Contacts of the helix formed by residues 172 - 188 (chain A) in PDB entry 4M04
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 SER 172 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 2.9 19.6 + - - +
168A GLY* 4.9 0.4 - - - -
170A GLU* 3.3 6.6 - - - -
171A GLY* 1.3 76.3 - - - +
173A GLU* 1.3 62.3 + - - +
174A GLY* 3.3 1.5 + - - -
175A ARG* 3.3 37.5 + - - +
176A LEU* 3.1 21.4 + - - +
1D G 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLY* 4.8 5.7 - - - +
171A GLY 3.3 10.2 + - - +
172A SER* 1.3 73.9 - - - +
174A GLY* 1.3 57.5 + - - +
176A LEU* 3.5 23.3 - - - +
177A LEU* 2.9 35.5 + - + +
442A ARG* 3.0 37.1 + - - +
4T C 6.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER* 3.3 1.8 + - - -
173A GLU* 1.3 78.4 - - - +
175A ARG* 1.3 58.5 + - - +
177A LEU* 3.3 1.8 + - - +
178A THR 3.0 23.0 + - - -
1D G 3.1 39.3 - - - +
4T C 3.6 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU 5.3 0.6 + - - -
167A ALA* 3.9 24.5 - - + +
170A GLU* 6.4 0.2 - - - +
172A SER* 3.3 27.0 + - - +
173A GLU 3.4 0.2 - - - -
174A GLY* 1.3 71.5 - - - +
176A LEU* 1.3 65.8 + - - +
178A THR* 3.2 1.9 + - - -
179A PHE* 3.0 38.2 + - + -
208A HIS* 3.7 18.4 - - - -
224A GLU* 4.7 5.3 + - - -
1D G 2.6 74.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.5 34.7 - - - +
165A GLU* 4.9 3.4 - - - -
167A ALA* 3.6 2.6 - - - +
168A GLY* 3.6 20.6 - - - +
172A SER 3.1 14.5 + - - +
173A GLU* 3.5 24.7 - - - +
174A GLY 3.3 0.2 - - - -
175A ARG* 1.3 76.8 - - - +
177A LEU* 1.3 64.7 + - + +
179A PHE 3.4 0.2 + - - -
180A CYS* 2.9 49.8 + - - -
442A ARG* 4.1 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 2.9 21.8 + - + +
174A GLY* 3.6 5.2 - - - +
175A ARG 3.2 0.2 - - - -
176A LEU* 1.3 82.7 - - + +
178A THR* 1.3 56.5 + - - +
180A CYS* 3.3 3.0 + - + +
181A ARG* 2.8 60.9 + - - +
439A LEU* 4.5 13.5 - - + -
442A ARG* 3.6 38.4 - - - +
443A GLU* 5.3 0.7 - - - +
4T C 3.5 48.5 - - + +
5T A 3.7 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY 3.0 7.7 + - - -
175A ARG 3.2 0.6 + - - -
177A LEU* 1.3 76.0 - - - +
179A PHE* 1.3 60.2 + - - +
181A ARG* 3.2 11.3 + - - +
182A ALA* 2.8 28.1 + - - +
204A HIS* 4.1 9.1 + - + +
209A SER* 4.6 3.6 - - - +
1D G 2.5 73.4 + - - +
2D C 3.6 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.6 29.2 - - + +
163A LEU* 3.8 44.0 - - + -
164A ALA* 3.6 12.1 - - + -
167A ALA* 4.8 0.2 - - + -
175A ARG* 3.0 38.8 + - + +
178A THR* 1.3 76.3 - - - +
180A CYS* 1.3 57.5 + - - +
182A ALA* 3.4 3.4 + - - +
183A ALA* 2.9 29.8 + - - +
208A HIS* 4.0 27.4 - + - -
209A SER* 3.6 26.0 - - - -
224A GLU* 5.9 0.2 - - - -
1D G 3.5 34.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLU* 4.9 10.8 - - - +
164A ALA* 3.7 16.8 - - - -
176A LEU* 2.9 40.4 + - + +
177A LEU* 3.7 5.6 - - + +
179A PHE* 1.3 77.7 - - - +
181A ARG* 1.3 57.9 - - - +
183A ALA* 3.4 8.0 + - - +
184A SER* 2.9 28.6 + - - -
439A LEU* 3.6 25.0 - - + +
494A ALA* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 6.4 0.4 - - + -
145A ARG* 4.1 2.5 + - - +
177A LEU* 2.8 55.7 + - - +
178A THR* 3.7 6.3 + - - +
180A CYS* 1.3 69.0 - - - +
182A ALA* 1.3 61.4 + - - +
184A SER* 3.2 7.2 + - - -
185A VAL* 2.9 33.8 + - - +
204A HIS* 3.7 38.8 + - + +
439A LEU* 4.4 9.9 - - + -
443A GLU* 2.9 29.3 + - - +
446A ARG* 3.1 41.5 - - - +
1D G 4.0 21.8 + - - -
2D C 5.2 1.2 + - - -
3T G 4.9 5.9 - - - +
4T C 4.1 8.3 + - - -
5T A 4.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.2 3.8 - - + -
178A THR 2.8 20.1 + - - +
179A PHE* 3.8 4.5 - - - +
181A ARG* 1.3 68.9 - - - +
183A ALA* 1.3 68.6 + - - +
185A VAL* 3.3 8.6 + - - -
186A LEU* 3.3 9.4 + - - +
204A HIS* 3.6 25.2 - - - +
205A PHE* 3.3 35.4 - - + -
209A SER* 4.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 3.8 17.6 - - - +
160A LEU* 4.0 14.7 - - + +
161A GLU* 3.6 33.2 - - + +
179A PHE 2.9 18.1 + - - +
180A CYS 3.5 5.6 - - - +
182A ALA* 1.3 77.2 - - - +
184A SER* 1.3 62.4 + - - +
186A LEU* 3.2 14.5 + - - +
187A LYS* 3.2 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.1 0.2 - - - +
145A ARG* 3.4 14.8 + - - -
147A THR* 4.3 2.9 + - - +
180A CYS 2.9 17.3 + - - -
181A ARG* 3.2 6.5 + - - -
183A ALA* 1.3 74.6 - - - +
185A VAL* 1.3 67.2 + - - +
187A LYS* 3.1 18.9 + - - +
188A ALA* 3.1 13.7 + - - +
439A LEU* 3.6 9.6 - - - +
494A ALA* 2.9 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A MET* 3.9 24.4 - - + +
145A ARG* 3.7 26.9 - - - +
181A ARG 2.9 19.4 + - - +
182A ALA 3.5 8.1 - - - +
184A SER* 1.3 75.8 - - - +
186A LEU* 1.3 62.7 + - - +
188A ALA* 3.1 13.5 + - - +
189A LEU* 3.3 12.2 + - + +
202A LEU* 4.2 21.8 - - + -
203A PRO* 3.5 22.4 - - + +
204A HIS* 4.2 7.9 - - + -
205A PHE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A HIS* 4.2 1.0 + - - -
153A ASN* 3.3 34.1 + - + +
156A LEU* 3.5 37.2 - - + -
157A SER* 4.3 3.4 - - - +
160A LEU* 3.8 22.9 - - + -
182A ALA 3.6 9.4 - - - +
183A ALA 3.2 7.6 + - - +
185A VAL* 1.3 78.5 - - - +
187A LYS* 1.3 61.0 + - - +
189A LEU* 3.3 29.4 + - + +
193A VAL* 4.0 13.2 - - + -
199A LEU* 4.2 7.6 - - + -
202A LEU* 4.7 1.8 - - + -
205A PHE* 3.6 20.9 - - + -
213A VAL* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 3.5 11.7 - - + -
148A PRO* 3.7 13.1 - - - +
151A HIS* 3.3 55.2 - - + +
157A SER* 4.2 7.2 - - - -
161A GLU* 2.8 34.7 + - - -
183A ALA 3.2 16.7 + - - +
184A SER* 3.1 10.0 + - - +
186A LEU* 1.3 76.2 - - - +
188A ALA* 1.3 60.0 + - - +
189A LEU 3.6 2.9 + - - +
493A ASN 3.9 11.5 + - - +
494A ALA* 3.0 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A MET* 4.2 10.4 - - + +
145A ARG* 3.9 27.8 - - + +
146A PRO 3.7 24.3 - - - +
147A THR* 4.3 4.5 - - - +
148A PRO* 4.7 2.8 - - - +
184A SER 3.1 9.6 + - - +
185A VAL 3.1 11.4 + - - +
187A LYS* 1.3 77.3 - - - +
189A LEU* 1.3 62.3 + - - +
190A PRO* 3.8 2.4 - - - +
----------------------------------------------------------
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