Contacts of the helix formed by residues 174 - 185 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 5.0 8.7 + - - -
173B SER* 1.3 74.3 + - - +
175B TYR* 1.3 64.7 + - - +
177B GLY* 3.0 2.6 + - - -
178B PHE 2.9 23.2 + - - -
197B GLU 2.9 12.1 + - - -
198B SER* 3.1 15.3 + - - -
199B PRO* 3.6 6.9 - - - +
200B MSE 3.7 12.4 + - - +
208B ASP* 4.9 1.4 + - - -
309B GLU* 4.2 4.2 + - - -
310B ASP* 3.3 7.8 + - - -
340B HIS* 2.9 32.6 + - - -
341B SER* 4.5 1.6 - - - -
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 3.5 26.5 - - + -
82B TYR* 3.6 23.0 + - + +
119B VAL* 4.9 2.5 - - + -
129B TYR* 2.7 38.1 + + - -
130B VAL 4.1 0.9 + - - -
131B MSE 4.3 5.2 - - - -
132B THR* 2.8 37.5 + - + -
133B ARG 4.4 0.9 + - - -
146B HIS* 4.4 9.1 + + - -
173B SER 3.3 0.2 + - - -
174B SER* 1.3 81.2 + - - +
176B GLU* 1.3 61.5 + - - +
178B PHE* 3.2 28.2 + + - +
179B THR* 3.2 21.5 + - + +
200B MSE 3.6 24.1 - - + -
222B TYR* 3.4 22.4 - - - -
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.5 18.8 - - + +
79B ARG 3.7 8.1 + - - +
80B THR* 2.6 40.1 + - - +
81B PRO* 4.5 0.2 - - + -
82B TYR* 3.9 14.0 - - + -
87B ARG* 2.9 43.3 + - - -
171B ILE 3.9 1.9 - - - +
172B GLY* 3.4 15.5 - - - -
173B SER* 3.1 23.5 + - - +
175B TYR* 1.3 77.8 - - - +
177B GLY* 1.3 56.7 + - - +
179B THR* 3.0 13.4 + - - -
180B VAL* 3.4 9.7 - - - +
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLY 3.1 24.2 + - - -
173B SER 3.5 0.4 - - - -
174B SER 3.0 8.2 + - - -
176B GLU* 1.3 74.3 - - - +
178B PHE* 1.3 65.0 + - - +
179B THR 3.2 1.8 - - - -
180B VAL* 3.0 17.2 + - - +
181B VAL* 3.1 16.1 + - - +
196B PRO* 3.9 1.6 - - - +
197B GLU 3.9 12.8 - - - -
199B PRO* 3.8 7.4 - - - -
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR* 3.6 47.1 - - + -
146B HIS* 3.6 26.0 - + - -
174B SER 2.9 11.5 + - - +
175B TYR* 3.2 29.4 + + - +
177B GLY* 1.3 78.4 - - - +
179B THR* 1.3 59.8 + - + +
181B VAL* 3.3 6.5 + - - +
182B MSE 3.1 64.2 + - + +
199B PRO* 4.0 6.9 - - - +
200B MSE 3.5 29.4 - - + +
284B GLN 6.1 0.2 - - - -
286B LEU* 3.7 9.2 - - + -
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 2.8 61.2 + - + +
119B VAL* 4.1 11.7 - - + -
146B HIS* 4.2 9.1 - - + +
150B ALA* 5.1 0.9 - - - +
170B MSE 3.8 5.4 - - - +
175B TYR* 3.2 13.2 + - + +
176B GLU 3.0 16.3 + - - -
178B PHE* 1.3 85.4 - - + +
180B VAL* 1.3 65.0 + - - +
182B MSE 3.5 7.5 + - - +
183B ALA* 3.3 20.4 + - - +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 6.1 0.2 - - - -
170B MSE 4.1 22.2 - - + -
171B ILE* 3.7 31.9 - - - +
172B GLY 4.1 2.0 - - - +
176B GLU 3.4 18.2 - - - +
177B GLY* 3.0 10.2 + - - +
179B THR* 1.3 76.6 - - - +
181B VAL* 1.3 63.1 + - - +
183B ALA* 3.1 6.4 + - - +
184B LEU* 3.1 20.3 + - + +
191B LEU* 6.2 0.4 - - + -
194B ALA* 3.7 29.4 - - + -
195B VAL 4.2 2.5 - - - +
196B PRO* 3.9 20.2 - - + -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLY 3.1 13.6 + - - +
178B PHE* 3.3 7.8 + - - +
180B VAL* 1.3 77.0 - - - +
182B MSE 1.3 61.8 + - - +
184B LEU* 3.1 19.3 + - - +
185B THR* 3.4 12.5 + - - +
196B PRO* 3.7 8.5 - - + -
199B PRO* 4.0 11.2 - - + -
201B ILE* 4.0 5.4 - - + -
286B LEU* 3.9 31.2 - - + -
290B MSE 3.9 20.8 - - + +
301B TRP* 3.5 34.5 - - + -
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Residues in contact with MSE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR 4.9 0.4 - - - +
133B ARG 3.7 14.8 - - - +
134B PRO* 4.5 3.4 - - + -
135B LEU* 3.4 41.5 - - + +
146B HIS* 3.5 35.0 - - + -
147B ALA* 3.2 11.2 - - - +
178B PHE* 3.1 54.5 + - + +
179B THR 3.8 4.3 - - - +
180B VAL 3.3 0.2 - - - -
181B VAL* 1.3 76.4 - - - +
183B ALA* 1.3 59.0 + - - +
185B THR* 2.6 28.2 + - - -
284B GLN 5.8 0.2 - - - +
286B LEU* 3.8 23.1 - - + -
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS 4.8 0.2 + - - -
147B ALA* 4.5 4.7 - - - +
150B ALA* 3.8 19.5 - - + -
154B ILE* 5.7 0.9 - - + -
170B MSE 3.5 28.9 - - - -
179B THR 3.3 7.1 + - - +
180B VAL 3.1 10.4 + - - +
182B MSE 1.3 79.7 - - - +
184B LEU* 1.3 58.3 + - - +
186B ASN 3.2 4.5 - - - +
187B PRO* 3.0 33.4 - - + +
191B LEU* 4.3 9.0 - - + -
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL 3.1 17.4 + - - +
181B VAL* 3.1 17.8 + - - +
183B ALA* 1.3 75.0 - - - +
185B THR* 1.3 63.2 + - - +
186B ASN 3.1 0.7 + - - -
187B PRO* 3.6 12.6 - - + +
191B LEU* 4.6 6.7 - - + -
194B ALA* 3.8 16.2 - - + -
196B PRO* 4.2 10.8 - - + -
290B MSE 4.4 10.5 - - - -
293B THR* 3.4 16.7 - - + +
294B PRO 5.3 0.5 - - - +
297B VAL* 3.8 26.7 - - + +
299B THR* 3.6 40.8 - - + +
301B TRP* 4.5 9.9 - - + -
321B MSE 5.9 2.9 - - + -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.6 23.3 - - + +
147B ALA* 3.4 12.6 - - - +
181B VAL* 3.4 15.7 + - + +
182B MSE 2.6 24.0 + - - +
184B LEU* 1.3 78.6 - - - +
186B ASN* 1.3 62.5 + - - +
187B PRO* 4.1 0.9 - - - +
286B LEU* 5.3 1.3 - - + -
289B VAL* 3.8 18.8 - - + -
290B MSE 3.8 14.4 - - + -
293B THR* 4.2 15.5 + - - +
294B PRO* 5.7 2.3 - - - +
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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