Contacts of the helix formed by residues 179 - 195 (chain C) 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 SER 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C SER 5.2 0.4 + - - -
177C THR 3.4 0.6 - - - -
178C ALA* 1.3 81.0 - - - +
180C PRO* 1.4 65.8 - - - +
181C ALA* 3.6 13.7 + - - +
182C VAL* 3.2 28.1 + - - +
183C ASN* 2.9 35.1 + - - +
246C GLU* 5.2 4.7 + - - +
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Residues in contact with PRO 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C THR 5.4 0.4 - - - +
178C ALA 4.1 5.4 - - - +
179C SER* 1.4 88.2 - - - +
181C ALA* 1.3 56.7 + - - +
183C ASN* 3.5 10.1 + - + +
184C SER* 3.1 30.0 + - - -
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Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP* 4.0 8.5 - - + -
179C SER* 3.2 7.0 + - - +
180C PRO* 1.3 80.2 - - - +
182C VAL* 1.3 57.1 + - + +
184C SER* 3.2 7.8 + - - -
185C ALA* 2.9 25.8 + - - +
242C VAL* 3.6 20.4 - - + +
246C GLU* 3.4 38.6 - - + -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP* 5.4 8.3 - - + -
112C ILE* 4.5 7.4 - - + +
115C ALA* 3.9 26.5 - - + +
116C CYS* 3.8 33.0 - - + -
176C SER 5.6 0.7 - - - +
179C SER* 3.2 29.1 + - - +
181C ALA* 1.3 73.3 - - + +
183C ASN* 1.3 62.7 + - - +
185C ALA* 3.8 5.3 - - + +
186C TYR* 3.0 28.1 + - - +
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Residues in contact with ASN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C CYS* 5.8 0.8 - - - +
175C VAL* 6.0 2.6 - - - +
176C SER 3.2 25.7 + - - -
177C THR* 3.1 30.9 + - - +
178C ALA 4.8 0.2 - - - +
179C SER 2.9 19.1 + - - +
180C PRO* 3.7 8.8 - - + +
181C ALA 3.3 0.2 - - - -
182C VAL* 1.3 79.9 - - - +
184C SER* 1.3 51.6 + - - +
186C TYR* 3.4 9.3 - - - +
187C ASN* 2.7 39.1 + - - +
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Residues in contact with SER 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PRO 3.1 14.8 + - - -
181C ALA* 3.2 12.0 - - - -
183C ASN* 1.3 72.5 - - - +
185C ALA* 1.3 55.7 + - - +
187C ASN* 3.1 8.1 + - - +
188C ALA* 2.7 37.1 + - - +
238C ILE* 5.6 0.2 - - - +
242C VAL* 3.4 23.5 - - - +
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP* 4.8 14.1 - - + -
112C ILE* 4.0 31.1 - - + +
181C ALA 2.9 15.5 + - - +
182C VAL* 3.8 8.5 - - + +
183C ASN 3.5 0.2 - - - -
184C SER* 1.3 73.2 - - - +
186C TYR* 1.3 52.8 + - - +
188C ALA* 3.1 8.7 + - - +
189C MET* 2.7 35.7 + - - +
239C ILE* 4.4 13.9 - - + +
242C VAL* 4.4 4.6 - - + +
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Residues in contact with TYR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 3.8 2.8 - - + +
113C LEU* 4.3 17.3 - - + -
116C CYS* 3.7 28.3 - - - -
117C THR* 5.0 3.4 - - - -
166C LEU* 4.5 6.1 + - + +
167C TYR* 3.5 37.3 + + - -
171C GLY 5.2 3.1 + - - -
174C ALA 4.9 5.7 + - - -
175C VAL* 4.7 30.7 - - + +
182C VAL 3.0 19.8 + - - +
183C ASN* 3.4 9.9 - - - +
185C ALA* 1.3 76.3 - - - +
187C ASN* 1.3 64.9 + - - +
189C MET* 3.6 22.2 - - + +
190C MET* 3.2 26.2 + - + +
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Residues in contact with ASN 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ASN* 2.7 23.2 + - - +
184C SER* 3.1 8.2 + - - +
186C TYR* 1.3 75.7 - - - +
188C ALA* 1.3 63.7 + - - +
190C MET* 3.3 25.2 + - - +
191C MET* 3.0 24.9 + - - +
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C SER 2.7 18.9 + - - +
185C ALA* 3.4 8.1 - - - +
187C ASN* 1.3 72.7 - - - +
189C MET* 1.3 55.7 + - - +
191C MET* 3.1 10.2 + - - +
192C ILE* 2.9 31.0 + - - +
235C PHE* 4.3 14.8 - - + -
238C ILE* 3.7 34.2 - - + +
239C ILE* 4.6 1.6 - - + -
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Residues in contact with MET 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 3.2 51.6 - - + +
112C ILE* 3.2 43.1 - - + -
113C LEU* 4.3 13.5 - - + -
166C LEU* 4.8 10.1 - - + -
167C TYR* 4.7 8.5 - - - +
185C ALA 2.7 16.1 + - - +
186C TYR* 3.6 22.2 - - + +
188C ALA* 1.3 72.5 - - - +
190C MET* 1.3 62.0 + - - +
192C ILE* 3.3 4.3 + - - +
193C ILE* 3.1 27.8 + - + +
235C PHE* 4.2 10.6 - - - -
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Residues in contact with MET 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C TYR* 2.9 44.5 + - + +
186C TYR* 3.2 15.4 + - + +
187C ASN* 3.4 26.2 - - - +
189C MET* 1.3 78.0 - - - +
191C MET* 1.3 73.7 + - - +
193C ILE* 3.4 1.8 - - - +
194C VAL* 2.9 45.4 + - + +
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Residues in contact with MET 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ASN* 3.0 12.4 + - - +
188C ALA* 3.3 13.7 - - - +
190C MET* 1.3 96.4 - - - +
192C ILE* 1.3 59.6 + - + +
194C VAL* 6.1 0.7 - - - -
195C VAL* 3.2 36.9 + - + +
196C GLY* 2.9 20.1 + - - -
238C ILE* 6.5 0.4 - - + -
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 4.8 0.7 - - + -
109C PHE* 4.0 25.4 - - + -
188C ALA 2.9 12.2 + - - +
189C MET 3.5 9.4 - - - +
190C MET 3.2 0.2 - - - -
191C MET* 1.3 78.6 - - + +
193C ILE* 1.3 58.5 + - - +
196C GLY* 2.7 10.6 + - - -
197C TRP* 2.5 41.1 + - - +
230C VAL* 4.1 15.0 - - + +
231C ASN* 3.0 28.3 - - + +
234C LEU* 5.2 0.9 - - + -
235C PHE* 3.9 45.3 - - + +
238C ILE* 4.9 9.6 - - + -
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Residues in contact with ILE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 3.6 28.9 - - + -
159C TRP* 2.7 38.3 + - + +
162C MET* 4.2 24.7 - - + -
163C ILE* 3.8 8.2 - - + +
166C LEU* 3.7 23.1 - - + -
167C TYR* 4.0 14.4 - - + +
189C MET* 3.1 17.5 + - + +
190C MET* 3.4 11.9 - - - +
192C ILE* 1.3 79.6 - - - +
194C VAL* 1.3 68.3 + - + +
197C TRP* 3.6 25.7 - - + +
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TRP* 3.2 25.2 - - + -
163C ILE* 4.0 29.6 - - + -
167C TYR* 4.7 2.7 - - + -
190C MET* 2.9 33.0 + - + +
191C MET* 5.2 1.1 - - - -
193C ILE* 1.3 84.1 - - + +
195C VAL* 1.3 70.0 + - + +
198C ALA* 3.4 7.1 - - - +
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C MET* 3.2 46.4 + - + +
194C VAL* 1.3 80.9 - - + +
196C GLY* 1.3 71.8 + - - +
198C ALA* 3.0 19.7 + - + +
199C ILE* 3.9 9.1 + - + +
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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