Contacts of the helix formed by residues 182 - 196 (chain B) in PDB entry 4KPE
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 ASN 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG* 3.5 6.7 - - - +
181B HIS* 1.3 72.3 - - - +
183B LEU* 1.3 69.6 + - - +
184B ALA* 3.1 18.7 + - - +
185B GLU* 3.2 37.8 + - - +
186B VAL* 3.0 20.5 + - - +
210B GLY 5.1 0.2 + - - -
212B ASP* 3.0 35.0 + - + +
476B THR* 2.8 28.6 + - - +
477B PRO 3.4 12.5 + - - -
478B ARG* 3.5 4.4 - - - +
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Residues in contact with LEU 183 (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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95B ARG* 5.2 1.6 - - - +
96B GLU* 4.5 18.3 + - - +
126B ILE* 4.9 7.0 - - + -
159B PHE* 3.7 29.4 - - + -
160B PRO* 4.6 0.7 - - + -
164B VAL* 3.3 29.7 - - + +
181B HIS 3.3 4.6 + - - -
182B ASN* 1.3 73.6 + - - +
184B ALA* 1.3 65.0 + - - +
186B VAL* 3.2 3.3 + - - +
187B ILE* 3.0 46.2 + - + +
470B VAL* 4.2 20.9 - - + +
471B LYS* 4.2 6.3 - - - -
474B PHE* 4.2 24.5 - - + +
475B ALA* 4.4 2.2 - - - +
476B THR* 5.5 2.7 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASN* 3.1 10.5 + - - +
183B LEU* 1.3 79.7 - - - +
185B GLU* 1.3 59.0 + - + +
187B ILE* 3.2 2.8 + - - +
188B ASP* 2.8 39.4 + - - +
471B LYS* 3.7 26.7 - - + -
475B ALA* 4.0 21.6 - - + +
476B THR 5.1 1.6 - - - +
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Residues in contact with GLU 185 (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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182B ASN* 3.2 24.8 + - + +
184B ALA* 1.3 77.2 - - + +
186B VAL* 1.3 62.7 + - - +
188B ASP* 3.3 7.2 + - - +
189B ALA* 2.9 23.6 + - - +
207B PHE 3.4 21.4 - - - +
208B LEU* 4.0 10.5 - - + +
209B PRO* 3.4 17.8 - - - +
210B GLY 3.7 6.4 - - - +
478B ARG* 2.5 51.4 + - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PRO* 3.7 32.3 - - + +
163B LEU* 4.0 28.0 - - + -
164B VAL* 4.1 10.5 - - + -
181B HIS* 3.5 27.1 - - + -
182B ASN 3.0 15.2 + - - +
183B LEU 3.6 5.8 - - - +
185B GLU* 1.3 75.4 - - - +
187B ILE* 1.3 57.7 + - - +
189B ALA* 3.3 2.8 + - - +
190B ALA* 2.9 26.2 + - - +
208B LEU* 4.1 14.6 - - + -
346B LEU* 4.4 6.3 - - + -
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 4.8 1.3 - - + -
160B PRO* 4.3 17.5 - - + -
183B LEU* 3.0 25.4 + - + +
184B ALA 3.7 5.8 - - - +
186B VAL* 1.3 73.4 - - - +
188B ASP* 1.3 59.9 + - - +
190B ALA* 3.1 6.0 + - - +
191B VAL* 2.7 41.6 + - + +
467B LEU* 3.2 52.5 - - + +
468B ARG* 4.7 1.6 - - + +
470B VAL* 3.8 15.9 - - + -
471B LYS* 3.8 30.1 - - + +
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Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ALA* 2.8 27.2 + - - +
185B GLU* 3.5 8.3 - - - +
187B ILE* 1.3 71.9 - - - +
189B ALA* 1.3 64.1 + - - +
191B VAL* 3.5 6.5 + - - +
192B TYR* 3.1 19.8 + - - +
207B PHE* 4.1 25.7 - - + +
471B LYS* 3.0 36.4 + - - +
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Residues in contact with ALA 189 (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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185B GLU 2.9 13.5 + - - +
186B VAL* 3.4 8.3 - - - +
188B ASP* 1.3 74.6 - - - +
190B ALA* 1.3 65.5 + - - +
192B TYR* 2.8 17.9 + - - +
193B MET* 3.0 11.4 + - - +
204B LEU* 4.4 11.1 - - + +
207B PHE* 3.8 15.1 - - + +
208B LEU* 4.0 23.1 - - + -
346B LEU* 4.1 20.2 - - + -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PRO* 4.9 4.9 - - + -
186B VAL 2.9 19.3 + - - +
187B ILE* 3.6 7.6 - - - +
189B ALA* 1.3 72.5 - - - +
191B VAL* 1.3 63.2 + - - +
193B MET* 3.3 5.9 + - - -
194B ILE* 3.0 29.1 + - - +
346B LEU* 3.8 22.3 - - + +
349B TYR* 4.8 12.8 - - + -
350B ILE* 3.6 9.0 - - + +
467B LEU* 4.5 13.7 - - + -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 2.7 38.2 + - + +
188B ASP* 3.9 6.1 - - - +
190B ALA* 1.3 71.8 - - - +
192B TYR* 1.3 65.0 + - - +
194B ILE* 3.1 21.8 + - - +
195B ASP* 3.5 12.4 + - - +
464B LYS* 3.9 13.6 - - + +
467B LEU* 4.0 22.0 - - + -
468B ARG* 3.9 40.2 - - + +
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Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ASP 3.1 12.4 + - - +
189B ALA* 2.8 11.0 + - - +
191B VAL* 1.3 78.3 - - - +
193B MET* 1.3 59.6 + - - +
195B ASP* 3.1 11.0 + - + +
196B HIS* 3.0 65.1 + + + +
199B ALA* 3.7 22.4 - - + -
203B LYS* 3.4 28.4 - - + +
204B LEU* 4.4 6.1 - - + -
207B PHE* 3.3 39.3 - + + -
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Residues in contact with MET 193 (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 ALA 3.0 10.8 + - - +
190B ALA* 3.7 10.5 - - - +
192B TYR* 1.3 76.8 - - - +
194B ILE* 1.3 63.9 + - - +
196B HIS 3.3 26.6 - - - +
197B PRO* 3.3 22.7 - - + +
199B ALA* 4.8 4.0 - - + +
204B LEU* 4.4 13.5 - - + -
343B VAL* 3.7 24.5 - - + +
346B LEU* 3.9 22.4 - - + +
347B SER* 3.1 44.6 - - - +
350B ILE* 3.9 11.9 - - + +
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Residues in contact with ILE 194 (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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190B ALA 3.0 15.7 + - - +
191B VAL* 3.3 9.6 - - - +
192B TYR 3.1 0.4 - - - -
193B MET* 1.3 79.2 - - - +
195B ASP* 1.3 59.5 + - - +
196B HIS 3.6 0.2 + - - -
197B PRO* 4.1 8.1 - - - +
350B ILE* 3.1 18.8 - - + -
460B TYR* 3.7 36.8 - - + +
463B MET* 3.0 41.5 - - + -
464B LYS* 3.5 28.5 - - + -
467B LEU* 3.9 17.9 - - + -
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Residues in contact with ASP 195 (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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191B VAL* 3.5 13.8 + - - +
192B TYR* 3.1 11.7 + - - +
194B ILE* 1.3 78.6 - - - +
196B HIS* 1.3 82.6 + - + +
197B PRO* 3.5 7.1 - - - +
464B LYS* 2.9 35.4 + - - +
468B ARG* 5.1 1.7 + - - -
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Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 3.0 63.1 + + + +
193B MET* 3.3 8.6 - - - +
194B ILE 3.3 0.2 - - - -
195B ASP* 1.3 103.0 + - + +
197B PRO* 1.3 59.2 - - - +
198B THR* 3.0 7.2 - - - +
199B ALA* 2.9 27.3 + - + +
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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