Contacts of the helix formed by residues 174 - 185 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C TYR* 4.8 9.9 + - - -
173C SER* 1.3 73.1 + - - +
175C TYR* 1.3 64.2 + - - -
177C GLY* 3.1 0.9 + - - -
178C PHE 3.0 22.2 + - - -
197C GLU 2.9 11.9 + - - -
198C SER* 3.1 15.2 + - - -
199C PRO* 3.6 0.5 - - - +
200C MSE 3.6 21.1 + - - +
208C ASP* 4.9 1.9 + - - -
309C GLU* 4.2 4.7 + - - -
310C ASP* 3.4 7.1 + - - -
340C HIS* 2.9 30.7 + - - -
341C SER* 4.5 2.2 - - - -
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Residues in contact with TYR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.4 24.9 - - + -
82C TYR* 3.6 22.4 - - + +
119C VAL* 4.8 3.1 - - + -
129C TYR* 2.8 36.4 + + - -
130C VAL 4.1 1.2 + - - -
131C MSE 4.3 4.5 - - - -
132C THR* 2.8 39.2 + - + -
133C ARG 4.3 1.2 + - - -
146C HIS* 4.4 9.7 + + - -
173C SER 3.3 0.2 + - - -
174C SER* 1.3 81.4 + - - +
176C GLU* 1.3 61.6 + - - +
178C PHE* 3.2 18.1 + + - +
179C THR* 3.2 30.1 + - + +
200C MSE 3.5 27.3 - - + -
222C TYR* 3.5 19.5 - - - -
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Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 3.4 19.3 - - + +
79C ARG 3.6 8.9 + - - +
80C THR* 2.6 42.2 + - - +
81C PRO* 4.5 0.2 - - + -
82C TYR* 3.8 13.5 - - + -
87C ARG* 3.0 41.1 + - - -
116C PHE* 4.0 0.4 - - - -
171C ILE 4.0 1.6 - - - +
172C GLY* 3.5 10.7 - - - -
173C SER* 3.1 23.7 + - - +
175C TYR* 1.3 78.1 - - - +
177C GLY* 1.3 54.8 + - - +
179C THR* 2.9 13.8 + - - -
180C VAL* 3.4 14.0 - - - +
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Residues in contact with GLY 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLY 3.0 24.9 + - - -
173C SER 3.6 0.6 - - - -
174C SER 3.1 7.6 + - - -
176C GLU* 1.3 74.8 - - - +
178C PHE* 1.3 65.6 + - - +
179C THR 3.2 0.4 - - - -
180C VAL* 3.1 18.2 + - - +
181C VAL* 3.2 16.8 + - - +
196C PRO* 3.9 1.2 - - - +
197C GLU 3.9 12.3 - - - -
199C PRO* 3.9 7.0 - - - -
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Residues in contact with PHE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C THR* 3.5 47.1 - - + -
133C ARG 4.0 1.1 - - - -
146C HIS* 3.7 24.7 - + - -
174C SER 3.0 12.2 + - - +
175C TYR* 3.2 26.0 + + - +
177C GLY* 1.3 77.8 - - - +
179C THR* 1.3 62.4 + - + +
181C VAL* 3.3 6.8 + - - +
182C MSE 3.1 64.5 + - + +
199C PRO* 4.0 4.9 - - - +
200C MSE 3.5 32.3 - - + +
286C LEU* 3.6 12.1 - - + -
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG* 2.8 63.1 + - + +
119C VAL* 4.1 8.5 - - + -
146C HIS* 4.1 12.6 - - - +
150C ALA* 5.1 0.5 - - - +
170C MSE 3.8 6.3 - - - +
175C TYR* 3.2 14.2 + - + +
176C GLU 2.9 15.1 + - - -
178C PHE* 1.3 84.8 - - + +
180C VAL* 1.3 63.7 + - - +
181C VAL 3.4 0.2 - - - -
182C MSE 3.6 7.8 + - - +
183C ALA* 3.3 21.0 + - - +
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Residues in contact with VAL 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 6.1 0.2 - - - -
170C MSE 4.1 24.0 - - + -
171C ILE* 3.8 30.7 - - - +
172C GLY 4.1 1.3 - - - +
176C GLU 3.4 18.4 - - - +
177C GLY* 3.1 10.0 + - - +
179C THR* 1.3 75.6 - - - +
181C VAL* 1.3 64.7 + - - +
183C ALA* 3.1 6.1 + - - +
184C LEU* 3.1 21.4 + - + +
191C LEU* 5.6 0.4 - - + +
194C ALA* 3.6 30.5 - - + -
195C VAL 4.2 3.1 - - - +
196C PRO* 3.9 18.8 - - + -
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C GLY 3.2 14.0 + - - +
178C PHE* 3.3 8.5 + - - +
180C VAL* 1.3 77.2 - - - +
182C MSE 1.3 61.3 + - - +
184C LEU* 3.1 20.0 + - - +
185C THR* 3.4 12.8 + - - +
196C PRO* 3.8 7.4 - - + -
199C PRO* 4.0 4.0 - - + -
201C ILE* 3.9 12.6 - - + -
286C LEU* 3.7 33.2 - - + -
290C MSE 3.7 23.9 - - + +
301C TRP* 3.6 29.4 - - + -
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Residues in contact with MSE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C THR 4.8 0.2 - - - +
133C ARG 3.5 16.6 - - - +
134C PRO* 4.3 3.6 - - + -
135C LEU* 3.4 49.8 - - + +
146C HIS* 3.5 34.1 - - + -
147C ALA* 3.2 10.6 - - - +
178C PHE* 3.1 54.3 + - + +
179C THR 3.7 4.7 - - - +
180C VAL 3.2 0.4 - - - -
181C VAL* 1.3 77.9 - - - +
183C ALA* 1.3 58.7 + - - +
185C THR* 2.5 28.2 + - - -
286C LEU* 4.0 14.6 - - + -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C HIS 4.7 0.4 + - - -
147C ALA* 4.4 5.8 - - - +
150C ALA* 3.8 20.9 - - + -
154C ILE* 5.6 1.3 - - + -
170C MSE 3.5 28.9 - - - -
179C THR 3.3 7.5 + - - +
180C VAL 3.1 10.6 + - - +
182C MSE 1.3 78.4 - - - +
184C LEU* 1.3 58.5 + - - +
186C ASN 3.2 4.2 - - - -
187C PRO* 3.0 33.8 - - + +
191C LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C VAL 3.1 18.4 + - - +
181C VAL* 3.1 13.0 + - - +
183C ALA* 1.3 72.9 - - - +
185C THR* 1.3 62.7 + - - +
186C ASN 3.2 3.1 + - - -
187C PRO* 3.7 11.3 - - - +
191C LEU* 4.3 7.0 - - + -
194C ALA* 3.8 18.6 - - + -
196C PRO* 4.2 11.7 - - + -
290C MSE 4.4 10.8 - - - -
293C THR* 3.4 16.8 - - + +
294C PRO 5.4 0.3 - - - +
296C LYS* 6.0 0.7 - - - +
297C VAL* 3.8 28.3 - - + +
299C THR* 3.6 39.7 - - + +
301C TRP* 4.5 9.6 - - + -
321C MSE 5.9 2.5 - - + -
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Residues in contact with THR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 3.8 21.4 - - + +
147C ALA* 3.4 13.5 - - - +
181C VAL* 3.4 15.7 + - + +
182C MSE 2.5 24.1 + - - +
184C LEU* 1.3 77.5 - - - +
186C ASN* 1.3 63.2 + - - +
187C PRO* 4.1 0.2 - - - -
286C LEU* 5.3 0.9 - - + -
289C VAL* 3.9 19.1 - - + -
290C MSE 3.7 14.1 - - + -
293C THR* 4.2 16.8 + - - +
294C PRO* 5.8 1.4 - - - +
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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