Contacts of the helix formed by residues 1044 - 1049 (chain D) in PDB entry 3IKM
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 VAL1044 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D LEU* 6.1 4.5 - - + -
1040D LYS 4.2 1.1 - - - +
1041D TRP* 3.4 63.3 - - + +
1042D GLU 2.7 0.8 + - - -
1043D VAL* 1.3 81.7 - - + +
1045D ALA* 1.3 57.6 + - - +
1047D ARG* 2.5 57.7 + - + +
1048D ALA* 3.3 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1045 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039D LYS* 5.7 2.9 - - + -
1040D LYS* 3.6 22.7 + - + +
1042D GLU 2.8 15.0 + - - +
1044D VAL* 1.3 69.9 - - - +
1046D GLU* 1.3 64.5 + - - +
1047D ARG 2.8 5.9 + - - -
1048D ALA* 3.2 12.3 + - - +
1049D TRP* 4.2 1.7 + - - -
1090D GLU* 3.4 31.2 - - + +
1092D PHE* 3.3 29.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1046 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042D GLU 3.8 2.2 + - - +
1043D VAL* 3.3 27.6 + - - +
1044D VAL 3.2 0.2 - - - -
1045D ALA* 1.3 78.8 - - - +
1047D ARG* 1.3 54.9 + - - +
1049D TRP* 2.7 76.3 + - + +
1050D LYS* 5.2 1.1 - - - -
1092D PHE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1047 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D LEU* 4.8 18.1 - - + +
1043D VAL* 3.3 4.5 + - + +
1044D VAL* 2.5 52.8 + - + +
1046D GLU* 1.3 68.1 - - - +
1048D ALA* 1.3 57.8 + - + +
1049D TRP 2.8 2.9 - - - -
1050D LYS* 2.3 47.7 + - + +
1051D GLY* 2.4 18.3 + - - +
1054D GLU* 3.4 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1048 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D PHE* 2.5 35.0 - - + -
311D LEU* 4.1 22.2 - - + -
1044D VAL 3.3 0.6 + - - +
1045D ALA* 3.2 12.2 + - - +
1047D ARG* 1.3 88.9 - - + +
1049D TRP* 1.3 49.2 + - - +
1051D GLY* 2.7 4.4 - - - +
1052D GLY 2.3 25.8 + - - -
1090D GLU* 4.0 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1049 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D PHE* 3.6 10.5 - - + -
960D PRO* 4.3 18.4 - - + -
961D PHE* 2.9 61.7 - + + -
1045D ALA 4.2 2.8 + - - -
1046D GLU* 2.7 64.1 + - + +
1047D ARG 2.6 4.9 + - - -
1048D ALA* 1.3 73.4 - - - +
1050D LYS* 1.3 96.2 + - + +
1052D GLY* 2.8 24.6 + - - +
1053D THR* 3.0 5.9 + - - -
1090D GLU 5.0 4.6 - - - +
1092D PHE* 4.8 15.4 - + + -
1093D MET 6.2 0.2 - - - -
1094D THR* 5.2 10.3 - - + -
1095D SER* 6.1 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