Contacts of the helix formed by residues 185 - 192 (chain M) in PDB entry 1MCW
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 THR 185 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133M LYS* 5.0 2.2 - - - +
184M LEU* 1.3 91.3 - - - +
186M PRO* 1.3 68.2 - - + +
187M GLU* 3.2 45.8 - - + +
188M GLN* 2.2 37.1 + - + +
189M TRP* 2.8 12.5 + - - +
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Residues in contact with PRO 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M LEU* 5.6 8.3 - - + -
132M ASN* 4.0 32.1 - - - +
133M LYS* 4.4 6.3 - - + -
134M ALA* 4.0 7.8 - - + +
184M LEU 3.6 6.8 - - - +
185M THR* 1.3 85.3 - - + -
187M GLU* 1.3 85.9 - - + +
189M TRP* 2.8 28.9 - - + +
190M LYS* 2.6 23.2 + - + +
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Residues in contact with GLU 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M THR* 3.2 22.8 - - + +
186M PRO* 1.3 94.6 - - - +
188M GLN* 1.3 52.6 + - + +
190M LYS* 3.5 2.1 - - - +
191M SER* 2.8 28.1 + - - -
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Residues in contact with GLN 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M LEU* 3.7 20.1 - - + +
185M THR* 2.2 41.5 + - + +
186M PRO 3.2 0.4 - - - -
187M GLU* 1.3 76.3 - - + +
189M TRP* 1.3 55.7 + - - +
191M SER* 2.3 30.1 + - - +
192M HIS* 3.0 22.1 + - + +
195M TYR* 4.2 7.3 + - - +
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Residues in contact with TRP 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M PRO* 4.1 13.0 - - + -
124M PRO* 4.1 20.8 - - + +
129M LEU* 4.4 18.7 - - + +
134M ALA* 4.6 5.4 - - + -
136M LEU* 3.8 29.6 - - + -
184M LEU* 3.7 15.8 - - + +
185M THR 2.8 15.8 + - - +
186M PRO* 2.8 40.9 - - + +
188M GLN* 1.3 74.6 - - - +
190M LYS* 1.3 90.7 + - + +
191M SER 3.3 0.7 - - - -
192M HIS* 4.1 4.6 + - - +
193M ARG 4.8 3.8 + - - -
195M TYR* 4.0 26.3 - + + -
210M VAL* 5.5 6.3 - - + -
211M ALA 5.7 2.7 - - - -
212M PRO* 5.1 21.8 - - + +
213M THR 6.0 2.0 - - - -
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Residues in contact with LYS 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M LEU* 5.8 2.5 - - + -
186M PRO* 2.6 19.1 + - + +
187M GLU* 3.5 1.8 - - - +
189M TRP* 1.3 110.5 - - + +
191M SER* 1.3 66.7 - - - +
212M PRO* 3.6 35.1 + - + +
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Residues in contact with SER 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M GLU 2.8 12.8 + - - -
188M GLN* 2.3 33.0 + - - +
190M LYS* 1.3 84.3 - - - +
192M HIS* 1.3 74.0 + - - +
193M ARG* 3.8 4.2 + - - +
212M PRO* 5.5 1.6 - - - +
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Residues in contact with HIS 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M ALA* 4.3 12.9 + - + +
155M ASP* 2.0 76.5 + - + +
157M SER* 5.5 0.9 + - - -
188M GLN* 3.0 12.8 + - - +
189M TRP 4.1 1.4 - - - +
190M LYS 3.6 1.0 - - - -
191M SER* 1.3 84.2 + - - +
193M ARG* 1.3 61.8 + - - +
194M SER 3.5 0.2 - - - -
195M TYR* 3.2 39.2 + + + -
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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