Contacts of the helix formed by residues 1125 - 1135 (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 ARG1125 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120D MET* 2.8 30.7 + - + +
1123D GLN* 3.0 8.7 + - + +
1124D LYS* 1.3 76.9 - - - +
1126D TRP* 1.3 64.5 + - - +
1127D ASP 4.0 0.2 - - - -
1128D GLU* 4.5 12.1 - - + -
1129D ALA* 3.4 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090D SER 5.6 3.4 - - - -
1091D LEU* 4.5 6.5 - - + -
1092D ASP* 5.0 0.7 - - - -
1095D ARG* 3.3 64.3 - - - +
1121D LEU* 3.4 40.4 - - + -
1124D LYS* 3.7 34.0 + - + +
1125D ARG* 1.3 72.1 - - - +
1127D ASP* 1.3 75.6 + - - +
1128D GLU 3.1 1.1 - - - -
1129D ALA* 2.9 16.0 + - - +
1130D ALA* 2.9 13.2 + - - +
1153D PHE* 3.7 4.4 - - - +
1154D ARG* 4.0 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126D TRP* 1.3 82.9 - - - +
1128D GLU* 1.3 61.3 - - - +
1130D ALA* 3.3 7.6 + - - +
1131D VAL* 2.9 31.7 + - + +
1154D ARG* 3.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120D MET* 3.4 25.7 - - + +
1125D ARG* 4.3 13.0 - - + +
1126D TRP 3.1 1.0 - - - +
1127D ASP* 1.3 75.5 - - - +
1129D ALA* 1.3 66.8 + - - +
1131D VAL* 3.2 8.7 + - - +
1132D ASN* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117D SER* 4.1 5.1 + - - +
1120D MET* 3.6 22.3 - - + -
1121D LEU* 4.0 28.9 - - + -
1125D ARG 3.4 14.9 + - - +
1126D TRP 2.9 9.4 + - - +
1128D GLU* 1.3 76.4 - - - +
1130D ALA* 1.3 55.5 + - - +
1132D ASN* 2.7 25.6 + - - +
1133D LEU* 2.9 19.2 + - + +
1153D PHE* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126D TRP 2.9 13.7 + - - +
1127D ASP 3.6 7.6 - - - +
1129D ALA* 1.3 71.5 - - - +
1131D VAL* 1.3 65.5 + - + +
1133D LEU* 2.9 18.2 + - - +
1134D ALA* 2.9 13.8 + - - +
1150D ILE* 3.4 33.5 - - + +
1153D PHE* 5.8 3.5 - - + +
1154D ARG* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127D ASP* 2.9 21.6 + - + +
1128D GLU* 3.5 10.3 - - - +
1130D ALA* 1.3 75.8 - - + +
1132D ASN* 1.3 64.1 + - - +
1134D ALA* 3.2 16.0 + - + +
1135D LYS* 3.2 40.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116D ASN* 3.3 28.5 + - - +
1117D SER* 3.6 11.4 + - - +
1120D MET* 3.4 31.6 - - + +
1128D GLU 2.9 6.3 + - - +
1129D ALA 2.7 16.6 + - - +
1131D VAL* 1.3 75.9 - - - +
1133D LEU* 1.3 57.2 + - - +
1134D ALA 3.6 0.2 + - - -
1135D LYS* 3.7 17.6 + - - +
1136D SER* 4.2 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102D MET* 5.0 9.6 - - + -
1114D PHE* 3.8 26.7 - - + -
1117D SER* 3.0 31.9 - - - +
1121D LEU* 5.3 5.8 - - + -
1129D ALA* 2.9 23.4 + - + +
1130D ALA* 2.9 10.8 + - - +
1132D ASN* 1.3 73.8 - - - +
1134D ALA* 1.3 62.4 + - - +
1135D LYS 3.2 2.2 - - - -
1136D SER* 2.8 26.0 + - - +
1138D TRP* 5.0 11.0 - - + -
1139D TYR* 3.5 8.2 - - - +
1150D ILE* 4.0 28.3 - - + +
1153D PHE* 4.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130D ALA 2.9 11.7 + - - +
1131D VAL* 3.2 14.1 + - - +
1133D LEU* 1.3 76.8 - - - +
1135D LYS* 1.3 59.7 - - + +
1136D SER 3.2 5.4 + - - +
1139D TYR* 3.5 43.6 - - + +
1140D ASN* 5.9 0.2 - - - +
1150D ILE* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131D VAL* 3.2 38.1 + - - +
1132D ASN* 3.7 10.7 + - - +
1133D LEU 3.2 1.0 - - - -
1134D ALA* 1.3 78.8 - - + +
1136D SER* 1.3 62.4 + - - +
----------------------------------------------------------
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