2 - - + -
1174A TYR* 3.9 25.7 - - + +
1177A LEU* 4.5 4.3 - - + -
5B ARG* 3.5 20.2 - - - -
61B PRO* 3.8 10.8 - - + -
62B PHE* 5.1 0.7 - + - -
95B PRO* 3.7 17.5 - - + -
96B ALA* 4.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A SER 3.2 24.9 - - - -
1119A ALA* 3.9 9.0 + - - +
1122A LYS* 3.5 41.5 - - + +
1135A ILE 2.9 17.4 + - - +
1136A GLU 3.6 4.7 - - - +
1138A PHE* 1.3 75.7 - - - +
1140A ASN* 1.3 66.4 + - - +
1142A PHE* 3.3 4.5 + - - +
1143A MET* 2.9 61.6 + - + +
1174A TYR* 3.1 33.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122A LYS* 5.4 1.0 + - - -
1136A GLU* 2.9 33.5 + - - +
1137A ASP* 3.1 13.7 + - - +
1139A HIS* 1.3 86.0 - - - +
1141A THR* 1.3 56.5 + - - +
1143A MET* 3.4 5.1 + - - +
1144A ASP* 2.9 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137A ASP 2.9 13.4 + - - -
1138A PHE 3.2 6.7 + - - -
1140A ASN* 1.3 75.6 - - - +
1142A PHE* 1.3 63.8 + - - +
1144A ASP* 3.3 7.0 + - - +
1145A LEU* 2.9 37.0 + - + +
1167A THR* 3.3 36.8 + - + +
1170A TYR* 3.8 24.0 - - + +
1171A LEU* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A GLY* 6.3 1.6 - - - -
1101A LEU* 5.2 6.3 - - + -
1114A PHE* 3.8 30.3 - + - -
1118A SER* 3.5 29.6 - - - -
1138A PHE 2.9 13.2 + - - +
1139A HIS 3.3 8.5 + - - +
1141A THR* 1.3 78.4 - - - +
1143A MET* 1.3 62.1 + - - +
1145A LEU* 3.0 9.8 + - + +
1146A ILE* 2.9 34.8 + - + +
1171A LEU* 3.6 28.5 - - + +
1174A TYR* 3.4 37.9 - + + -
1175A LEU* 4.4 20.0 - - + -
1178A LEU* 4.4 5.6 - - + -
1227A LEU* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115A LYS* 4.1 28.0 - - + +
1118A SER* 3.5 24.5 - - - +
1119A ALA* 4.0 22.2 - - + -
1139A HIS* 2.9 57.6 + - + +
1140A ASN* 4.0 4.7 - - - +
1142A PHE* 1.3 74.1 - - + +
1144A ASP* 1.3 58.1 + - - +
1146A ILE* 3.2 11.7 + - + +
1147A GLU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140A ASN* 2.9 22.5 + - - +
1141A THR* 3.6 7.9 - - - +
1143A MET* 1.3 75.8 - - - +
1145A LEU* 1.3 63.4 + - + +
1147A GLU* 3.0 23.9 + - - +
1148A GLN* 2.9 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A LEU* 3.9 19.9 - - + +
1141A THR* 2.9 37.4 + - + +
1142A PHE* 3.3 7.9 - - - +
1144A ASP* 1.3 79.4 - - + +
1146A ILE* 1.3 59.6 + - - +
1147A GLU 3.5 0.2 + - - -
1148A GLN* 3.4 32.5 + - - +
1149A VAL* 3.6 18.2 + - - +
1158A LEU* 4.9 5.9 - - + +
1161A SER* 4.1 10.3 - - - -
1162A PHE* 4.5 15.9 - - + -
1167A THR* 4.1 20.2 - - + +
1168A SER* 5.6 0.9 - - - -
1171A LEU* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A LEU* 4.3 7.6 - - + -
1104A LEU* 5.4 0.7 - - + -
1111A LEU* 4.1 20.2 - - + -
1114A PHE* 3.8 30.5 - - + -
1115A LYS* 4.2 22.2 - - + -
1118A SER* 3.2 31.0 - - - +
1142A PHE* 2.9 22.8 + - + +
1143A MET* 3.5 18.8 - - + +
1144A ASP 3.2 0.2 - - - -
1145A LEU* 1.3 75.8 - - + +
1147A GLU* 1.3 58.9 + - - +
1149A VAL* 3.1 11.9 - - + +
1150A GLU* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143A MET 2.9 11.2 + - - +
1144A ASP* 3.0 34.8 + - - +
1146A ILE* 1.3 75.2 - - - +
1148A GLN* 1.3 62.8 + - + +
1149A VAL 3.1 1.6 - - - -
1150A GLU* 3.2 34.3 + - + +
1151A LYS* 4.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144A ASP* 2.9 24.2 + - - +
1145A LEU* 3.4 28.6 - - - +
1146A ILE 3.4 0.2 - - - -
1147A GLU* 1.3 77.4 - - + +
1149A VAL* 1.3 57.5 + - - +
1151A LYS 3.3 12.5 - - - +
1153A THR* 3.2 29.6 + - + +
1157A ASP* 4.1 2.9 - - - +
1158A LEU* 3.8 17.2 + - + +
1161A SER* 2.5 33.6 + - - -
1167A THR* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A LEU* 3.4 39.5 - - + +
1104A LEU* 4.4 4.2 - - + +
1105A LEU* 3.5 37.4 - - + +
1111A LEU* 3.2 25.5 - - + +
1145A LEU 3.6 7.9 + - - +
1146A ILE* 3.1 28.0 + - + +
1147A GLU 3.1 0.4 - - - -
1148A GLN* 1.3 78.7 - - - +
1150A GLU* 1.3 67.7 + - - +
1151A LYS 3.6 1.8 - - - -
1152A GLN* 3.9 10.3 + - - +
1153A THR* 5.2 0.4 - - - -
1158A LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111A LEU* 3.4 26.8 - - + +
1115A LYS* 3.0 40.5 + - - +
1146A ILE 2.9 12.2 + - - +
1147A GLU* 3.2 34.2 + - + +
1149A VAL* 1.3 80.6 - - - +
1151A LYS* 1.3 60.3 + - + +
1152A GLN* 3.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A GLU 4.1 2.9 + - - +
1148A GLN 3.3 12.0 - - - +
1149A VAL 3.9 0.2 - - - -
1150A GLU* 1.3 78.4 - - + +
1152A GLN* 1.3 70.2 + - - +
1153A THR* 3.2 3.8 + - - -
----------------------------------------------------------
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