Contacts of the helix formed by residues 136 - 150 (chain A) 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 GLY 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASN* 1.3 65.6 - - - +
138A SER* 2.8 19.6 + - - -
139A HIS* 3.5 11.3 + - - +
140A SER* 4.1 3.7 + - - -
298A ILE* 5.8 1.2 - - - +
12E T 4.5 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 1.3 70.3 - - - +
138A SER* 1.3 51.6 + - - +
140A SER* 2.5 41.5 + - - -
141A LYS* 2.5 46.7 + - + -
300A ASN 5.1 4.4 + - - -
342D THR* 5.0 1.6 - - - +
12E T 3.8 30.6 + - - +
13E C 3.2 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 2.8 17.8 + - - -
137A ASN* 1.3 78.1 - - - +
139A HIS* 1.3 62.5 + - - -
141A LYS* 3.3 5.9 + - - +
142A LYS* 3.1 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 3.5 5.8 + - - +
137A ASN 3.0 0.8 + - - -
138A SER* 1.3 78.4 - - - +
140A SER* 1.3 64.8 + - - +
142A LYS* 3.2 16.7 + - + +
143A MET* 3.2 33.8 + - + +
298A ILE* 3.4 42.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 4.1 1.9 + - - -
137A ASN* 2.5 37.2 + - - -
139A HIS* 1.3 76.0 - - - +
141A LYS* 1.3 59.5 + - - +
142A LYS 3.1 1.2 + - - -
143A MET 3.2 0.9 + - - -
144A LEU* 3.1 21.9 + - - +
295A ILE* 3.4 10.0 - - - +
298A ILE* 3.5 24.3 - - - +
299A LYS 5.8 0.2 - - - -
300A ASN 5.6 0.4 - - - -
301A GLY* 3.7 6.4 - - - -
302A PRO* 3.4 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASN* 2.5 42.1 + - + +
138A SER* 3.8 5.6 - - - +
140A SER* 1.3 74.1 - - - +
142A LYS* 1.3 60.3 + - - +
144A LEU* 4.0 15.7 - - + +
145A LYS* 3.2 31.1 + - + +
341D THR* 3.1 15.2 + - - +
342D THR* 3.0 43.1 - - - +
345D HIS* 4.6 9.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER 3.1 12.4 + - - +
139A HIS* 3.5 17.5 - - + +
140A SER 3.1 1.2 - - - -
141A LYS* 1.3 76.3 - - - +
143A MET* 1.3 66.9 + - - +
145A LYS* 3.1 15.2 + - + +
146A ALA* 2.8 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 3.4 26.0 - - + +
140A SER 3.2 0.8 + - - -
142A LYS* 1.3 80.7 - - - +
144A LEU* 1.3 55.3 + - - +
146A ALA* 3.0 12.8 + - + +
147A LEU* 2.7 36.4 + - - +
294A PRO* 3.1 42.4 - - + +
295A ILE* 3.5 27.2 - - + +
298A ILE* 3.0 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.1 27.3 + - - +
141A LYS* 4.0 8.7 - - + +
142A LYS 3.3 0.2 - - - -
143A MET* 1.3 79.0 - - - +
145A LYS* 1.3 63.8 + - - +
147A LEU* 3.5 20.1 - - + +
148A LEU* 3.6 6.4 + - - +
295A ILE* 3.3 22.0 - - + -
302A PRO* 3.9 26.7 - - + -
306A ILE* 4.0 16.2 - - + -
309A HIS* 4.9 10.5 - - + +
345D HIS* 3.4 52.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 3.2 19.0 + - - +
142A LYS* 3.1 18.6 + - + +
144A LEU* 1.3 79.0 - - - +
146A ALA* 1.3 61.9 + - - +
148A LEU* 3.3 1.6 + - - -
149A SER* 2.7 32.4 + - - +
344D THR* 3.7 12.4 + - - +
345D HIS* 3.8 29.8 - - + +
346D GLN* 3.6 21.0 - - - +
347D ILE* 4.9 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 2.8 15.2 + - + +
143A MET* 3.0 23.8 - - + +
145A LYS* 1.3 75.2 - - - +
147A LEU* 1.3 57.7 + - - +
149A SER* 2.5 31.8 + - - -
150A GLU* 2.9 28.7 + - + +
294A PRO* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET 2.7 15.0 + - - +
144A LEU* 3.5 17.0 - - + +
146A ALA* 1.3 74.4 - - - +
148A LEU* 1.3 78.8 + - + +
150A GLU* 3.6 16.7 + - - +
152A GLU* 4.9 4.3 - - - +
157A ILE* 3.9 20.5 - - + +
161A ILE* 5.8 1.3 - - + -
293A TYR* 3.3 50.7 - - + -
294A PRO* 5.5 4.9 - - + +
295A ILE* 4.6 11.4 - - + -
296A PHE* 5.8 0.7 - - + -
306A ILE* 4.4 18.6 - - + -
310A LEU* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU 3.7 10.8 - - - +
145A LYS 3.3 0.6 + - - -
146A ALA 3.2 0.8 - - - -
147A LEU* 1.3 96.4 - - + +
149A SER* 1.3 63.7 + - - +
150A GLU 3.4 7.3 - - - +
152A GLU 4.6 4.8 - - - +
154A ILE* 3.8 24.7 - - + -
157A ILE* 4.0 8.7 - - + -
310A LEU* 4.2 5.4 - - + -
313A SER* 3.6 34.3 - - - +
345D HIS* 3.6 28.7 - - + +
346D GLN* 3.7 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 2.7 25.5 + - - +
146A ALA* 2.5 23.4 + - - -
148A LEU* 1.3 68.9 - - - +
150A GLU* 1.3 66.5 + - - +
345D HIS 5.1 1.7 + - - -
346D GLN* 5.0 9.3 - - - +
347D ILE* 5.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 2.9 28.5 + - - +
147A LEU* 3.6 9.9 + - - +
148A LEU 3.4 8.9 - - - +
149A SER* 1.3 84.9 - - - +
151A GLY* 1.3 71.7 - - - +
152A GLU* 3.8 2.5 - - - +
294A PRO* 5.6 5.5 - - - +
----------------------------------------------------------
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