Contacts of the helix formed by residues 179 - 196 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E SER 3.8 2.9 - - - +
177E THR 3.5 5.3 - - - +
178E ALA* 1.3 79.8 - - - +
180E PRO* 1.3 73.5 - - - +
181E ALA* 3.2 15.3 + - - +
182E VAL* 3.2 29.9 - - - +
183E ASN* 3.1 25.6 + - - +
246E GLU* 4.2 10.9 + - - +
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Residues in contact with PRO 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E THR* 4.3 3.8 - - + +
179E SER* 1.3 90.5 - - - +
181E ALA* 1.3 54.7 + - + +
183E ASN* 3.4 9.0 - - + +
184E SER* 2.7 35.7 + - - -
246E GLU* 6.2 1.1 - - + -
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Residues in contact with ALA 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 4.0 12.3 - - + -
179E SER* 3.2 4.9 - - - +
180E PRO* 1.3 78.8 - - + +
182E VAL* 1.3 64.9 + - + +
183E ASN 3.1 1.1 - - - -
184E SER* 3.0 11.3 + - - -
185E ALA* 3.0 13.5 + - - +
242E VAL* 3.4 20.3 - - + +
246E GLU* 3.1 41.7 - - + -
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Residues in contact with VAL 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LYS* 6.3 3.1 - - + -
58E TRP* 4.8 13.5 - - + -
112E ILE* 4.6 2.6 - - - +
115E ALA* 4.0 28.0 - - + +
116E CYS* 4.3 5.3 - - - -
176E SER* 3.5 26.9 - - - +
178E ALA* 4.7 1.6 - - + -
179E SER* 3.2 33.1 + - - +
181E ALA* 1.3 76.3 - - - +
183E ASN* 1.3 59.6 + - - +
185E ALA* 3.7 6.2 + - - +
186E TYR* 3.0 29.5 + - - +
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Residues in contact with ASN 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E VAL* 3.7 23.0 - - - +
176E SER* 2.9 22.7 + - - +
177E THR* 5.1 2.4 - - - +
179E SER 3.1 18.7 + - - +
180E PRO* 3.4 11.1 - - + +
181E ALA 3.1 0.2 - - - -
182E VAL* 1.3 80.4 - - - +
184E SER* 1.3 56.2 + - - +
186E TYR* 3.5 5.8 - - - +
187E ASN* 3.1 48.6 + - - +
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Residues in contact with SER 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E PRO 2.7 21.5 + - - -
181E ALA* 3.0 8.0 + - - -
183E ASN* 1.3 73.3 - - - +
185E ALA* 1.3 53.9 + - - +
187E ASN* 2.9 11.0 + - - +
188E ALA* 2.8 34.9 + - - +
242E VAL* 4.0 22.3 - - - +
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Residues in contact with ALA 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 4.4 18.4 - - + -
112E ILE* 3.6 21.3 - - + +
181E ALA 3.0 14.7 + - - +
182E VAL* 3.9 5.4 - - - +
184E SER* 1.3 75.0 - - - +
186E TYR* 1.3 62.4 + - - +
188E ALA* 3.5 3.5 + - - +
189E MET* 3.0 24.4 + - - +
239E ILE* 4.0 25.3 - - + +
242E VAL* 4.3 5.6 - - + +
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Residues in contact with TYR 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ILE* 3.5 10.2 - - + +
113E LEU* 4.4 11.7 - - + -
116E CYS* 3.7 30.5 - - + -
117E THR* 6.3 0.2 - - + -
166E LEU* 4.3 6.5 + - + -
171E GLY 4.4 9.0 + - - -
174E ALA 4.7 9.4 + - - -
175E VAL* 4.4 28.7 - - + +
182E VAL 3.0 19.0 + - - +
183E ASN* 3.5 7.9 - - - +
185E ALA* 1.3 75.2 - - - +
187E ASN* 1.3 72.3 + - - +
189E MET* 3.1 26.1 + - + +
190E MET* 2.9 67.0 + - + +
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Residues in contact with ASN 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E VAL* 5.7 0.3 - - - +
183E ASN* 3.1 35.3 + - - +
184E SER* 2.9 11.2 + - - +
186E TYR* 1.3 92.0 - - - +
188E ALA* 1.3 58.0 + - - +
190E MET* 3.4 5.3 + - - +
191E MET* 2.9 30.0 + - - +
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Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E SER 2.8 15.3 + - - +
185E ALA* 3.7 8.7 - - - +
187E ASN* 1.3 75.7 - - - +
189E MET* 1.3 56.6 + - - +
191E MET* 3.3 10.8 + - - +
192E ILE* 2.8 33.8 + - - +
235E PHE* 3.8 14.8 - - + -
238E ILE* 3.9 31.4 - - + -
239E ILE* 4.7 2.0 - - + -
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Residues in contact with MET 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E PHE* 3.3 54.1 - - + +
112E ILE* 3.9 18.2 - - + -
113E LEU* 3.8 21.5 - - + -
166E LEU* 4.1 11.4 - - + -
185E ALA 3.0 13.8 + - - +
186E TYR* 3.4 38.1 - - + +
188E ALA* 1.3 77.0 - - - +
190E MET* 1.3 74.2 + - - +
192E ILE* 3.2 23.7 - - - +
193E ILE* 3.3 11.6 + - - +
235E PHE* 4.0 3.3 - - - -
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Residues in contact with MET 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 3.6 38.1 - - + +
167E TYR* 2.7 63.4 + - + +
186E TYR* 2.9 57.1 + - + +
187E ASN* 3.8 6.3 - - - +
188E ALA 3.3 0.4 - - - -
189E MET* 1.3 92.4 - - - +
191E MET* 1.3 61.2 + - - +
193E ILE* 3.7 5.4 - - - +
194E VAL* 3.4 12.6 - - - +
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Residues in contact with MET 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E TYR* 4.7 0.9 - - - -
187E ASN 2.9 18.2 + - - +
188E ALA* 3.6 10.8 - - + +
190E MET* 1.3 76.7 - - - +
192E ILE* 1.3 79.2 + - + +
194E VAL* 3.2 3.3 + - - +
195E VAL* 2.8 69.0 + - + +
235E PHE* 5.6 0.2 - - + -
238E ILE* 4.1 25.6 - - + -
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Residues in contact with ILE 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E LEU* 5.1 0.2 - - + -
109E PHE* 3.9 16.6 - - + -
188E ALA 2.8 20.1 + - - +
189E MET* 3.2 13.9 - - - +
191E MET* 1.3 90.6 - - + +
193E ILE* 1.3 62.4 + - - +
194E VAL 3.0 0.2 - - - -
196E GLY* 2.7 33.8 + - - -
197E TRP* 2.8 19.0 + - + +
230E VAL* 4.5 11.4 - - + +
231E ASN* 3.4 27.4 - - + +
235E PHE* 3.6 47.8 - - + +
238E ILE* 5.6 1.3 - - + -
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Residues in contact with ILE 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E PHE* 4.1 19.3 - - + -
127E LEU* 4.9 1.6 - - + -
159E TRP* 3.0 34.8 + - - +
162E MET* 4.0 23.8 - - + -
163E ILE* 3.5 11.0 - - + +
166E LEU* 3.9 32.3 - - + -
167E TYR* 4.9 3.4 - - + -
189E MET 3.3 15.7 + - - +
190E MET* 3.7 10.3 - - - +
192E ILE* 1.3 79.2 - - - +
194E VAL* 1.3 64.0 + - + +
197E TRP* 3.6 42.7 - - + +
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Residues in contact with VAL 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E TRP* 3.6 6.1 - - + -
163E ILE* 4.1 20.6 - - + -
167E TYR* 3.3 39.9 - - + +
190E MET 3.4 8.1 - - - +
191E MET* 3.2 3.7 + - - +
192E ILE 3.0 2.0 - - - -
193E ILE* 1.3 80.3 - - + +
195E VAL* 1.3 75.8 + - + +
198E ALA* 3.2 23.9 + - - +
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E MET* 2.8 53.7 + - + +
194E VAL* 1.3 82.7 - - + +
196E GLY* 1.3 64.5 + - - +
198E ALA* 3.6 14.5 + - - +
199E ILE* 4.0 8.7 - - - +
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Residues in contact with GLY 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ILE* 2.7 29.2 + - - +
195E VAL* 1.3 81.9 - - - +
197E TRP* 1.3 61.2 + - - -
199E ILE* 3.2 19.3 - - - +
230E VAL* 4.7 4.3 - - - -
231E ASN* 3.0 30.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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