Contacts of the helix formed by residues 198 - 209 (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 ALA 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B TRP* 3.5 26.9 - - + -
194B VAL 3.7 8.2 + - - +
195B VAL* 3.5 13.9 + - - +
196B GLY 3.1 2.0 + - - -
197B TRP* 1.3 77.6 - - - +
199B ILE* 1.3 61.1 + - - +
200B TYR 3.1 0.2 - - - -
201B PRO* 3.0 17.1 - - + +
202B ALA* 3.1 12.6 + - - +
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Residues in contact with ILE 199 (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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195B VAL 4.3 5.2 - - - +
196B GLY* 3.2 20.2 - - - +
197B TRP 3.1 0.6 - - - -
198B ALA* 1.3 78.2 - - + +
200B TYR* 1.3 57.0 + - - +
202B ALA* 3.3 6.3 - - + +
203B GLY 2.9 21.7 + - - -
223B ILE* 3.3 28.8 - - + +
226B LEU* 4.8 11.0 - - + -
227B ALA* 3.6 26.2 - - + +
230B VAL* 4.2 31.9 - - + -
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Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.4 32.3 - + - -
197B TRP* 3.3 19.4 + + - -
199B ILE* 1.3 74.7 - - - +
201B PRO* 1.4 62.1 - - + +
203B GLY* 2.7 21.0 + - - -
204B TYR* 2.7 16.8 + - - +
224B TYR* 3.5 14.7 - + - -
227B ALA* 3.5 22.8 + - + -
228B ASP* 2.7 40.6 + - - -
231B ASN* 3.4 25.9 - - - +
301B RET 3.3 64.7 - - + +
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Residues in contact with PRO 201 (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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152B PHE* 3.6 11.5 - - + -
156B MET* 3.6 29.4 - - + -
159B TRP* 3.8 24.7 - - + -
197B TRP 3.2 8.7 - - - +
198B ALA* 3.0 19.1 - - + +
200B TYR* 1.4 93.9 - - + +
202B ALA* 1.3 49.4 + - - +
204B TYR* 3.3 6.3 + - + +
205B ALA* 2.7 36.4 + - - +
301B RET 3.9 18.4 - - + -
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Residues in contact with ALA 202 (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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198B ALA 3.1 15.0 + - - +
199B ILE* 3.3 15.0 - - + +
200B TYR 3.1 0.2 - - - -
201B PRO* 1.3 75.1 - - - +
203B GLY* 1.3 57.6 + - - +
205B ALA* 3.3 6.5 + - - +
206B ALA* 2.9 30.7 + - - +
223B ILE* 4.1 9.4 - - + +
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Residues in contact with GLY 203 (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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199B ILE 2.9 12.4 + - - -
200B TYR 2.7 13.4 + - - -
202B ALA* 1.3 68.2 - - - +
204B TYR* 1.3 63.6 + - - -
206B ALA* 3.3 4.2 + - - +
207B GLY 3.1 18.0 + - - -
220B LEU* 3.4 16.2 - - - +
223B ILE* 3.7 24.6 - - - +
224B TYR* 4.1 7.4 - - - -
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Residues in contact with TYR 204 (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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138B GLY* 3.8 11.2 - - - -
141B GLY* 3.4 14.4 - - - -
142B GLU* 3.7 33.0 - - + -
148B VAL* 3.1 42.2 + - + +
151B ALA* 3.8 1.8 - - + +
152B PHE* 3.5 25.1 - + + -
200B TYR 2.7 12.5 + - - +
201B PRO* 3.5 7.2 - - + +
203B GLY* 1.3 71.0 - - - +
205B ALA* 1.3 63.5 + - - +
207B GLY 3.2 1.6 + - - -
208B TYR* 2.9 45.5 + + + +
209B LEU* 4.0 8.5 - - + -
220B LEU* 4.1 3.6 - - - -
224B TYR* 3.8 11.0 + - - +
301B RET 3.6 33.0 - - + -
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Residues in contact with ALA 205 (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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152B PHE* 4.6 8.1 - - + -
201B PRO 2.7 20.8 + - - +
202B ALA* 3.5 8.3 - - - +
204B TYR* 1.3 73.7 - - - +
206B ALA* 1.3 59.7 + - - +
209B LEU* 2.8 53.1 + - + +
210B MET* 3.7 3.5 + - - +
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Residues in contact with ALA 206 (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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202B ALA 2.9 12.5 + - - +
203B GLY 3.3 2.7 + - - +
205B ALA* 1.3 73.5 - - - +
207B GLY* 1.3 61.4 + - - +
210B MET* 3.3 38.2 - - + +
216B TYR* 3.3 15.5 - - - +
219B ASN* 4.6 11.2 - - + -
223B ILE* 3.5 33.0 - - + -
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Residues in contact with GLY 207 (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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203B GLY 3.1 10.8 + - - -
204B TYR 3.7 2.0 - - - -
206B ALA* 1.3 81.2 - - - +
208B TYR* 1.3 62.4 + - - +
210B MET 5.3 0.2 - - - -
215B VAL* 3.4 13.6 - - - +
216B TYR* 3.1 42.5 + - - -
220B LEU* 4.0 13.2 - - - +
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Residues in contact with TYR 208 (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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89B THR* 5.5 0.5 - - - +
91B THR* 4.7 2.9 + - - -
141B GLY 4.9 0.4 - - - -
142B GLU* 2.5 67.1 + - + +
148B VAL* 3.9 27.3 - - + +
204B TYR* 2.9 40.3 + + + +
207B GLY* 1.3 76.9 - - - +
209B LEU* 1.3 78.3 + - + +
210B MET 3.6 5.2 + - - +
215B VAL* 3.7 32.5 - - + +
220B LEU* 3.8 19.3 - - + +
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Residues in contact with LEU 209 (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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148B VAL* 3.4 32.1 - - + -
149B LEU* 4.4 15.9 - - + +
152B PHE* 3.6 47.1 - - + -
204B TYR* 4.0 8.7 - - + -
205B ALA* 2.8 28.3 + - + +
208B TYR* 1.3 87.6 - - + +
210B MET* 1.3 64.5 + - - +
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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