Contacts of the helix formed by residues 179 - 195 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LYS* 5.3 8.7 + - - -
177A THR* 3.5 8.8 - - - +
178A ALA* 1.3 78.3 - - - +
180A PRO* 1.4 73.5 - - - +
181A ALA* 3.1 18.9 + - - +
182A VAL* 3.6 25.8 - - - +
183A ASN* 3.1 27.5 + - - +
246A GLU* 4.5 9.0 + - - +
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Residues in contact with PRO 180 (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 THR* 4.8 5.2 - - + -
178A ALA 4.9 0.4 - - - +
179A SER* 1.4 90.4 - - - +
181A ALA* 1.3 55.5 + - - +
183A ASN* 3.9 7.5 + - + +
184A SER* 3.1 29.5 + - - -
246A GLU* 6.3 0.4 - - + -
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Residues in contact with ALA 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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58A TRP* 3.7 16.2 - - + -
179A SER* 3.1 5.2 + - - +
180A PRO* 1.3 77.1 - - - +
182A VAL* 1.3 60.6 + - + +
184A SER* 3.1 4.3 + - - -
185A ALA* 2.9 29.8 + - - +
242A VAL* 3.6 14.4 - - + +
246A GLU* 3.4 40.8 - - + +
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Residues in contact with VAL 182 (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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57A LYS* 5.3 12.6 - - - +
58A TRP* 4.7 11.4 - - + -
112A ILE* 4.6 4.7 - - + +
115A ALA* 3.8 30.3 - - + +
116A CYS* 3.7 27.1 - - - -
175A VAL 5.9 0.2 - - - +
176A SER 4.9 4.0 - - - +
178A ALA* 4.7 6.5 - - + -
179A SER* 3.6 27.3 - - - +
181A ALA* 1.3 76.9 - - + +
183A ASN* 1.3 59.4 + - - +
185A ALA* 3.3 6.5 + - - +
186A TYR* 2.8 29.6 + - - +
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Residues in contact with ASN 183 (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 VAL* 4.3 18.8 - - - +
176A SER 6.1 0.2 - - - -
177A THR* 3.6 30.5 + - + +
179A SER 3.1 20.3 + - - +
180A PRO* 4.0 7.0 + - + +
181A ALA 3.2 0.2 - - - -
182A VAL* 1.3 79.0 - - - +
184A SER* 1.3 59.7 + - - +
186A TYR* 3.7 6.4 + - - +
187A ASN* 2.6 56.2 + - - +
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Residues in contact with SER 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 PRO 3.1 19.7 + - - -
181A ALA* 3.1 6.6 + - - -
183A ASN* 1.3 75.1 + - - +
185A ALA* 1.3 60.4 + - - +
187A ASN* 3.4 6.1 + - - +
188A ALA* 3.0 28.7 + - - +
238A ILE* 5.6 0.2 - - - +
242A VAL* 3.7 24.5 - - - +
245A LYS* 5.6 2.8 + - - -
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Residues in contact with ALA 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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58A TRP* 4.0 22.2 - - + -
112A ILE* 3.9 27.8 - - + +
181A ALA 2.9 16.5 + - - +
182A VAL* 3.7 4.0 - - - +
184A SER* 1.3 72.5 - - - +
186A TYR* 1.3 59.6 + - - +
188A ALA* 3.2 9.7 + - - +
189A MET* 2.9 28.6 + - - +
239A ILE* 4.3 10.5 - - + +
242A VAL* 4.5 5.5 - - + +
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Residues in contact with TYR 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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112A ILE* 3.6 13.6 - - + +
113A LEU* 4.2 13.5 - - + -
116A CYS* 4.0 23.6 - - - -
166A LEU* 4.4 5.6 + - + -
171A GLY 4.4 8.7 + - - -
174A ALA 4.9 7.9 + - - -
175A VAL* 4.7 30.8 - - + +
182A VAL 2.8 21.0 + - - +
183A ASN* 3.8 10.1 - - - +
185A ALA* 1.3 73.8 - - - +
187A ASN* 1.3 75.1 + - - +
189A MET* 3.2 22.5 + - + +
190A MET* 2.9 74.0 + - + +
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Residues in contact with ASN 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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175A VAL* 5.7 1.6 - - - +
183A ASN* 2.6 46.3 + - - +
184A SER* 3.8 5.5 - - - +
186A TYR* 1.3 90.3 - - - +
188A ALA* 1.3 60.5 + - - +
190A MET* 3.4 6.5 + - - +
191A MET* 3.0 47.8 + - + +
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Residues in contact with ALA 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 SER 3.0 15.0 + - - +
185A ALA* 3.2 13.7 + - - +
187A ASN* 1.3 73.6 - - - +
189A MET* 1.3 63.6 + - - +
191A MET* 3.5 4.3 + - - +
192A ILE* 3.2 27.0 + - - +
235A PHE* 3.7 14.2 - - + -
238A ILE* 3.7 32.2 - - + +
239A ILE* 4.6 2.2 - - + -
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Residues in contact with MET 189 (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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109A PHE* 3.5 57.2 - - + +
112A ILE* 3.8 22.4 - - + -
113A LEU* 3.9 20.2 - - + -
166A LEU* 4.5 13.5 - - + -
185A ALA 2.9 12.1 + - - +
186A TYR* 3.2 39.9 + - + +
188A ALA* 1.3 78.9 - - - +
190A MET* 1.3 66.7 + - - +
191A MET 3.3 0.2 + - - -
192A ILE* 3.3 22.1 + - - +
193A ILE* 3.4 12.5 - - - +
235A PHE* 4.1 4.4 - - - -
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Residues in contact with MET 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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166A LEU* 3.7 41.3 - - + +
167A TYR* 3.0 59.6 + - + +
186A TYR* 2.9 65.2 + - + +
187A ASN* 3.4 9.6 + - - +
189A MET* 1.3 80.4 - - - +
191A MET* 1.3 67.0 + - + +
193A ILE* 4.2 4.4 + - - +
194A VAL* 3.5 13.0 + - - +
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Residues in contact with MET 191 (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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167A TYR* 4.5 8.3 - - + +
187A ASN* 3.0 38.6 + - + +
188A ALA* 4.1 4.7 - - - +
190A MET* 1.3 84.8 - - + +
192A ILE* 1.3 57.9 + - - +
194A VAL* 3.0 6.2 + - - +
195A VAL* 2.7 50.3 + - + +
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Residues in contact with ILE 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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105A LEU* 6.0 0.4 - - + -
109A PHE* 3.9 20.6 - - + -
188A ALA 3.2 14.8 + - - +
189A MET 3.3 11.0 - - - +
191A MET* 1.3 77.9 - - - +
193A ILE* 1.3 59.9 + - - +
195A VAL* 4.9 0.2 - - - -
196A GLY* 2.9 16.6 + - - +
197A TRP* 2.7 38.1 + - + +
230A VAL* 4.4 12.6 - - + +
231A ASN* 3.2 25.8 - - - +
235A PHE* 3.9 45.5 - - + -
238A ILE* 5.4 5.4 - - + -
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Residues in contact with ILE 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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109A PHE* 3.5 35.0 - - + -
127A LEU* 4.7 10.3 - - + -
159A TRP* 3.0 23.9 + - + +
162A MET* 5.0 5.4 - - + -
163A ILE* 3.7 25.6 - - + +
166A LEU* 3.4 31.6 - - + -
167A TYR* 6.1 1.3 - - + -
189A MET 3.4 16.2 - - - +
190A MET 4.5 4.5 - - - +
191A MET 3.4 0.6 - - - -
192A ILE* 1.3 76.8 - - - +
194A VAL* 1.3 58.7 + - + +
197A TRP* 2.9 42.3 - - + +
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Residues in contact with VAL 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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159A TRP* 3.6 9.6 - - + -
163A ILE* 4.2 20.2 - - + -
167A TYR* 3.9 23.6 - - + +
190A MET 3.5 17.0 - - - +
191A MET* 3.0 6.5 + - - +
193A ILE* 1.3 77.8 - - + +
195A VAL* 1.3 72.4 + - + +
198A ALA* 3.1 28.5 + - + +
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Residues in contact with VAL 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 MET* 2.7 43.9 + - + +
192A ILE* 4.9 0.2 - - - -
194A VAL* 1.3 79.9 - - + +
196A GLY* 1.3 62.0 + - - +
198A ALA* 3.5 13.2 + - - +
199A ILE* 4.0 8.7 - - - +
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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