Contacts of the helix formed by residues 186 - 197 (chain A) in PDB entry 2MKJ
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 ALA 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A TRP* 5.1 0.2 - - - -
159A SER* 5.2 0.6 - - - +
161A PHE* 3.5 32.8 - - + -
185A ARG* 1.3 70.6 - - - +
187A VAL* 1.3 56.0 + - - +
188A GLU 3.4 1.8 - - - -
189A LEU* 3.8 9.9 - - + -
190A ALA* 2.9 32.1 + - - +
203A ALA 4.9 0.2 - - - -
204A GLY* 3.8 32.1 - - - +
205A ILE* 4.0 16.2 - - + +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.7 23.3 - - + -
185A ARG* 2.8 25.8 + - + +
186A ALA* 1.3 76.9 - - - +
188A GLU* 1.3 59.9 + - + +
190A ALA* 4.8 0.6 - - - +
191A MET* 2.9 36.7 + - + +
241A HIS* 5.8 3.6 - - + +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 3.4 31.5 - - + +
181A PRO* 3.5 11.7 - - - +
184A LEU* 3.3 29.3 - - + +
185A ARG 3.9 13.1 - - - +
187A VAL* 1.3 77.2 - - + +
189A LEU* 1.3 62.3 + - + +
191A MET* 3.9 7.4 - - - -
192A ILE* 3.0 37.2 + - + +
241A HIS* 3.5 37.5 - - + +
242A GLY* 5.6 0.5 - - - -
244A ILE* 4.6 10.2 - - - +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.0 33.0 - - + -
180A VAL* 4.2 16.2 - - + -
186A ALA* 3.6 13.5 - - + +
188A GLU* 1.3 80.4 - - + +
190A ALA* 1.3 71.8 + - + +
192A ILE* 3.3 22.1 - - - +
193A MET* 3.3 16.8 - - + +
203A ALA* 4.1 8.1 - - + -
204A GLY 3.6 20.9 - - - +
205A ILE* 4.0 13.7 - - + -
218A GLY* 4.2 7.2 - - - -
219A ARG 4.2 2.2 - - - +
220A VAL* 3.5 30.1 - - + -
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 4.0 15.9 - - + -
186A ALA 2.9 16.6 + - - +
187A VAL 4.8 0.2 - - - +
189A LEU* 1.3 81.5 - - - +
191A MET* 1.3 58.4 + - - +
193A MET* 4.1 3.6 - - - +
194A ASP* 3.1 28.8 + - - +
200A VAL* 5.1 8.9 - - + +
203A ALA* 3.9 25.6 - - + -
220A VAL* 5.7 0.4 - - - -
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Residues in contact with MET 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 2.9 30.4 + - + +
188A GLU* 3.8 4.0 - - - +
190A ALA* 1.3 76.3 - - - +
192A ILE* 1.3 89.2 + - + +
194A ASP* 3.3 5.4 + - - +
195A ARG* 3.1 71.2 + - - +
241A HIS* 3.4 44.0 - - + +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 6.0 1.1 - - + -
188A GLU* 3.0 25.1 - - + +
189A LEU* 3.3 13.0 - - - +
191A MET* 1.3 99.2 - - + +
193A MET* 1.3 84.7 + - + +
195A ARG* 3.0 13.9 + - - +
196A LEU* 3.0 24.5 - - - +
239A LEU* 3.7 47.8 - - + -
241A HIS* 5.0 3.8 - - + -
248A VAL* 5.3 4.0 - - + -
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Residues in contact with MET 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 4.2 18.8 - - + -
189A LEU* 3.3 21.4 + - + +
190A ALA* 4.4 3.8 - - - +
191A MET 3.4 0.4 - - - -
192A ILE* 1.3 95.7 - - + +
194A ASP* 1.3 57.0 - - - +
195A ARG 3.4 0.2 - - - -
196A LEU* 3.6 14.1 - - - -
197A TYR* 2.9 38.7 + - + +
198A GLY* 3.0 0.3 + - - -
200A VAL* 6.0 8.1 - - + -
220A VAL* 5.6 7.2 - - + -
222A PHE* 5.5 10.3 - - + -
231A ALA* 4.7 15.0 - - - -
237A VAL* 5.6 7.2 - - + -
239A LEU* 6.3 0.4 - - - -
248A VAL* 5.0 7.4 - - + -
250A VAL* 3.5 33.0 - - + -
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Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A MET* 4.6 18.2 - - - +
190A ALA 3.1 20.9 + - - +
191A MET* 3.7 7.1 - - - +
192A ILE 3.1 0.6 - - - -
193A MET* 1.3 78.4 - - - +
195A ARG* 1.3 61.3 + - - +
196A LEU 3.5 0.4 - - - -
198A GLY* 3.8 22.3 + - - -
199A GLY 4.4 4.3 + - - -
200A VAL* 4.8 11.4 - - + +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A MET* 3.1 52.4 + - - +
192A ILE* 3.0 8.3 + - - +
194A ASP* 1.3 82.6 - - - +
196A LEU* 1.3 59.5 + - + +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ILE* 3.0 24.5 - - + +
193A MET* 3.6 15.5 - - - -
195A ARG* 1.3 81.9 - - + +
197A TYR* 1.3 114.2 + - + +
198A GLY 3.8 1.6 - - - -
237A VAL* 4.7 18.8 - - + -
238A GLN 5.3 1.8 - - - +
239A LEU* 4.7 16.4 - - + -
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A MET* 2.9 19.8 + - + +
196A LEU* 1.3 118.2 - - + +
198A GLY* 1.3 68.9 + - - +
200A VAL* 5.1 0.3 + - - +
222A PHE* 3.7 18.5 - - - -
227A SER* 3.5 20.5 - - - +
230A ALA* 3.4 42.3 + - + -
231A ALA* 3.4 24.9 - - + -
234A ALA* 3.8 19.1 - - + +
237A VAL* 5.1 10.1 - - + +
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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