Contacts of the helix formed by residues 1142 - 1156 (chain D) in PDB entry 4DAJ
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 THR1142 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020D ASP* 5.8 0.2 - - - +
1021D THR* 4.1 18.4 - - + +
1022D GLU* 3.8 22.2 + - + +
1105D GLN* 4.2 11.5 + - - +
1138D TRP* 3.1 21.6 + - - +
1139D TYR 3.4 3.4 - - - -
1141D GLN* 1.3 87.5 - - + +
1143D PRO* 1.3 67.2 - - - +
1144D ASN* 3.3 3.7 + - - -
1145D ARG* 3.8 8.8 + - - +
1146D ALA* 3.5 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139D TYR* 3.0 38.3 - - + +
1140D ASN* 4.3 4.9 - - - +
1141D GLN 3.9 5.8 - - - +
1142D THR* 1.3 85.1 - - - +
1144D ASN* 1.3 68.7 + - - +
1146D ALA* 3.6 2.9 - - + +
1147D LYS* 2.9 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142D THR* 3.3 2.8 + - - -
1143D PRO* 1.3 82.9 - - - +
1145D ARG* 1.3 66.2 + - - +
1147D LYS* 2.9 25.9 + - - +
1148D ARG* 3.0 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007D LEU* 3.9 9.5 - - - +
1010D ASP* 3.5 39.1 + - + +
1011D GLU* 3.3 32.5 + - - +
1101D ASN* 3.4 23.5 + - - -
1104D PHE* 3.8 22.8 - - - -
1105D GLN* 3.2 47.3 - - - +
1138D TRP* 5.2 1.6 - - + +
1142D THR* 3.8 12.2 + - - +
1143D PRO 3.6 0.2 - - - -
1144D ASN* 1.3 79.4 - - - +
1146D ALA* 1.3 65.3 + - - +
1148D ARG* 3.1 20.2 + - - +
1149D VAL* 2.9 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138D TRP* 4.0 26.1 - - + -
1139D TYR* 3.8 32.1 - - + -
1142D THR 3.5 16.3 + - - +
1143D PRO 3.6 4.3 - - - +
1144D ASN 3.1 0.2 - - - -
1145D ARG* 1.3 80.2 - - - +
1147D LYS* 1.3 63.3 + - - +
1149D VAL* 3.1 1.2 + - - +
1150D ILE* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139D TYR* 3.8 28.5 + - + +
1143D PRO* 2.9 33.0 + - - +
1144D ASN* 3.0 14.6 - - - +
1146D ALA* 1.3 75.6 - - - +
1148D ARG* 1.3 63.8 + - + +
1150D ILE* 3.9 6.1 - - - +
1151D THR* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009D ILE* 4.5 15.4 + - - +
1010D ASP* 2.6 32.0 + - - +
1144D ASN* 3.0 39.5 + - - +
1145D ARG* 3.1 15.8 + - - +
1147D LYS* 1.3 81.4 - - + +
1149D VAL* 1.3 65.7 + - - +
1151D THR* 3.2 2.6 + - - -
1152D THR* 3.0 23.0 + - - -
1160D ALA* 3.9 21.4 - - + +
1161D TYR* 3.4 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006D MET* 4.6 1.3 - - - -
1098D ALA* 3.8 13.9 - - + +
1101D ASN* 3.7 22.2 - - - +
1102D MET* 3.8 17.3 - - + -
1138D TRP* 4.1 13.2 - - + -
1145D ARG* 2.9 25.0 + - + +
1146D ALA 3.5 4.9 - - - +
1148D ARG* 1.3 71.3 - - - +
1150D ILE* 1.3 57.0 + - - +
1152D THR* 3.2 11.2 - - - +
1153D PHE* 3.0 52.2 + - + -
1161D TYR* 3.5 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130D ALA* 3.4 36.6 - - + +
1133D LEU* 4.0 35.4 - - + +
1134D ALA* 4.8 1.3 - - + +
1138D TRP* 4.6 10.1 - - + -
1139D TYR* 4.2 21.8 - - + -
1146D ALA* 2.9 28.6 + - + +
1147D LYS* 3.9 4.0 - - - +
1149D VAL* 1.3 73.2 - - + +
1151D THR* 1.3 60.5 + - - +
1152D THR 3.0 1.1 - - - -
1153D PHE* 2.5 32.3 + - + +
1154D ARG* 2.9 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147D LYS* 2.9 23.4 + - - +
1148D ARG 3.5 3.6 - - - -
1150D ILE* 1.3 77.3 - - - +
1152D THR* 1.3 60.2 + - - +
1154D ARG* 3.2 18.1 + - - +
1155D THR* 2.9 48.1 + - + +
1160D ALA* 3.8 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006D MET* 5.6 1.6 - - + -
1094D VAL* 3.4 30.7 - - + +
1095D ARG* 4.0 2.8 - - - +
1098D ALA* 4.0 18.4 - - + +
1148D ARG 3.0 8.7 + - - -
1149D VAL* 3.2 12.8 - - - +
1151D THR* 1.3 79.1 - - - +
1153D PHE* 1.3 54.9 + - - +
1155D THR* 3.7 7.0 - - - -
1156D GLY* 2.9 25.1 + - - -
1157D THR 3.2 11.2 + - - -
1158D TRP* 4.6 5.4 - - + -
1160D ALA* 4.0 3.8 - - - +
1161D TYR* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091D LEU* 4.3 8.5 - - + -
1095D ARG* 2.7 52.5 + - + +
1098D ALA* 3.5 13.2 - - + -
1099D LEU* 3.7 17.7 - - + -
1102D MET* 3.8 16.8 - - - -
1121D LEU* 3.6 43.5 - - + -
1126D TRP* 3.7 10.3 - - - +
1129D ALA* 6.0 1.1 - - + -
1130D ALA* 5.8 2.9 - - + +
1133D LEU* 4.6 13.2 - - + -
1149D VAL* 3.0 47.7 + - + -
1150D ILE* 2.5 25.8 + - + +
1152D THR* 1.3 73.4 - - - +
1154D ARG* 1.3 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095D ARG* 2.7 26.5 + - - -
1126D TRP* 4.0 17.3 - - + -
1127D ASP* 3.8 36.9 + - - +
1130D ALA* 3.9 28.9 - - + -
1150D ILE* 2.9 12.0 + - - +
1151D THR* 3.8 17.1 + - - +
1153D PHE* 1.3 73.9 - - + +
1155D THR* 1.3 71.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095D ARG* 4.0 2.9 + - - -
1151D THR* 2.9 37.6 + - + +
1152D THR* 3.7 0.9 - - - -
1154D ARG* 1.3 90.2 - - + +
1156D GLY* 1.3 61.9 + - - +
1157D THR* 3.0 42.0 + - - +
1159D ASP* 5.1 3.5 - - + +
1160D ALA 5.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092D ASP* 4.0 3.4 - - - +
1094D VAL* 3.2 31.2 - - - +
1095D ARG* 3.8 25.1 - - - -
1152D THR 2.9 19.5 + - - -
1154D ARG 3.1 2.2 - - - -
1155D THR* 1.3 77.4 + - - +
1157D THR* 1.3 60.3 + - - +
----------------------------------------------------------
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