Contacts of the helix formed by residues 177 - 199 (chain A) in PDB entry 4KM5
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 ASP 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LYS* 3.2 23.5 + - - +
174A LEU* 4.5 9.1 - - + +
175A SER 3.3 0.6 - - - -
176A ARG* 1.3 80.9 - - - +
178A ASP* 1.3 63.3 + - - +
179A ILE 3.2 0.7 - - - -
180A SER* 3.7 17.4 + - - -
181A THR* 4.8 4.0 + - - +
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Residues in contact with ASP 178 (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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174A LEU 4.2 6.7 + - - +
175A SER* 3.5 15.8 + - - +
176A ARG 3.3 0.4 - - - -
177A ASP* 1.3 78.9 - - - +
179A ILE* 1.3 63.7 + - - +
180A SER 3.3 0.4 + - - -
181A THR* 3.2 26.8 + - - +
182A ALA* 4.2 1.9 + - - +
223A PRO* 5.9 3.1 - - - +
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Residues in contact with ILE 179 (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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175A SER 3.2 13.5 - - - +
176A ARG* 3.4 29.2 - - + +
177A ASP 3.2 0.2 - - - -
178A ASP* 1.3 77.5 - - - +
180A SER* 1.3 51.6 + - - +
182A ALA* 2.7 13.2 + - - +
183A ALA* 2.7 36.8 + - + -
214A TYR* 4.3 16.6 - - + +
217A HIS* 3.6 29.8 - - + +
223A PRO* 3.6 26.9 - - + +
226A PHE* 3.5 27.6 - - + -
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG 3.9 4.0 + - - -
177A ASP* 3.7 15.4 + - - -
178A ASP 3.3 0.8 - - - -
179A ILE* 1.3 79.3 - - - +
181A THR* 1.3 61.1 + - - +
183A ALA* 3.7 10.3 - - - +
184A GLY* 3.4 15.2 + - - -
214A TYR* 5.9 2.5 - - - -
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Residues in contact with THR 181 (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 ASP 5.0 4.3 - - - +
178A ASP* 3.2 25.6 + - - +
180A SER* 1.3 79.0 - - - +
182A ALA* 1.3 71.9 + - - +
184A GLY* 3.4 8.5 + - - -
185A MET* 3.4 25.3 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP 4.9 1.1 - - - +
179A ILE* 2.7 13.4 + - - +
181A THR* 1.3 79.4 + - - +
183A ALA* 1.3 66.0 + - - +
184A GLY 3.2 0.2 - - - -
185A MET* 3.1 12.2 + - - +
186A VAL* 3.1 26.4 + - - +
224A ASN* 5.7 0.9 - - - +
226A PHE* 4.4 7.6 - - + -
316A ILE* 3.8 32.8 - - + +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 2.7 28.4 + - + +
180A SER* 3.7 13.2 - - - +
181A THR 3.2 0.2 - - - -
182A ALA* 1.3 74.1 - - - +
184A GLY* 1.3 59.8 + - - +
186A VAL* 3.3 6.0 + - - +
187A LYS 3.2 15.2 + - - -
213A SER* 3.1 24.8 + - - +
214A TYR* 4.3 17.9 - - + +
226A PHE* 4.1 13.2 - - + -
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Residues in contact with GLY 184 (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 SER 3.4 10.6 + - - -
181A THR 3.4 4.6 + - - -
182A ALA 3.2 0.4 - - - -
183A ALA* 1.3 78.0 - - - +
185A MET* 1.3 64.9 + - - +
187A LYS* 3.8 6.7 - - - +
188A GLY* 3.2 18.7 + - - -
213A SER* 4.3 5.4 - - - -
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Residues in contact with MET 185 (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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181A THR* 3.4 21.1 - - - +
182A ALA* 3.1 13.4 + - - +
184A GLY* 1.3 78.3 - - - +
186A VAL* 1.3 63.1 + - - +
188A GLY* 3.6 1.7 + - - +
189A VAL* 3.3 27.9 + - - +
294A THR* 5.6 10.6 - - + +
312A ILE* 4.4 20.6 - - + +
313A SER* 5.9 2.2 - - - +
316A ILE* 4.9 3.1 - - + -
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Residues in contact with VAL 186 (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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182A ALA 3.1 15.6 + - - +
183A ALA* 3.5 7.6 - - - +
184A GLY 3.3 0.2 - - - -
185A MET* 1.3 74.3 - - - +
187A LYS* 1.3 60.7 + - - +
189A VAL* 3.1 7.2 + - - +
190A VAL* 2.8 47.7 + - + +
212A GLY 5.2 6.5 - - - +
213A SER* 6.0 1.1 - - - -
214A TYR 6.1 0.9 - - - +
226A PHE* 3.9 23.3 - - + -
228A VAL* 4.2 15.3 - - + -
312A ILE* 5.3 2.0 - - - -
316A ILE* 3.7 20.0 - - + -
318A VAL* 3.8 25.1 - - + -
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Residues in contact with LYS 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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183A ALA 3.2 5.7 + - - +
184A GLY* 3.8 7.6 - - - +
186A VAL* 1.3 80.5 - - - +
188A GLY* 1.3 57.3 + - - +
190A VAL* 4.3 5.8 - - - -
191A ASP* 2.8 61.0 + - - +
208A LEU* 6.2 1.3 - - + -
212A GLY* 5.4 2.5 - - - -
213A SER* 3.8 40.8 - - - +
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Residues in contact with GLY 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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184A GLY 3.2 13.1 + - - -
185A MET* 3.6 2.7 + - - -
186A VAL 3.2 0.2 - - - -
187A LYS* 1.3 79.5 - - - +
189A VAL* 1.3 60.3 + - - +
191A ASP* 4.1 5.4 - - - +
192A HIS* 3.3 21.8 + - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A MET 3.3 15.2 + - - +
186A VAL* 3.1 6.8 + - - +
188A GLY* 1.3 74.1 - - - +
190A VAL* 1.3 62.4 + - + +
192A HIS* 3.2 5.9 + - - +
193A LEU* 3.0 47.1 + - + +
288A ILE* 5.8 1.8 - - + -
291A ILE* 5.4 12.3 - - + -
294A THR* 5.0 8.1 - - + -
296A VAL* 4.2 16.2 - - + -
310A LEU* 4.3 14.6 - - + -
312A ILE* 3.7 28.5 - - + -
320A ILE* 5.9 0.7 - - + -
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Residues in contact with VAL 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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186A VAL* 2.8 36.8 + - + +
187A LYS* 3.8 7.0 - - - +
189A VAL* 1.3 78.3 - - + +
191A ASP* 1.3 63.5 + - - +
193A LEU* 3.3 7.6 + - - +
194A LEU* 3.0 33.7 + - + +
208A LEU* 4.0 18.6 - - + -
212A GLY* 5.8 3.8 - - - +
228A VAL* 4.2 18.4 - - + -
230A PHE* 3.6 27.5 - - + -
318A VAL* 5.1 2.2 - - + -
320A ILE* 5.0 8.3 - - + -
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 2.8 58.3 + - - +
188A GLY* 4.1 5.3 - - - +
190A VAL* 1.3 73.9 - - - +
192A HIS* 1.3 61.5 + - - +
194A LEU* 3.6 9.9 + - - +
195A LEU* 3.2 21.7 + - - +
208A LEU* 4.5 15.6 - - - +
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Residues in contact with HIS 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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188A GLY 3.3 16.6 + - - +
189A VAL* 3.2 7.5 + - - +
190A VAL 3.2 0.4 - - - -
191A ASP* 1.3 78.4 - - - +
193A LEU* 1.3 68.3 + - - +
195A LEU* 3.3 28.5 + - + +
196A ARG* 3.3 11.1 + - - +
287A GLU* 3.7 28.1 - - + +
290A ASP* 5.8 2.2 - - + -
291A ILE* 3.5 37.5 - - + +
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Residues in contact with LEU 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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189A VAL* 3.0 28.6 + - + +
190A VAL* 3.7 5.4 - - - +
192A HIS* 1.3 78.1 - - - +
194A LEU* 1.3 61.2 + - - +
196A ARG* 3.2 6.7 + - - +
197A LEU* 2.9 38.6 + - + +
230A PHE* 4.7 9.4 - - + -
284A ILE* 3.9 28.0 - - + +
287A GLU* 4.0 27.8 - - + -
288A ILE* 4.7 7.2 - - + -
291A ILE* 5.4 2.2 - - + -
310A LEU* 3.8 27.4 - - + -
320A ILE* 3.8 20.0 - - + -
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Residues in contact with LEU 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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190A VAL* 3.0 27.8 + - + +
191A ASP* 3.8 10.1 - - - +
193A LEU* 1.3 76.4 - - - +
195A LEU* 1.3 61.8 + - - +
197A LEU* 3.9 3.9 - - + +
198A LYS* 3.1 45.3 + - - +
206A VAL* 4.4 7.9 - - + -
207A GLY* 3.9 22.7 - - - +
208A LEU* 3.8 37.2 - - + +
230A PHE* 3.6 36.1 - - + -
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Residues in contact with LEU 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 ASP 3.2 14.1 + - - +
192A HIS* 3.4 29.2 - - + +
193A LEU 3.2 0.4 - - - -
194A LEU* 1.3 78.8 - - - +
196A ARG* 1.3 66.1 + - + +
198A LYS* 3.8 9.9 + - - +
199A CYS* 3.2 29.6 + - - -
287A GLU* 5.8 0.9 - - - +
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Residues in contact with ARG 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 HIS 3.3 7.0 + - - +
193A LEU* 3.2 8.3 + - - +
195A LEU* 1.3 84.7 - - + +
197A LEU* 1.3 60.3 + - - +
198A LYS 3.2 0.4 - - - -
199A CYS* 2.9 36.2 + - - +
200A ASP* 3.5 23.1 + - - +
283A ILE* 3.7 28.4 - - + +
286A GLU* 2.6 26.2 + - - -
287A GLU* 3.0 48.8 + - + +
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Residues in contact with LEU 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 LEU* 2.9 25.4 + - + +
194A LEU* 3.4 6.0 + - + +
196A ARG* 1.3 76.1 - - - +
198A LYS* 1.3 56.5 + - - +
200A ASP* 3.1 13.2 + - - +
203A PHE* 2.8 35.8 - - + +
206A VAL* 3.7 17.5 - - + -
230A PHE* 3.9 23.6 - - + -
280A PHE* 3.6 39.7 - - + -
283A ILE* 3.7 36.1 - - + -
284A ILE* 4.8 9.2 - - + -
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Residues in contact with LYS 198 (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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194A LEU* 3.1 37.9 + - - +
195A LEU* 3.9 8.7 - - - +
197A LEU* 1.3 77.2 - - - +
199A CYS* 1.3 60.3 + - - +
200A ASP 3.1 8.8 + - - +
203A PHE 3.5 6.3 - - - -
204A ARG* 3.9 28.4 - - - +
206A VAL* 3.6 26.7 - - + -
207A GLY* 4.8 4.1 - - - -
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Residues in contact with CYS 199 (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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195A LEU* 3.2 27.8 - - - -
196A ARG* 2.9 24.1 + - - +
198A LYS* 1.3 77.5 - - - +
200A ASP* 1.3 60.4 + - - +
201A SER 4.1 0.3 + - - -
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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