Contacts of the helix formed by residues 180 - 195 (chain B) in PDB entry 4KNF
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 PRO 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B SER* 1.3 85.3 - - - +
181B ALA* 1.3 55.6 + - + +
183B ASN* 2.9 10.5 + - + +
184B SER* 2.8 33.8 + - - -
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Residues in contact with ALA 181 (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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58B TRP* 4.0 9.8 - - + -
179B SER* 3.4 0.6 - - - -
180B PRO* 1.3 77.9 - - + +
182B VAL* 1.3 65.2 + - + +
184B SER* 3.0 20.4 + - - -
185B ALA* 3.1 11.6 + - - +
242B VAL* 3.5 12.6 - - + +
246B GLU* 3.4 37.9 - - + -
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Residues in contact with VAL 182 (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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58B TRP* 4.9 10.1 - - + -
112B ILE* 4.4 25.3 - - + +
175B VAL* 3.8 31.4 - - + -
179B SER* 3.4 32.6 + - - +
180B PRO 3.3 0.2 - - - -
181B ALA* 1.3 77.6 - - + +
183B ASN* 1.3 59.4 + - - +
185B ALA* 3.6 5.7 + - - +
186B TYR* 2.9 27.9 + - + +
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Residues in contact with ASN 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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175B VAL* 3.3 31.4 + - - +
176B SER 5.0 1.1 - - - +
179B SER 3.2 11.7 + - - +
180B PRO* 2.9 14.1 + - + +
182B VAL* 1.3 75.5 - - - +
184B SER* 1.3 54.7 + - - +
186B TYR* 3.7 8.8 - - - +
187B ASN* 2.7 54.8 + - - +
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Residues in contact with SER 184 (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 PRO 2.8 14.7 + - - -
181B ALA* 3.0 21.7 + - - -
183B ASN* 1.3 72.0 - - - +
185B ALA* 1.3 59.9 + - - +
187B ASN* 3.6 11.8 - - - +
188B ALA* 3.1 26.2 + - - +
242B VAL* 4.0 18.3 - - - +
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Residues in contact with ALA 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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58B TRP* 4.1 19.3 - - + -
112B ILE* 3.9 17.9 - - + -
181B ALA 3.1 17.3 + - - +
182B VAL 3.6 4.3 - - - +
184B SER* 1.3 74.9 - - - +
186B TYR* 1.3 55.1 + - - +
188B ALA* 3.1 6.6 + - - +
189B MET* 2.6 38.5 + - - +
238B ILE* 5.2 1.9 - - - +
239B ILE* 4.6 10.5 - - + -
242B VAL* 4.1 12.4 - - + +
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Residues in contact with TYR 186 (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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109B PHE* 4.1 19.1 - + - -
112B ILE* 4.5 21.0 - - + +
123B LEU* 5.5 5.5 - - + +
166B LEU* 3.4 31.4 + - + +
171B GLY* 4.2 13.8 + - - -
175B VAL* 4.8 19.7 - - + -
182B VAL* 2.9 25.3 + - + +
183B ASN* 3.7 10.5 - - - +
185B ALA* 1.3 72.6 - - - +
187B ASN* 1.3 57.5 + - - +
189B MET* 3.2 7.2 + - - -
190B MET* 2.6 76.4 + - + +
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Residues in contact with ASN 187 (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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183B ASN* 2.7 48.9 + - - +
184B SER* 3.6 11.0 - - - +
186B TYR* 1.3 77.2 - - - +
188B ALA* 1.3 53.6 + - + +
190B MET* 3.0 10.8 - - - +
191B MET* 2.8 38.4 + - + +
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Residues in contact with ALA 188 (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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184B SER 3.1 14.3 + - - +
185B ALA 3.5 2.2 - - - +
187B ASN* 1.3 77.8 - - + +
189B MET* 1.3 59.4 + - - +
191B MET* 3.4 6.9 + - - +
192B ILE* 3.0 29.3 + - - +
235B PHE* 4.4 3.6 - - - -
238B ILE* 3.3 42.7 - - + +
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Residues in contact with MET 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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108B GLU* 3.6 9.0 - - + +
109B PHE* 3.0 76.1 - - + +
112B ILE* 3.5 25.1 - - + -
185B ALA 2.6 25.8 + - - +
186B TYR* 3.7 4.3 - - - +
188B ALA* 1.3 73.0 - - - +
190B MET* 1.3 63.9 + - - +
192B ILE* 3.2 4.9 - - - +
193B ILE* 3.1 27.7 - - - +
235B PHE* 3.6 29.6 - - + -
238B ILE* 6.2 0.2 - - + -
239B ILE* 3.6 22.9 - - + -
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Residues in contact with MET 190 (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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109B PHE* 4.2 0.4 - - - -
166B LEU* 3.1 50.3 - - + +
167B TYR* 3.5 33.7 - - + +
186B TYR* 2.6 52.4 + - + +
187B ASN* 3.0 17.9 - - - +
189B MET* 1.3 76.1 - - - +
191B MET* 1.3 63.2 + - + +
193B ILE* 3.7 2.6 + - - +
194B VAL* 3.1 27.4 + - - +
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Residues in contact with MET 191 (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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167B TYR* 6.0 2.0 - - - -
187B ASN* 2.8 21.4 + - + +
188B ALA* 3.9 7.4 - - - +
189B MET 3.3 0.2 - - - -
190B MET* 1.3 77.4 - - + +
192B ILE* 1.3 58.0 + - - +
194B VAL* 3.2 13.4 + - + -
195B VAL* 2.9 69.7 + - + +
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Residues in contact with ILE 192 (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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105B LEU* 6.1 1.3 - - + -
188B ALA 3.0 16.4 + - - +
189B MET* 3.2 15.7 - - - +
191B MET* 1.3 76.0 - - - +
193B ILE* 1.3 67.7 + - + +
196B GLY* 2.9 15.5 + - - +
197B TRP* 2.7 36.2 + - + +
230B VAL* 4.8 7.2 - - + +
231B ASN* 3.5 25.8 - - + +
234B LEU* 5.2 2.5 - - + -
235B PHE* 3.5 52.3 - - + +
238B ILE* 4.8 9.9 - - + -
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Residues in contact with ILE 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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105B LEU* 5.0 5.8 - - + -
109B PHE* 3.8 25.1 - - + -
159B TRP* 2.9 34.7 + - + +
162B MET* 4.7 13.5 - - + -
163B ILE* 4.2 13.0 - - + +
166B LEU* 5.3 10.8 - - + -
189B MET 3.1 17.7 + - - +
190B MET* 4.1 4.0 - - - +
191B MET 3.4 0.4 - - - -
192B ILE* 1.3 84.9 - - + +
194B VAL* 1.3 58.5 + - + +
197B TRP* 3.2 61.4 - - + +
235B PHE* 5.9 0.9 - - + -
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Residues in contact with VAL 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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159B TRP* 3.3 25.3 - - - -
163B ILE* 4.3 31.6 - - + -
167B TYR* 4.4 11.9 - - - +
190B MET* 3.1 19.7 - - - +
191B MET* 3.2 15.7 + - + +
192B ILE 3.1 0.2 - - - -
193B ILE* 1.3 79.6 - - + +
195B VAL* 1.3 69.3 + - + +
198B ALA* 3.7 6.9 + - - +
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Residues in contact with VAL 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 MET* 2.9 49.7 + - + +
194B VAL* 1.3 74.8 - - + +
196B GLY* 1.3 68.2 + - - +
198B ALA* 3.5 16.1 + - - +
199B ILE* 4.3 6.8 - - - +
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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