Contacts of the helix formed by residues 170 - 185 (chain A) in PDB entry 3MA0
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 LEU 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 5.4 0.4 - - - +
13A ARG* 3.6 43.3 - - + +
166A VAL* 3.5 6.2 - - - +
167A ASP 3.2 11.9 + - - +
168A GLY* 3.1 22.9 - - - +
169A TRP* 1.3 76.2 - - - +
171A PRO* 1.3 73.4 - - + +
172A GLU* 4.4 16.6 - - - +
173A ASN* 3.0 30.6 + - - +
174A ALA* 2.9 19.1 + - - +
199A THR* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 6.1 3.1 - - + +
14A LEU* 5.8 0.9 - - + -
169A TRP 3.7 8.3 - - - +
170A LEU* 1.3 88.2 - - + +
172A GLU* 1.3 57.6 + - - +
174A ALA* 3.0 7.5 + - + +
175A LEU* 2.8 26.4 + - - +
198A ALA* 3.7 36.6 - - + +
201A GLY 5.5 0.2 - - - -
202A GLY* 3.6 13.5 - - - +
159C LYS* 4.0 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 5.4 4.5 + - - -
170A LEU* 3.2 16.5 - - + +
171A PRO* 1.3 78.9 - - + +
173A ASN* 1.3 67.8 + - - +
175A LEU* 3.3 9.6 + - + +
176A LYS* 3.2 23.4 + - - +
125C ASN* 5.3 7.5 + - - +
159C LYS* 5.5 5.1 - - - +
185C ASN 4.8 4.2 - - - +
186C ASN* 5.8 1.4 - - - +
188C LYS* 4.3 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 3.7 14.8 - - + -
167A ASP* 3.0 37.9 + - - +
170A LEU* 3.0 28.6 + - - +
172A GLU* 1.3 83.9 - - - +
174A ALA* 1.3 57.3 + - - +
176A LYS* 3.5 5.2 + - - +
177A ILE* 3.1 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A MET* 3.4 21.4 - - - +
166A VAL* 3.7 7.0 - - + +
170A LEU 2.9 9.7 + - - +
171A PRO 3.4 7.4 - - - +
173A ASN* 1.3 75.4 - - - +
175A LEU* 1.3 64.3 + - - +
177A ILE* 3.6 0.8 + - - -
178A MET* 3.0 21.1 + - - +
199A THR* 3.4 46.9 - - + +
203A ALA 4.1 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PRO 2.8 13.0 + - - +
172A GLU* 3.3 11.8 + - + +
174A ALA* 1.3 75.3 - - - +
176A LYS* 1.3 59.9 + - + +
178A MET 3.2 1.6 + - - -
179A GLU* 2.9 58.1 + - - +
202A GLY* 3.7 21.9 - - - +
205A GLN* 3.6 33.0 - - + +
206A ALA* 3.6 13.7 - - + +
124C GLY* 6.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU 3.2 12.9 + - - +
173A ASN* 3.9 5.6 - - - +
175A LEU* 1.3 78.5 - - + +
177A ILE* 1.3 69.2 + - + +
179A GLU* 3.2 22.2 + - - +
180A ASN* 3.0 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.7 30.5 - - + -
129A MET* 4.1 8.3 - - + -
164A GLN* 3.7 24.9 - - + +
165A TRP 3.5 25.1 - - - +
166A VAL* 4.0 17.0 - - + -
167A ASP 5.2 0.4 - - - +
173A ASN* 3.1 26.6 + - + +
174A ALA 3.9 3.4 - - - +
175A LEU 3.3 0.2 - - - -
176A LYS* 1.3 77.9 - - + +
178A MET* 1.3 57.5 + - - +
180A ASN* 3.3 8.8 + - - +
181A ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 4.4 7.4 - - + -
129A MET* 4.2 7.0 - - + -
174A ALA 3.0 18.9 + - - +
175A LEU 3.2 4.0 + - - +
177A ILE* 1.3 77.1 - - - +
179A GLU* 1.3 58.0 + - - +
181A ALA* 4.1 6.5 - - + -
182A LEU* 2.9 50.5 + - + +
189A ILE* 3.7 31.6 - - + -
192A VAL* 3.6 35.7 - - + -
203A ALA* 3.7 35.7 - - + +
206A ALA* 3.7 10.1 - - + -
207A LEU* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 2.9 35.7 + - - +
176A LYS* 3.3 29.0 + - - +
178A MET* 1.3 76.9 - - - +
180A ASN* 1.3 65.5 + - - +
182A LEU* 3.4 6.1 + - - +
183A THR* 3.1 27.4 + - - +
206A ALA* 3.7 13.6 - - + +
209A ALA* 5.7 3.6 - - - +
210A GLN* 6.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.0 51.3 + - - +
177A ILE* 3.8 6.6 - - - +
179A GLU* 1.3 79.0 - - - +
181A ALA* 1.3 57.0 + - - +
183A THR* 3.1 8.6 + - - -
184A ALA* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.9 33.7 - - + -
177A ILE 2.9 17.6 + - - +
178A MET* 3.7 15.7 - - + +
180A ASN* 1.3 76.9 - - - +
182A LEU* 1.3 60.7 + - - +
184A ALA* 3.5 4.2 + - - -
185A ASN* 2.9 35.3 + - - +
189A ILE* 3.7 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A MET* 2.9 28.9 + - + +
179A GLU* 3.6 6.1 - - - +
181A ALA* 1.3 73.2 - - - +
183A THR* 1.3 65.6 + - - +
185A ASN 3.3 1.0 + - - -
186A ASN* 3.1 3.8 + - - -
187A ASN* 2.9 46.9 + - - +
189A ILE* 4.1 18.6 - - + -
206A ALA* 3.5 34.3 - - + +
207A LEU* 4.0 18.4 - - + +
210A GLN* 3.9 14.4 - - + +
212A LEU* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 3.1 17.2 + - - +
180A ASN* 3.4 10.9 - - - -
182A LEU* 1.3 76.6 - - - +
184A ALA* 1.3 63.6 + - - +
185A ASN 3.1 1.6 + - - -
186A ASN* 3.3 15.0 + - - +
187A ASN* 5.1 0.7 - - - -
210A GLN* 5.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN 2.8 19.7 + - - +
181A ALA* 3.8 7.6 - - - +
182A LEU 3.4 0.2 - - - -
183A THR* 1.3 74.5 - - - +
185A ASN* 1.3 66.6 + - - +
186A ASN* 3.9 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 5.7 0.3 - - - -
161A VAL* 3.5 47.3 + - - +
181A ALA* 2.9 27.7 + - - +
182A LEU 4.4 0.4 - - - +
183A THR 3.1 0.2 - - - -
184A ALA* 1.3 84.4 + - - +
186A ASN* 1.3 67.6 + - - +
187A ASN 3.2 0.4 - - - -
188A LYS* 2.9 39.8 + - - +
189A ILE* 4.2 11.5 - - + +
----------------------------------------------------------
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