Contacts of the helix formed by residues 135 - 148 (chain M) in PDB entry 3Q2K
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 135 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M GLN 4.2 2.1 - - - +
132M ASN* 3.0 33.8 + - - +
134M ARG* 1.3 78.4 - - - +
136M ALA* 1.3 59.7 + - - +
137M THR* 3.5 13.0 - - - +
138M LEU* 3.9 7.3 - - + +
139M GLN* 3.0 27.0 + - - +
267M ALA 3.9 4.4 + - - -
268M VAL* 3.5 35.8 + - - +
293M THR* 3.5 19.1 - - + +
296M VAL* 5.8 4.9 - - - +
300M GLY* 6.1 0.9 - - - -
303M LEU* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M ARG 3.3 3.9 + - - -
135M ASN* 1.3 72.3 - - - +
137M THR* 1.3 63.7 + - - +
139M GLN* 3.7 7.8 - - - +
140M LEU* 3.1 27.9 + - + +
289M ALA* 3.9 20.4 - - + +
292M GLU* 3.7 31.5 + - - +
293M THR* 3.0 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M ASN* 3.5 5.9 - - - +
136M ALA* 1.3 75.0 - - - +
138M LEU* 1.3 65.5 + - - +
140M LEU* 3.3 10.9 + - - +
141M VAL* 3.3 16.9 + - - +
263M VAL* 3.8 9.2 - - - -
268M VAL 2.8 22.4 + - - -
269M ASN 3.7 23.3 - - - +
270M ARG 3.8 2.7 - - - +
271M ILE* 4.0 17.1 - - + +
289M ALA* 4.0 8.8 - - - +
290M ASN* 3.4 25.6 - - - +
293M THR* 3.0 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132M ASN* 3.5 24.9 - - + +
133M ARG 5.3 0.2 - - - +
135M ASN* 3.3 9.6 + - + +
137M THR* 1.3 86.3 + - - +
139M GLN* 1.3 60.1 + - - +
140M LEU 3.3 0.2 - - - -
141M VAL* 3.3 5.7 + - + +
142M LYS* 2.9 29.5 + - - +
195M LEU* 3.8 24.9 - - + -
198M TRP* 4.4 14.3 - - + -
199M LEU* 4.0 15.1 - - + +
252M ILE* 4.1 26.9 - - + -
263M VAL* 4.2 10.3 - - + -
268M VAL* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ARG* 2.8 24.9 + - - +
134M ARG* 3.3 34.3 + - - +
135M ASN 3.0 22.8 + - - +
136M ALA* 3.7 8.1 - - - +
137M THR 3.2 0.2 - - - -
138M LEU* 1.3 77.4 - - - +
140M LEU* 1.3 58.1 + - + +
142M LYS* 3.4 9.9 + - - +
143M LYS* 3.0 41.2 + - - +
198M TRP* 3.9 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M ALA* 3.1 16.7 + - + +
137M THR 3.4 9.6 - - - +
138M LEU 3.3 0.2 - - - -
139M GLN* 1.3 74.1 - - + +
141M VAL* 1.3 59.9 + - - +
143M LYS* 3.2 14.8 + - + +
144M ALA 2.9 23.4 + - - -
271M ILE* 4.1 14.6 - - + -
274M TRP* 3.7 27.2 - - + -
282M ASP* 3.9 45.4 - - + +
285M LYS* 4.3 15.5 - - + +
286M ILE* 4.4 3.8 - - + -
289M ALA* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M THR 3.3 15.4 + - - +
138M LEU* 3.3 11.2 + - + +
140M LEU* 1.3 76.9 - - - +
142M LYS* 1.3 64.8 + - - +
144M ALA* 3.0 6.0 + - - +
145M ILE* 3.0 41.6 + - + +
150M PHE* 4.5 9.2 - - + -
199M LEU* 4.2 9.9 - - + -
252M ILE* 6.3 0.2 - - + -
254M ILE* 4.0 18.2 - - + -
261M VAL* 4.3 13.2 - - + -
263M VAL* 3.7 27.6 - - + -
271M ILE* 5.4 0.2 - - + -
274M TRP* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138M LEU 2.9 17.6 + - - +
139M GLN* 3.6 14.4 - - - +
141M VAL* 1.3 76.3 - - - +
143M LYS* 1.3 64.4 + - + +
145M ILE* 3.2 7.0 + - + +
146M GLU* 3.0 55.3 + - + +
198M TRP* 2.7 58.9 + - + +
199M LEU* 3.6 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M GLN* 3.0 24.5 + - - +
140M LEU* 3.3 17.3 - - + +
142M LYS* 1.3 76.2 - - + +
144M ALA* 1.3 67.6 + - - +
145M ILE 3.0 0.2 + - - -
146M GLU* 3.3 9.3 + - - +
147M GLN* 2.8 45.9 + - - +
280M HIS* 5.3 0.9 - - + -
282M ASP* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M LEU 2.9 16.0 + - - +
141M VAL* 3.0 9.6 + - - +
143M LYS* 1.3 72.8 - - - +
145M ILE* 1.3 62.8 + - - +
147M GLN* 3.5 10.2 + - - +
148M GLY 3.2 3.1 + - - -
149M ARG* 2.9 40.3 + - - +
150M PHE* 3.9 7.1 + - + -
274M TRP* 4.3 5.6 - - + -
276M PHE* 3.6 32.3 - - + -
282M ASP* 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M VAL* 3.0 32.1 + - + +
142M LYS* 3.6 7.6 - - + +
144M ALA* 1.3 78.1 - - - +
146M GLU* 1.3 68.8 + - + +
148M GLY* 3.0 14.9 + - - -
149M ARG 5.0 0.2 - - - +
150M PHE* 3.6 26.5 - - + +
153M ILE* 4.7 17.0 - - + -
199M LEU* 3.2 43.7 - - + +
200M VAL* 4.6 3.8 - - - +
254M ILE* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M LYS* 3.0 54.4 + - + +
143M LYS* 4.1 7.9 - - - +
145M ILE* 1.3 82.4 - - + +
147M GLN* 1.3 62.2 + - + +
148M GLY* 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M LYS* 2.8 46.7 + - - +
144M ALA* 3.8 6.9 + - - +
146M GLU* 1.3 71.3 - - + +
148M GLY* 1.3 60.0 + - - +
149M ARG* 3.0 34.1 + - + +
280M HIS* 3.3 37.8 + - + -
282M ASP* 4.0 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M ALA 3.2 0.2 + - - -
145M ILE 3.0 14.7 + - - -
146M GLU 3.0 1.7 - - - -
147M GLN* 1.3 78.5 - - - +
149M ARG* 1.3 64.2 + - - +
150M PHE 3.2 3.6 - - - -
151M GLY* 3.1 14.3 + - - -
258M LYS* 3.4 12.8 + - - -
278M GLU* 5.2 1.1 - - - -
----------------------------------------------------------
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