Contacts of the helix formed by residues 174 - 185 (chain A) in PDB entry 1MPX
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 174 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 5.0 8.6 + - - -
173A SER* 1.3 72.0 + - - +
175A TYR* 1.3 63.7 + - - +
177A GLY* 3.0 1.9 + - - -
178A PHE* 2.9 26.5 + - - +
197A GLU 2.9 12.1 + - - -
198A SER* 3.1 15.1 + - - -
199A PRO* 3.7 0.2 - - - +
200A MSE 3.6 16.4 + - - +
208A ASP* 4.8 1.6 + - - -
309A GLU* 4.2 4.0 + - - -
310A ASP* 3.2 8.3 + - - -
340A HIS* 2.9 32.2 + - - -
341A SER* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 3.5 25.6 - - + -
82A TYR* 3.6 22.4 - - + +
119A VAL* 4.9 4.7 - - + -
129A TYR* 2.7 36.8 + + - -
130A VAL 4.1 1.4 + - - -
131A MSE 4.3 5.2 - - - -
132A THR* 2.8 39.1 + - + -
146A HIS* 4.3 7.8 + + - -
173A SER 3.3 0.2 + - - -
174A SER* 1.3 80.8 + - - +
176A GLU* 1.3 61.8 + - - +
178A PHE* 3.1 19.3 + + - +
179A THR* 3.1 29.5 + - + +
200A MSE 3.6 23.1 - - + -
222A TYR* 3.4 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.5 18.4 - - + +
79A ARG 3.7 2.0 + - - +
80A THR* 2.5 41.8 + - - +
82A TYR* 3.9 14.0 - - + -
87A ARG* 2.9 42.9 + - - -
171A ILE 4.0 1.7 - - - +
172A GLY* 3.4 11.2 - - - -
173A SER* 3.1 23.2 + - - +
175A TYR* 1.3 77.3 - - - +
177A GLY* 1.3 57.2 + - - +
179A THR* 3.0 20.1 + - - -
180A VAL* 3.4 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 3.0 23.8 + - - -
173A SER 3.5 0.6 - - - -
174A SER 3.0 7.4 + - - -
176A GLU* 1.3 75.8 - - - +
178A PHE* 1.3 65.7 + - - +
179A THR 3.2 0.7 - - - -
180A VAL* 3.1 17.2 + - - +
181A VAL* 3.2 15.9 + - - +
196A PRO* 3.9 1.5 - - - +
197A GLU 3.9 14.1 - - - -
199A PRO* 3.9 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 3.6 44.6 - - + -
146A HIS* 3.5 26.7 - + - -
174A SER 2.9 11.8 + - - +
175A TYR* 3.1 28.2 + + - +
177A GLY* 1.3 77.6 - - - +
179A THR* 1.3 66.2 + - + +
181A VAL* 3.2 6.6 + - - +
182A MSE 3.1 60.2 + - + +
199A PRO* 4.1 2.6 - - - +
200A MSE 3.5 34.8 - - + +
286A LEU* 3.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 2.8 61.3 + - + +
119A VAL* 4.1 11.9 - - + -
146A HIS* 4.4 9.4 - - - +
150A ALA* 5.1 0.9 - - - +
170A MSE 3.8 5.6 - - - +
175A TYR* 3.1 14.2 + - + +
176A GLU 3.0 15.8 + - - -
178A PHE* 1.3 88.6 - - + +
180A VAL* 1.3 61.7 + - - +
182A MSE 3.6 8.2 + - - +
183A ALA* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 6.2 0.4 - - - -
170A MSE 4.1 20.6 - - + -
171A ILE* 3.7 31.6 - - - +
172A GLY 4.0 1.3 - - - +
176A GLU 3.4 18.2 - - - +
177A GLY* 3.1 10.2 + - - +
179A THR* 1.3 76.0 - - - +
181A VAL* 1.3 65.0 + - - +
183A ALA* 3.1 6.2 + - - +
184A LEU* 3.1 20.4 + - + +
194A ALA* 3.7 29.8 - - + -
195A VAL 4.1 4.3 - - - +
196A PRO* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLY 3.2 13.8 + - - +
178A PHE* 3.2 7.2 + - - +
180A VAL* 1.3 75.2 - - - +
182A MSE 1.3 62.7 + - - +
184A LEU* 3.1 19.0 + - - +
185A THR* 3.4 12.8 + - - +
196A PRO* 3.7 8.1 - - + -
199A PRO* 3.9 11.2 - - + -
201A ILE* 3.9 3.8 - - + -
286A LEU* 3.9 31.2 - - + -
290A MSE 3.9 25.5 - - + +
301A TRP* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR 4.8 0.4 - - - +
133A ARG 3.6 15.7 - - - +
134A PRO* 4.3 3.8 - - + -
135A LEU* 3.5 42.4 - - + +
146A HIS* 3.5 35.4 - - + -
147A ALA* 3.3 10.5 - - - +
178A PHE* 3.1 54.3 + - + +
179A THR 3.8 4.3 - - - +
180A VAL 3.2 0.2 - - - -
181A VAL* 1.3 76.7 - - - +
183A ALA* 1.3 59.7 + - - +
185A THR* 2.6 28.4 + - - -
286A LEU* 3.8 22.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
146A HIS 4.7 0.4 + - - -
147A ALA* 4.5 5.4 - - - +
150A ALA* 3.8 19.7 - - + -
154A ILE* 5.6 0.9 - - + -
170A MSE 3.5 28.9 - - - -
179A THR 3.3 6.9 + - - +
180A VAL 3.1 10.0 + - - +
182A MSE 1.3 80.2 - - - +
184A LEU* 1.3 57.7 + - - +
186A ASN 3.2 5.1 - - - -
187A PRO* 3.0 33.3 - - + +
191A LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL 3.1 17.9 + - - +
181A VAL* 3.1 17.4 + - - +
183A ALA* 1.3 75.2 - - - +
185A THR* 1.3 63.7 + - - +
186A ASN 3.1 0.7 + - - -
187A PRO* 3.5 12.9 - - - +
191A LEU* 4.5 6.1 - - + -
194A ALA* 3.8 17.9 - - + -
196A PRO* 4.3 7.6 - - + -
290A MSE 4.4 11.0 - - - -
293A THR* 3.4 16.7 - - + +
294A PRO 5.3 0.5 - - - +
296A LYS* 5.9 0.9 - - - +
297A VAL* 3.8 27.6 - - + +
299A THR* 3.6 42.2 - - + +
301A TRP* 4.5 9.4 - - + -
321A MSE 5.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.6 22.6 - - + +
147A ALA* 3.5 13.3 - - - +
181A VAL* 3.4 14.3 + - + +
182A MSE 2.6 23.5 + - - +
184A LEU* 1.3 78.1 - - - +
186A ASN* 1.3 63.7 + - - +
187A PRO* 4.1 0.6 - - - +
286A LEU* 5.4 1.1 - - + -
289A VAL* 3.8 19.1 - - + -
290A MSE 3.7 15.5 - - + -
293A THR* 4.2 16.0 + - - +
294A PRO* 5.6 1.9 - - - +
----------------------------------------------------------
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