Contacts of the helix formed by residues 198 - 215 (chain B) in PDB entry 4KMR
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B THR* 4.0 24.1 - - + +
138B ASP* 6.2 4.0 - - + -
196B GLU* 5.5 3.4 - - + +
197B ARG* 1.3 80.8 - - - +
199B GLY* 1.3 69.1 + - - +
200B VAL 3.4 0.3 + - - -
201B ALA* 3.3 9.8 + - - +
202B ALA* 3.2 13.5 + - - -
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Residues in contact with GLY 199 (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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136B THR* 5.0 11.0 - - - +
154B GLU* 5.3 7.0 - - - -
198B THR* 1.3 75.5 - - - +
200B VAL* 1.3 64.8 + - - -
202B ALA* 3.1 13.7 + - - +
203B LEU* 3.3 19.1 + - - +
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Residues in contact with VAL 200 (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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153B GLY* 6.3 0.7 - - - -
154B GLU* 4.1 13.5 - - - +
168B HIS* 3.6 44.4 - - + +
198B THR 3.4 0.4 + - - -
199B GLY* 1.3 72.2 - - - -
201B ALA* 1.3 64.8 + - - +
203B LEU* 3.1 10.4 + - - +
204B ARG* 3.0 29.6 + - + +
230B TRP* 4.0 24.5 - - + -
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 4.7 0.7 - - - +
192B ALA* 4.2 25.9 - - + +
193B HIS 5.5 0.4 - - - +
197B ARG* 4.2 11.0 - - + -
198B THR 3.3 8.4 + - - +
199B GLY 3.3 0.6 - - - -
200B VAL* 1.3 80.5 - - - +
202B ALA* 1.3 58.9 + - - +
204B ARG* 3.4 7.5 + - - +
205B TYR* 2.9 31.0 + - - +
230B TRP* 4.6 17.1 - - + -
255B MSE 5.7 0.7 - - - -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ARG* 4.0 24.6 - - + +
198B THR* 3.2 16.0 + - - -
199B GLY 3.1 11.2 + - - +
201B ALA* 1.3 80.1 - - - +
203B LEU* 1.3 60.7 + - + +
205B TYR* 3.6 5.9 + - - +
206B ALA* 3.1 26.5 + - - +
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Residues in contact with LEU 203 (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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154B GLU* 3.8 35.7 - - + -
165B THR* 5.7 1.1 - - + -
168B HIS* 3.8 22.0 - - + -
169B GLU* 3.4 34.5 - - + +
199B GLY 3.3 12.3 + - - +
200B VAL* 3.1 6.6 + - - +
202B ALA* 1.3 79.0 - - + +
204B ARG* 1.3 64.8 + - - +
206B ALA* 3.3 5.4 + - + +
207B GLY 3.3 16.5 + - - -
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Residues in contact with ARG 204 (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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166B MSE 4.2 2.4 - - - +
168B HIS* 3.1 44.2 + - + -
172B ALA* 3.3 21.7 - - + +
189B LEU* 5.0 1.8 - - + -
200B VAL* 3.0 30.7 + - + +
201B ALA* 3.8 4.9 - - - +
203B LEU* 1.3 74.9 - - - +
205B TYR* 1.3 64.2 + - - +
207B GLY 3.1 2.4 + - - -
208B TYR* 3.0 21.8 + - - +
230B TRP* 4.0 7.0 - - + -
253B PHE* 5.1 0.7 - - - -
255B MSE 2.8 66.2 + - + +
283B PHE* 3.3 46.7 - - - -
284B ASP* 5.1 1.0 + - - -
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Residues in contact with TYR 205 (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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189B LEU* 4.0 27.7 - - + +
192B ALA* 5.2 0.2 - - + -
194B ALA 4.7 4.7 + - - -
197B ARG* 3.4 55.1 + - - +
201B ALA 2.9 17.7 + - - +
202B ALA 3.7 4.0 - - - +
203B LEU 3.3 0.2 - - - -
204B ARG* 1.3 77.6 - - - +
206B ALA* 1.3 57.3 + - - +
208B TYR* 3.3 6.6 + + - +
209B ARG* 2.8 60.4 + - + +
219B VAL* 3.6 27.0 - - + +
221B ASP* 4.9 2.1 + - - -
224B VAL* 4.1 24.2 - - + -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 3.9 21.1 - - - +
202B ALA 3.1 14.8 + - - +
203B LEU* 3.6 11.0 - - + +
204B ARG 3.2 0.6 - - - -
205B TYR* 1.3 78.4 - - - +
207B GLY* 1.3 55.5 + - - +
209B ARG* 3.7 29.2 + - - +
210B GLU* 3.0 34.4 + - - +
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 3.5 29.9 - - - +
173B ARG* 3.4 25.9 - - - +
203B LEU 3.3 4.8 + - - -
204B ARG 3.1 6.2 + - - -
206B ALA* 1.3 75.2 - - - +
208B TYR* 1.4 65.5 + - - +
210B GLU* 3.4 3.4 + - - -
211B ALA* 3.0 18.2 + - - +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA* 4.2 3.3 - - + +
176B THR* 3.6 28.9 - - + +
187B VAL* 2.7 42.9 + - + -
189B LEU* 3.9 48.5 + - + -
204B ARG 3.0 12.2 + - - +
205B TYR* 3.5 16.4 - + - +
207B GLY* 1.4 76.8 - - - +
209B ARG* 1.3 66.2 + - - +
211B ALA* 3.3 4.0 + - - +
212B LEU* 3.0 52.1 + - + +
219B VAL* 4.1 14.0 - - + +
220B ASP 5.1 0.9 + - - -
223B LEU* 4.1 12.8 + - - +
224B VAL* 4.2 13.8 - - + +
253B PHE* 4.9 0.9 - + - -
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 5.6 0.4 + - - -
197B ARG* 5.6 0.6 - - - +
205B TYR* 2.8 53.8 + - + +
206B ALA* 3.7 26.0 + - - +
208B TYR* 1.3 77.4 - - + +
210B GLU* 1.3 83.2 + - - +
212B LEU* 3.3 3.9 + - - +
213B THR* 2.9 38.9 + - - +
219B VAL* 4.1 22.0 - - + -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 4.9 7.9 - - - +
173B ARG* 3.7 27.8 + - - +
206B ALA 3.0 22.6 + - - +
207B GLY* 4.0 5.2 - - - +
208B TYR 3.3 0.2 - - - -
209B ARG* 1.3 107.6 + - - +
211B ALA* 1.3 60.8 + - - +
213B THR* 3.8 14.3 + - - +
214B ALA* 3.0 25.3 + - - +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 3.8 21.2 - - + +
176B THR* 3.6 31.2 - - + -
177B GLU* 4.0 14.3 - - + +
180B LEU* 3.6 12.5 - - + +
207B GLY 3.0 16.3 + - - +
208B TYR 3.7 0.2 - - - +
210B GLU* 1.3 76.6 - - - +
212B LEU* 1.3 64.4 + - - +
214B ALA* 3.3 6.0 + - - +
215B ALA* 3.3 15.4 + - - +
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Residues in contact with LEU 212 (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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176B THR* 4.1 17.5 - - + -
180B LEU* 4.2 11.0 - - + -
187B VAL* 4.5 14.1 - - + +
208B TYR* 3.0 51.5 + - + +
209B ARG* 3.7 4.3 - - - +
211B ALA* 1.3 77.4 - - - +
213B THR* 1.3 63.9 + - - +
215B ALA* 3.0 8.0 + - - -
216B GLY 3.2 0.2 + - - -
217B LEU* 2.9 54.8 + - + +
218B ALA 4.2 13.5 - - - +
219B VAL* 4.0 17.0 - - + -
402B NA 4.2 5.8 - - - -
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Residues in contact with THR 213 (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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209B ARG* 2.9 25.2 + - - +
210B GLU* 3.8 16.8 + - - +
212B LEU* 1.3 75.5 - - - +
214B ALA* 1.3 63.1 + - - +
216B GLY* 3.0 15.1 + - - -
217B LEU 3.5 11.6 + - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 3.7 20.9 - - - +
177B GLU* 5.8 0.7 - - - +
210B GLU 3.0 17.2 + - - +
211B ALA* 3.8 6.1 - - - +
212B LEU 3.2 0.2 - - - -
213B THR* 1.3 79.0 - - - +
215B ALA* 1.3 56.8 + - - +
216B GLY 3.3 0.7 + - - -
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Residues in contact with ALA 215 (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 LEU* 3.9 21.1 - - + -
185B ARG* 3.5 24.0 + - - +
211B ALA 3.3 11.2 + - - +
212B LEU 3.0 9.4 + - - +
214B ALA* 1.3 75.4 - - - +
216B GLY* 1.3 61.9 + - - +
217B LEU* 3.4 11.7 + - + +
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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