Contacts of the helix formed by residues 184 - 195 (chain M) in PDB entry 6CNB
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 LYS 184 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M GLU* 6.6 0.4 - - - -
147M THR* 4.4 23.5 + - + +
182M PHE* 4.1 19.5 - - + -
183M PHE* 1.3 72.7 - - - +
185M TYR* 1.3 64.9 + - + +
186M ILE 3.3 0.4 - - - -
187M ASP* 2.9 52.5 + - + +
188M ASP* 3.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I PRO* 4.9 7.6 - - + +
125M LEU* 5.4 2.6 - - - +
140M TRP* 3.6 47.3 - + + +
141M ASN 3.2 21.7 + - - -
142M GLY* 3.3 28.4 + - - -
144M ASN* 4.0 5.5 + - + +
145M VAL 3.5 19.8 + - - -
146M GLN* 5.2 1.1 - - - -
147M THR* 5.2 6.7 - - - -
183M PHE* 2.7 54.6 - + + -
184M LYS* 1.3 85.7 - - + +
186M ILE* 1.3 61.6 + - + +
188M ASP* 3.0 10.7 + - + +
189M ALA* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 5.7 1.8 - - + -
296B TYR* 4.0 30.3 - - + -
299B GLN* 2.7 28.1 + - + +
300B GLN* 3.4 36.3 - - + +
28I SER* 4.5 13.0 - - - +
140M TRP* 5.7 10.8 - - + -
183M PHE* 3.4 13.5 + - + +
184M LYS 3.3 0.4 - - - -
185M TYR* 1.3 79.3 - - + +
187M ASP* 1.3 57.9 + - - +
189M ALA* 3.1 19.2 + - + -
190M ASN 2.9 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLN* 3.8 14.3 - - - +
183M PHE 4.0 2.2 + - - +
184M LYS* 2.9 48.1 + - - +
186M ILE* 1.3 77.7 - - - +
188M ASP* 1.3 55.6 + - - +
190M ASN* 3.0 10.9 + - - +
191M VAL* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M GLU* 3.2 27.6 - - - +
140M TRP* 3.2 30.2 + - + -
141M ASN 4.6 0.5 + - - -
184M LYS 3.1 6.8 + - - +
185M TYR* 3.0 16.9 + - - +
187M ASP* 1.3 74.6 - - - +
189M ALA* 1.3 62.5 + - - +
191M VAL* 3.0 31.7 + - - +
192M THR* 3.5 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M GLU* 5.4 5.3 - - - +
140M TRP* 5.8 5.6 - - + -
185M TYR 2.9 6.9 + - - +
186M ILE* 3.1 37.9 + - + +
188M ASP* 1.3 75.6 - - - +
190M ASN* 1.3 56.3 + - - +
192M THR* 3.3 15.7 - - - +
193M ARG* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 190 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLN* 3.1 37.0 + - - +
186M ILE 2.9 5.5 + - - -
187M ASP* 3.0 17.2 + - - +
189M ALA* 1.3 73.7 - - - +
191M VAL* 1.3 56.3 + - - +
192M THR 3.1 2.2 - - - -
193M ARG* 2.6 30.2 + - - +
194M LYS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M ASP* 2.9 27.1 + - - +
188M ASP* 3.0 24.6 + - + +
190M ASN* 1.3 76.1 - - - +
192M THR* 1.3 59.9 + - - +
194M LYS* 4.2 8.9 + - - +
195M GLN* 4.3 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M GLU* 4.3 20.0 - - + +
188M ASP 3.5 7.3 + - - +
189M ALA* 3.3 17.3 - - - +
191M VAL* 1.3 78.1 - - - +
193M ARG* 1.3 66.2 + - - +
194M LYS 3.5 0.2 - - - -
195M GLN* 4.6 1.3 - - - -
196M GLU 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189M ALA* 3.2 24.4 + - - +
190M ASN* 2.6 21.0 + - - +
192M THR* 1.3 78.6 - - - +
194M LYS* 1.3 62.8 + - - +
195M GLN 4.9 0.5 - - - -
196M GLU 4.8 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190M ASN* 2.9 25.8 + - - +
191M VAL* 4.9 5.2 - - - +
193M ARG* 1.3 79.4 - - - +
195M GLN* 1.3 89.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191M VAL 4.3 12.7 + - - +
192M THR* 4.3 1.1 + - - +
193M ARG 3.6 0.8 - - - -
194M LYS* 1.3 101.2 + - - +
196M GLU* 1.3 89.9 + - + +
----------------------------------------------------------
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