Contacts of the helix formed by residues 186 - 192 (chain W) 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 PRO 186 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129W LEU* 4.4 13.2 - - + +
132W ASN* 4.3 9.9 - - + -
133W LYS 4.2 4.9 - - - +
184W LEU* 3.6 0.4 - - - -
185W THR* 1.3 111.7 - - - +
187W GLU* 1.3 84.0 + - + +
188W GLN 3.5 1.8 - - - -
189W TRP* 3.3 10.2 + - + -
190W LYS* 2.8 59.6 + - - +
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Residues in contact with GLU 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185W THR* 4.7 0.9 - - - +
186W PRO* 1.3 96.6 - - + +
188W GLN* 1.3 70.8 - - - +
190W LYS* 4.9 1.3 + - - +
191W SER* 2.5 48.2 + - - -
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Residues in contact with GLN 188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183W SER 4.5 2.8 - - - +
184W LEU* 3.7 40.7 + - + +
187W GLU* 1.3 89.1 - - - +
189W TRP* 1.3 59.1 + - - +
191W SER* 2.6 21.5 + - - -
192W HIS* 2.8 43.0 + - + +
195W TYR* 3.0 14.8 - - - +
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Residues in contact with TRP 189 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123W PRO* 3.1 32.8 - - + -
124W PRO* 3.2 18.8 - - + -
129W LEU* 3.3 38.1 - - + +
134W ALA* 4.3 4.9 - - + -
136W LEU* 3.0 24.9 - - + -
184W LEU* 3.5 25.2 - - + +
186W PRO* 3.3 9.5 + - + +
188W GLN* 1.3 78.5 - - - +
190W LYS* 1.3 78.3 + - + +
192W HIS 4.3 3.5 + - - +
195W TYR* 4.1 15.4 - + - -
210W VAL* 4.9 4.5 - - + -
211W ALA 2.9 29.2 - - - -
212W PRO* 3.3 39.8 - - + +
213W THR* 5.0 3.3 + - - -
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Residues in contact with LYS 190 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129W LEU* 5.0 15.3 + - + +
186W PRO* 2.8 42.2 + - - +
187W GLU* 4.9 1.4 + - - +
189W TRP* 1.3 91.2 - - + +
191W SER* 1.3 58.3 + - - +
192W HIS 3.0 19.0 + - - +
212W PRO* 5.3 4.9 - - + -
213W THR 4.9 12.3 - - - +
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Residues in contact with SER 191 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187W GLU* 2.5 35.8 + - - -
188W GLN* 2.6 8.6 + - - -
190W LYS* 1.3 71.9 - - - +
192W HIS* 1.3 68.8 - - - -
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Residues in contact with HIS 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154W ALA* 3.8 14.7 + - + +
155W ASP* 2.7 19.3 + - - +
188W GLN* 2.8 47.0 + - + +
189W TRP 4.4 2.2 - - - +
190W LYS* 3.0 12.5 - - - +
191W SER* 1.3 91.4 - - - +
193W ARG* 1.3 62.8 + - - +
194W SER 4.4 0.2 - - - +
195W TYR* 3.0 39.9 + + + -
212W PRO* 4.3 8.7 - - - +
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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