Contacts of the helix formed by residues 198 - 209 (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 ALA 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159E TRP* 3.6 21.2 - - + -
194E VAL 3.2 21.5 + - - +
195E VAL* 3.7 9.6 - - - +
196E GLY 3.2 1.2 - - - -
197E TRP* 1.3 76.0 - - - +
199E ILE* 1.3 60.1 + - - +
200E TYR 3.2 0.4 - - - -
201E PRO* 3.3 16.3 - - + +
202E ALA* 3.3 13.2 + - - +
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Residues in contact with ILE 199 (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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195E VAL 4.0 9.6 - - - +
196E GLY* 3.2 17.9 - - - +
197E TRP 2.7 0.8 + - - -
198E ALA* 1.3 79.1 - - - +
200E TYR* 1.3 61.2 + - - +
202E ALA* 3.4 7.6 - - + +
203E GLY 3.2 15.9 + - - -
223E ILE* 3.3 24.9 - - + +
226E LEU* 4.5 15.3 - - + +
227E ALA* 3.7 23.1 - - + +
230E VAL* 4.2 34.1 - - + -
231E ASN* 4.5 1.6 - - - +
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Residues in contact with TYR 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TRP* 3.4 36.8 - + - -
197E TRP* 2.8 23.9 + - - +
199E ILE* 1.3 74.0 - - - +
201E PRO* 1.4 72.1 - - + +
203E GLY 2.9 11.4 + - - -
204E TYR* 3.3 10.4 + - - +
224E TYR* 3.4 14.5 - + - -
227E ALA* 3.3 32.4 + - + -
228E ASP* 2.7 25.2 + - - -
231E ASN* 3.5 27.9 - - - +
301E RET 3.3 65.8 - - + +
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Residues in contact with PRO 201 (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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152E PHE* 3.8 13.5 - - + -
156E MET* 3.9 23.8 - - + -
159E TRP* 4.2 13.5 - - + -
197E TRP 3.2 16.6 - - - +
198E ALA* 3.3 21.3 - - + +
200E TYR* 1.4 88.6 - - + +
202E ALA* 1.3 60.2 + - - +
204E TYR* 3.4 5.7 + - + +
205E ALA* 2.9 24.8 + - - +
301E RET 3.9 30.7 - - + -
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Residues in contact with ALA 202 (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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198E ALA 3.3 13.3 + - - +
199E ILE* 3.4 15.3 - - + +
200E TYR 3.1 0.8 - - - -
201E PRO* 1.3 79.7 - - - +
203E GLY* 1.3 56.5 + - - +
205E ALA* 3.6 6.9 - - - +
206E ALA* 3.0 26.7 + - - +
223E ILE* 4.3 7.7 - - + +
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Residues in contact with GLY 203 (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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199E ILE 3.2 3.0 + - - -
200E TYR 2.9 8.1 + - - -
202E ALA* 1.3 77.3 - - - +
204E TYR* 1.3 59.0 + - - +
206E ALA* 3.1 6.2 + - - +
207E GLY* 2.9 25.1 + - - -
220E LEU* 3.8 8.5 - - - +
223E ILE* 3.4 31.2 - - - -
224E TYR* 3.9 9.2 - - - -
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Residues in contact with TYR 204 (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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138E GLY* 3.6 24.7 - - - -
141E GLY* 3.5 13.0 - - - -
142E GLU* 3.7 26.7 - - + -
148E VAL* 2.8 39.9 + - + +
151E ALA* 3.8 4.9 - - + +
152E PHE* 3.4 33.9 - + + -
200E TYR 3.3 8.2 + - - +
201E PRO* 3.6 11.0 - - + +
203E GLY* 1.3 71.9 - - - +
205E ALA* 1.3 68.4 + - - +
207E GLY* 2.8 1.9 + - - -
208E TYR* 2.8 38.7 + + + -
209E LEU* 4.0 11.4 - - + -
220E LEU* 4.1 5.4 - - - -
224E TYR* 3.6 14.5 - - - +
301E RET 4.1 13.9 - - + -
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Residues in contact with ALA 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PHE* 4.7 7.0 - - + -
201E PRO 2.9 17.4 + - - +
202E ALA* 3.6 8.7 - - - +
204E TYR* 1.3 75.5 - - - +
206E ALA* 1.3 64.3 + - - +
209E LEU* 3.0 55.2 + - + +
210E MET* 3.8 3.6 - - - +
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Residues in contact with ALA 206 (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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202E ALA 3.0 15.8 + - - +
203E GLY 3.1 10.1 + - - +
205E ALA* 1.3 75.4 - - - +
207E GLY* 1.3 60.0 + - - +
210E MET* 3.3 29.2 - - + +
216E TYR* 3.7 16.2 - - - +
219E ASN* 4.4 13.0 - - + +
223E ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 207 (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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203E GLY 2.9 10.2 + - - -
204E TYR 2.8 8.2 + - - -
206E ALA* 1.3 79.0 - - - +
208E TYR* 1.3 64.1 - - - -
209E LEU 3.8 0.4 - - - -
210E MET* 5.3 0.8 - - - +
215E VAL* 3.3 10.2 - - - -
216E TYR* 2.8 41.9 + - - +
220E LEU* 4.3 10.3 - - - -
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Residues in contact with TYR 208 (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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89E THR* 5.0 1.7 - - - +
91E THR* 4.3 4.7 + - - -
141E GLY 5.2 0.4 - - - -
142E GLU* 2.5 63.3 + - + +
148E VAL* 3.3 39.1 - - + +
204E TYR* 2.8 37.3 + + + +
207E GLY* 1.3 74.4 - - - +
209E LEU* 1.3 66.7 + - + +
210E MET 3.7 2.8 + - - -
211E GLY 5.3 4.5 - - - +
215E VAL* 3.7 34.5 - - + +
220E LEU* 3.6 26.8 - - + +
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Residues in contact with LEU 209 (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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148E VAL* 3.3 26.9 - - + +
149E LEU* 4.7 16.2 - - + -
152E PHE* 3.7 37.0 - - + -
204E TYR* 4.0 13.2 - - + -
205E ALA* 3.0 33.2 + - + +
207E GLY 3.8 0.2 - - - -
208E TYR* 1.3 92.4 - - + +
210E MET* 1.3 69.2 + - - +
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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