Contacts of the helix formed by residues 137 - 149 (chain D) in PDB entry 1M6X
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 ASN 137 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 4.4 7.0 + - - -
138D SER* 1.3 77.3 + - - +
139D HIS* 3.2 6.7 - - - +
140D SER* 2.9 27.8 + - - -
141D LYS* 2.6 34.5 + - - +
12H T 4.5 20.4 + - - +
13H C 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASN* 5.5 1.7 + - - -
345B HIS* 5.6 11.0 - - - +
137D ASN* 1.3 85.8 + - - +
139D HIS* 1.3 72.4 + - - +
141D LYS* 2.8 20.9 + - - +
142D LYS* 3.0 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER* 5.8 4.9 - - - -
268B ASN* 3.1 34.1 + - - +
137D ASN 3.1 5.0 + - - +
138D SER* 1.3 82.6 + - - +
140D SER* 1.3 57.8 + - - +
142D LYS* 3.2 8.6 + - + +
143D MET* 2.9 61.9 + - + +
298D ILE* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 3.6 19.6 - - - -
137D ASN* 2.9 15.6 + - - -
139D HIS* 1.3 78.8 - - - +
141D LYS* 1.3 56.9 - - - +
143D MET 3.3 0.2 + - - -
144D LEU* 2.8 28.4 + - - +
295D ILE* 3.2 24.4 - - - +
298D ILE* 3.5 26.7 - - - +
301D GLY* 3.6 13.2 - - - -
302D PRO* 3.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 3.0 64.2 - - + +
344B THR* 3.5 16.3 - - - +
345B HIS* 4.2 17.8 + - + +
346B GLN 5.2 0.2 - - - +
137D ASN* 2.6 43.0 + - - +
138D SER* 2.8 17.9 + - - +
140D SER* 1.3 75.5 - - - +
142D LYS* 1.3 60.2 + - - +
144D LEU* 3.5 2.9 + - - +
145D LYS* 3.1 21.0 + - - +
13H C 4.6 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP* 5.1 8.5 + - - -
218B LEU* 5.9 6.3 - - - +
268B ASN* 4.3 20.6 + - - +
345B HIS* 4.9 19.9 - - + +
138D SER 3.0 10.3 + - - +
139D HIS* 3.6 12.3 - - + +
141D LYS* 1.3 75.2 - - - +
143D MET* 1.3 59.5 + - - +
145D LYS* 3.2 16.5 - - + +
146D ALA* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D HIS* 2.9 49.7 + - + +
140D SER 3.6 4.5 - - - +
142D LYS* 1.3 76.3 - - + +
144D LEU* 1.3 60.2 + - - +
146D ALA* 3.2 11.4 + - - +
147D LEU* 2.9 28.4 + - - +
294D PRO* 3.7 37.5 - - + +
295D ILE* 3.7 20.7 - - + +
298D ILE* 3.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 3.3 42.0 - - + +
140D SER 2.8 16.7 + - - +
141D LYS 3.8 4.5 - - - +
143D MET* 1.3 72.7 - - - +
145D LYS* 1.3 69.5 + - - +
147D LEU* 3.2 24.7 + - + +
148D LEU* 2.9 58.2 + - + +
295D ILE* 4.1 8.0 - - + +
302D PRO* 6.3 0.7 - - + -
306D ILE* 4.8 11.4 - - + -
309D HIS* 4.1 17.0 - - + -
310D LEU* 4.9 3.8 - - + -
313D SER* 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 3.4 28.0 - - - +
229B HIS* 6.3 1.0 - - - -
345B HIS* 5.6 14.9 - - + +
141D LYS 3.1 11.7 + - - +
142D LYS* 3.2 20.4 - - + +
143D MET 3.2 0.2 - - - -
144D LEU* 1.3 80.7 - - - +
146D ALA* 1.3 54.2 + - - +
148D LEU* 3.5 8.9 - - - +
149D SER* 2.6 55.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS 3.0 12.6 + - - +
143D MET* 3.4 18.2 - - - +
144D LEU 3.2 0.2 - - - -
145D LYS* 1.3 78.5 - - - +
147D LEU* 1.3 66.7 + - - +
148D LEU 2.8 1.4 + - - -
149D SER* 3.0 6.4 + - - +
150D GLU* 2.9 40.7 - - - +
294D PRO* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D MET 2.9 16.4 + - - +
144D LEU* 3.2 30.1 - - + +
146D ALA* 1.3 73.5 - - - +
148D LEU* 1.3 64.9 + - + +
150D GLU* 4.2 13.2 + - - +
152D GLU* 5.0 2.3 + - - +
157D ILE* 3.6 32.8 - - + +
161D ILE* 5.7 0.2 - - + -
293D TYR* 3.1 52.4 - - + -
294D PRO* 5.6 6.1 - - + +
295D ILE* 4.4 20.4 - - + -
296D PHE* 5.6 1.6 - - + -
306D ILE* 4.8 7.0 - - + -
310D LEU* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 2.9 50.2 + - + +
145D LYS* 3.5 7.2 - - - +
146D ALA 2.8 2.6 + - - -
147D LEU* 1.3 72.4 - - + +
149D SER* 1.3 55.3 + - - +
150D GLU 2.5 29.1 + - - +
152D GLU 3.5 9.2 - - - +
154D ILE* 3.4 30.7 - - + -
157D ILE* 3.8 15.7 - - + -
310D LEU* 4.2 6.3 - - + -
313D SER* 3.8 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LYS* 2.6 46.3 + - - +
146D ALA* 4.1 2.2 - - - -
148D LEU* 1.3 69.0 - - - +
150D GLU* 1.3 67.6 + - - +
----------------------------------------------------------
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