Contacts of the helix formed by residues 174 - 185 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D TYR* 4.9 9.8 + - - -
173D SER* 1.3 73.2 + - - +
175D TYR* 1.3 63.3 + - - -
177D GLY* 3.0 1.7 + - - -
178D PHE 2.9 22.5 + - - -
197D GLU 3.0 11.7 + - - -
198D SER 3.1 15.0 + - - -
199D PRO* 3.6 0.2 - - - +
200D MSE 3.6 19.3 + - - +
208D ASP* 4.8 1.4 + - - -
309D GLU* 4.0 4.9 + - - -
310D ASP* 3.3 7.9 + - - -
340D HIS* 2.8 31.3 + - - -
341D SER* 4.5 2.2 - - - -
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 3.5 26.0 - - + -
82D TYR* 3.5 22.4 - - + +
119D VAL* 4.8 3.1 - - + -
129D TYR* 2.8 37.0 + + - -
130D VAL 4.0 1.2 + - - -
131D MSE 4.4 4.5 - - - -
132D THR* 2.9 37.4 + - + -
146D HIS* 4.3 9.9 + + - -
173D SER 3.3 0.2 + - - -
174D SER* 1.3 81.0 + - - +
176D GLU* 1.3 57.4 + - - +
178D PHE* 3.2 19.3 + + - +
179D THR* 3.1 33.4 + - + +
200D MSE 3.6 24.8 - - + -
222D TYR* 3.4 20.6 - - - -
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D THR* 3.5 18.6 - - + +
79D ARG 3.6 8.8 + - - +
80D THR* 2.6 41.1 + - - +
81D PRO* 4.5 0.2 - - + -
82D TYR* 3.9 13.2 - - + -
87D ARG* 2.9 43.6 + - - -
171D ILE 4.0 1.4 - - - +
172D GLY* 3.4 11.3 - - - -
173D SER* 3.0 24.5 + - - +
175D TYR* 1.3 76.0 - - - +
177D GLY* 1.3 57.9 + - - +
179D THR* 2.9 13.8 + - - -
180D VAL* 3.4 14.0 - - - +
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Residues in contact with GLY 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLY 3.1 24.4 + - - -
173D SER 3.5 0.6 - - - -
174D SER 3.0 8.4 + - - -
176D GLU* 1.3 74.0 - - - +
178D PHE* 1.3 65.8 + - - +
179D THR 3.2 0.4 - - - -
180D VAL* 3.1 17.6 + - - +
181D VAL* 3.1 17.0 + - - +
196D PRO* 3.9 0.9 - - - +
197D GLU 4.0 12.3 - - - -
199D PRO* 3.9 7.2 - - - -
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Residues in contact with PHE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D THR* 3.6 45.3 - - + -
133D ARG 4.0 1.3 - - - -
146D HIS* 3.6 24.5 - + - -
174D SER 2.9 11.7 + - - +
175D TYR* 3.2 29.8 + + - +
177D GLY* 1.3 77.7 - - - +
179D THR* 1.3 58.9 + - + +
181D VAL* 3.3 7.0 + - - +
182D MSE 3.1 65.4 + - + +
199D PRO* 4.0 2.6 - - - +
200D MSE 3.5 34.8 - - + +
284D GLN 6.1 0.2 - - - -
286D LEU* 3.7 11.7 - - + -
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Residues in contact with THR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ARG* 2.8 59.2 + - + +
119D VAL* 4.1 15.3 - - + -
146D HIS* 4.1 10.0 - - + +
150D ALA* 5.1 0.5 - - - +
170D MSE 3.8 6.2 - - - +
175D TYR* 3.1 12.9 + - + +
176D GLU 2.9 15.8 + - - -
178D PHE* 1.3 85.3 - - + +
180D VAL* 1.3 64.8 + - - +
182D MSE 3.5 7.8 + - - +
183D ALA* 3.3 20.8 + - - +
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Residues in contact with VAL 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D THR* 6.0 0.4 - - - -
170D MSE 4.1 21.5 - - + -
171D ILE* 3.7 31.4 - - - +
172D GLY 4.0 1.6 - - - +
176D GLU 3.4 18.2 - - - +
177D GLY* 3.1 9.1 + - - +
179D THR* 1.3 76.9 - - - +
181D VAL* 1.3 63.5 + - - +
183D ALA* 3.2 5.7 + - - +
184D LEU* 3.1 20.4 + - + +
191D LEU* 5.6 0.6 - - + +
194D ALA* 3.7 29.2 - - + -
195D VAL 4.1 4.0 - - - +
196D PRO* 3.8 21.3 - - + -
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D GLY 3.1 13.6 + - - +
178D PHE 3.3 7.4 + - - +
180D VAL* 1.3 77.9 - - - +
182D MSE 1.3 60.5 + - - +
184D LEU* 3.1 19.7 + - - +
185D THR* 3.4 13.2 + - - +
196D PRO* 3.7 8.1 - - + -
199D PRO* 4.0 11.4 - - + -
201D ILE* 4.0 5.6 - - + -
286D LEU* 3.7 33.0 - - + -
290D MSE 3.6 20.0 - - + +
301D TRP* 3.5 33.7 - - + -
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Residues in contact with MSE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D THR 4.7 0.7 - - - +
133D ARG 3.5 15.9 - - - +
134D PRO* 4.3 2.9 - - + -
135D LEU* 3.5 41.5 - - + +
146D HIS* 3.5 33.2 - - + -
147D ALA* 3.3 12.3 - - - +
178D PHE* 3.1 53.6 + - + +
179D THR 3.7 7.9 - - - +
180D VAL 3.2 0.2 - - - -
181D VAL* 1.3 76.3 - - - +
183D ALA* 1.3 59.2 + - - +
185D THR* 2.6 27.4 + - - -
284D GLN 5.9 0.4 - - - +
286D LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D HIS 4.7 0.4 + - - -
147D ALA* 4.5 5.6 - - - +
150D ALA* 3.8 19.5 - - + -
154D ILE* 5.6 1.3 - - + -
170D MSE 3.5 28.7 - - - -
179D THR 3.3 7.5 + - - +
180D VAL 3.2 10.4 + - - +
182D MSE 1.3 79.8 - - - +
184D LEU* 1.3 58.2 + - - +
186D ASN 3.2 4.5 - - - +
187D PRO* 3.0 32.9 - - + +
191D LEU* 4.4 8.3 - - + -
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D VAL 3.1 18.2 + - - +
181D VAL* 3.1 13.8 + - - +
183D ALA* 1.3 74.7 - - - +
185D THR* 1.3 63.4 + - - +
186D ASN 3.2 0.6 + - - -
187D PRO* 3.6 12.5 - - + +
191D LEU* 4.4 5.2 - - + -
194D ALA* 3.9 15.7 - - + -
196D PRO* 4.2 13.5 - - + -
290D MSE 4.3 11.9 - - + -
293D THR* 3.4 16.5 - - + +
294D PRO 5.4 0.2 - - - +
297D VAL* 3.8 27.6 - - + +
299D THR* 3.6 41.7 - - + +
301D TRP* 4.5 10.3 - - + -
321D MSE 5.9 2.2 - - + -
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 3.6 22.6 - - + +
147D ALA* 3.5 12.1 - - - +
181D VAL 3.4 14.7 + - - +
182D MSE 2.6 23.8 + - - +
184D LEU* 1.3 76.7 - - - +
186D ASN* 1.3 62.8 + - - +
187D PRO* 4.0 0.4 - - - +
286D LEU* 5.2 2.5 - - + -
289D VAL* 3.7 20.2 - - + -
290D MSE 3.6 17.9 - - + -
293D THR* 4.3 13.2 + - - +
294D PRO* 5.7 1.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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