Contacts of the helix formed by residues 198 - 215 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 5.7 5.0 - - - +
197A ARG* 1.3 76.0 - - - +
199A GLY* 1.3 73.7 + - - +
200A VAL 3.5 0.5 + - - -
201A ALA* 3.4 11.1 + - - +
202A ALA* 3.3 15.6 + - - -
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 5.5 4.5 - - - -
198A THR* 1.3 75.5 + - - +
200A VAL* 1.3 66.9 + - - -
202A ALA* 3.2 8.4 + - - +
203A LEU* 3.1 27.0 + - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLU* 4.3 14.3 - - + +
168A HIS* 3.5 44.9 - - + +
198A THR 3.5 0.6 + - - -
199A GLY* 1.3 71.4 - - - -
201A ALA* 1.3 64.6 + - - +
203A LEU* 3.0 10.6 + - - +
204A ARG* 2.9 30.8 + - + +
230A TRP* 4.2 20.2 - - + -
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Residues in contact with ALA 201 (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 GLY 4.6 1.8 - - - +
192A ALA* 4.4 22.3 - - + +
193A HIS 5.6 0.2 - - - +
197A ARG* 4.3 10.8 - - + -
198A THR 3.4 10.2 + - - +
199A GLY 3.3 0.4 - - - -
200A VAL* 1.3 79.4 - - - +
202A ALA* 1.3 56.9 + - - +
204A ARG* 3.4 8.3 + - - +
205A TYR* 2.9 31.2 + - - +
230A TRP* 4.6 17.4 - - + -
255A MSE 5.8 0.9 - - - -
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Residues in contact with ALA 202 (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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197A ARG* 4.3 16.5 - - + +
198A THR* 3.3 20.9 + - - -
199A GLY 3.2 10.9 + - - +
200A VAL 3.2 0.6 - - - -
201A ALA* 1.3 79.6 - - - +
203A LEU* 1.3 59.6 + - + +
205A TYR* 3.5 6.5 + - - +
206A ALA* 3.1 27.4 + - - +
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Residues in contact with LEU 203 (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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154A GLU* 3.5 39.5 - - + +
168A HIS* 3.8 20.4 - - + -
169A GLU* 3.4 32.2 - - + +
199A GLY 3.1 13.8 + - - +
200A VAL* 3.0 7.4 + - - +
202A ALA* 1.3 76.4 - - + +
204A ARG* 1.3 64.4 + - - +
206A ALA* 3.3 8.1 + - + +
207A GLY 3.3 16.6 + - - -
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MSE 3.9 3.6 - - - +
168A HIS* 3.0 49.3 + - + -
172A ALA* 3.3 18.3 - - + +
189A LEU* 5.0 2.9 - - + +
200A VAL* 2.9 29.6 + - + +
201A ALA* 3.8 6.1 - - - +
203A LEU* 1.3 76.6 - - - +
205A TYR* 1.3 62.8 + - - +
207A GLY 3.2 1.7 + - - -
208A TYR* 3.0 22.0 + - - +
230A TRP* 4.2 7.0 - - + -
253A PHE* 5.1 0.2 - - - -
255A MSE 2.9 65.0 + - - +
283A PHE* 3.5 43.7 - - - -
284A ASP* 4.8 2.4 + - - -
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Residues in contact with TYR 205 (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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189A LEU* 4.0 26.8 - - + +
194A ALA 4.5 5.2 + - - -
197A ARG* 3.4 54.8 + - - -
201A ALA 2.9 19.0 + - - +
202A ALA* 3.7 4.5 - - - +
204A ARG* 1.3 78.0 - - - +
206A ALA* 1.3 58.8 + - - +
208A TYR* 3.3 5.8 + + - +
209A ARG* 2.8 63.6 + - + +
219A VAL* 3.7 30.4 - - + +
221A ASP* 5.1 0.9 + - - -
224A VAL* 4.2 23.6 - - + -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 4.4 13.9 - - + +
202A ALA 3.1 17.0 + - - +
203A LEU* 3.6 10.3 - - + +
204A ARG 3.3 0.4 - - - -
205A TYR* 1.3 76.8 - - - +
207A GLY* 1.3 56.9 + - - +
209A ARG* 3.5 28.0 + - - +
210A GLU* 3.0 35.0 + - + +
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 3.5 24.8 - - - +
173A ARG* 3.4 19.1 - - - -
203A LEU 3.3 4.9 + - - -
204A ARG 3.2 5.8 + - - -
206A ALA* 1.3 75.8 - - - +
208A TYR* 1.3 66.9 + - - +
210A GLU* 3.3 14.9 + - - +
211A ALA* 3.1 18.2 + - - +
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Residues in contact with TYR 208 (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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172A ALA* 4.1 3.9 - - + +
176A THR* 3.6 31.3 - - + +
187A VAL* 2.7 44.0 + - + -
189A LEU* 3.9 40.4 - - + -
204A ARG 3.0 13.3 + - - +
205A TYR* 3.5 15.9 - + - +
207A GLY* 1.3 75.7 - - - +
209A ARG* 1.3 65.1 + - - +
211A ALA* 3.2 4.2 + - - +
212A LEU* 3.0 52.8 + - + +
219A VAL* 4.1 10.0 - - + +
220A ASP 5.4 0.9 + - - -
223A LEU* 4.1 14.2 + - - +
224A VAL* 4.1 22.4 - - + +
253A PHE* 4.8 0.7 - + - -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 5.0 3.6 - - - +
205A TYR* 2.8 54.3 + - + +
206A ALA* 3.7 29.2 + - - +
208A TYR* 1.3 76.3 - - + +
210A GLU* 1.3 66.4 + - - +
212A LEU* 3.3 8.6 + - + +
213A THR* 2.9 36.1 + - - +
219A VAL* 5.3 13.0 - - + +
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Residues in contact with GLU 210 (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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169A GLU* 2.8 38.8 - - - +
173A ARG* 3.3 36.2 + - - +
206A ALA* 3.0 23.7 + - + +
207A GLY* 3.5 9.6 - - - +
208A TYR 3.3 0.2 - - - -
209A ARG* 1.3 75.1 - - - +
211A ALA* 1.3 64.2 + - - +
213A THR* 3.2 7.5 + - - -
214A ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 211 (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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173A ARG* 3.9 17.7 - - + +
176A THR* 3.6 31.9 - - + -
177A GLU* 4.1 15.7 - - + +
180A LEU* 3.5 12.6 - - + +
207A GLY 3.1 7.6 + - - +
208A TYR 3.2 2.9 + - - +
210A GLU* 1.3 80.7 - - - +
212A LEU* 1.3 62.6 + - - +
214A ALA* 3.3 8.8 + - - +
215A ALA* 3.3 16.3 + - - +
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Residues in contact with LEU 212 (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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176A THR* 4.1 17.9 - - + -
180A LEU* 4.3 11.7 - - + -
187A VAL* 4.6 9.9 - - + +
208A TYR* 3.0 55.8 + - + +
209A ARG* 3.3 8.7 + - + +
211A ALA* 1.3 76.9 - - - +
213A THR* 1.3 63.5 + - - +
215A ALA* 3.1 8.9 + - - -
217A LEU* 3.0 51.7 + - + +
218A ALA 4.4 4.7 - - - +
219A VAL* 4.2 22.9 - - + +
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Residues in contact with THR 213 (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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209A ARG* 2.9 25.7 + - - +
210A GLU* 3.2 7.3 + - - -
212A LEU* 1.3 76.2 - - - +
214A ALA* 1.3 59.2 + - - +
216A GLY* 3.0 18.5 + - - -
217A LEU 3.7 12.0 + - - +
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Residues in contact with ALA 214 (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 GLU* 6.0 2.0 - - + +
210A GLU 3.0 17.0 + - - +
211A ALA* 3.7 8.7 - - - +
212A LEU 3.2 0.4 - - - -
213A THR* 1.3 77.9 - - - +
215A ALA* 1.3 57.4 + - - +
216A GLY 3.4 1.2 + - - -
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Residues in contact with ALA 215 (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 LEU* 3.9 27.6 - - + -
211A ALA 3.3 10.7 + - - +
212A LEU 3.1 8.5 + - - +
214A ALA* 1.3 74.7 - - - +
216A GLY* 1.3 60.5 + - - +
217A LEU* 3.3 13.9 + - + +
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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