Contacts of the helix formed by residues 210 - 225 (chain B) in PDB entry 4NKU
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 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASN* 3.5 1.6 - - - -
204B PRO* 3.5 19.6 - - - +
209B LEU* 1.3 80.3 - - - +
211B SER* 1.3 64.3 + - - +
212B TYR* 3.7 3.5 + - - +
213B GLY* 3.0 26.5 + - - -
214B TYR* 3.2 12.3 + - - -
338B VAL* 3.8 17.7 + - - +
341B THR* 4.6 1.6 + - - -
58H A 3.8 25.6 - - - -
59H U 3.8 7.7 + - - -
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 3.9 28.1 - - - +
202B ASN* 3.1 29.4 + - - -
210B SER* 1.3 72.8 - - - +
212B TYR* 1.3 62.5 + - - +
214B TYR* 3.1 10.9 + - - +
215B VAL* 3.0 26.3 + - - +
402B BR 4.7 0.2 - - - -
58H A 5.2 0.6 + - - -
59H U 3.6 20.7 + - - -
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Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASN* 3.3 22.6 + - + +
175B LEU* 3.8 30.9 - - + +
210B SER* 3.1 2.2 - - - +
211B SER* 1.3 75.8 - - - +
213B GLY* 1.3 64.2 + - - +
215B VAL* 3.2 2.6 + - + +
216B LEU* 3.0 44.4 + - + +
330B ASP* 2.9 28.2 + - - -
331B PRO* 3.7 14.6 - - - +
338B VAL* 3.8 10.8 - - + -
402B BR 4.2 6.9 - - + +
59H U 3.2 80.7 + + + +
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Residues in contact with GLY 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.7 17.7 - - - -
210B SER* 3.0 19.1 + - - -
212B TYR* 1.3 75.3 - - - +
214B TYR* 1.3 56.8 + - - +
216B LEU* 3.3 6.2 + - - +
217B MET* 3.0 30.0 + - - +
328B ILE* 4.0 4.0 - - - +
338B VAL* 3.7 20.3 - - - +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL* 4.0 26.9 - - + +
193B LYS* 5.4 7.2 - - + -
195B TRP* 4.2 17.3 - + - -
196B ALA* 3.8 20.0 - - + -
201B ILE* 2.7 45.8 + - - +
202B ASN* 4.3 4.0 - - - -
209B LEU* 3.6 31.2 - - + -
210B SER 3.2 21.9 + - - -
211B SER* 3.1 9.2 + - - +
213B GLY* 1.3 72.8 - - - +
215B VAL* 1.3 60.7 + - - +
217B MET* 3.2 15.5 + - - +
218B VAL* 2.9 33.3 + - - +
275B PHE* 5.2 1.1 - + - -
350B ILE* 3.6 13.8 - - + +
354B PHE* 4.6 11.9 - + - -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.3 10.3 - - + -
175B LEU* 3.9 31.9 - - + -
185B LEU* 6.2 1.1 - - + -
189B VAL* 3.8 32.5 - - + -
193B LYS* 3.8 13.7 - - + -
211B SER 3.0 19.1 + - - +
212B TYR* 3.2 8.7 + - - +
214B TYR* 1.3 75.0 - - - +
216B LEU* 1.3 58.6 + - + +
218B VAL* 3.1 9.8 + - - +
219B LEU* 2.9 35.8 + - + +
402B BR 3.9 11.4 - - + -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 6.0 0.2 - - + -
175B LEU* 4.5 4.9 - - + -
212B TYR* 3.0 46.2 + - + +
213B GLY 3.6 7.4 - - - +
215B VAL* 1.3 78.0 - - - +
217B MET* 1.3 57.8 + - - +
219B LEU* 4.4 13.7 - - + +
220B TYR* 2.9 28.3 + - - +
290B VAL* 4.7 1.8 - - - -
292B PHE* 3.3 28.6 - - + -
328B ILE* 3.9 20.0 - - + -
329B GLU 4.4 1.1 - - - +
331B PRO* 3.8 21.5 - - + -
338B VAL* 3.7 29.8 - - + -
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.5 29.4 - - - -
213B GLY 3.0 13.9 + - - +
214B TYR* 3.2 17.0 + - - +
216B LEU* 1.3 75.0 - - - +
218B VAL* 1.3 63.0 + - - +
220B TYR* 4.5 1.3 - - - -
221B TYR* 3.1 11.3 + - - +
275B PHE* 3.9 6.1 - - + -
279B TYR* 2.8 70.0 + - + +
290B VAL* 4.9 4.7 - - + -
326B LEU* 4.7 12.8 - - + -
328B ILE* 3.8 18.8 - - + -
350B ILE* 5.5 2.0 - - + -
354B PHE* 3.7 23.6 - - + -
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.9 15.0 - - + -
188B MET* 3.9 16.8 - - + -
189B VAL* 4.1 13.0 - - + -
192B VAL* 3.9 23.6 - - + -
214B TYR 2.9 17.6 + - - +
215B VAL* 3.5 9.9 - - - +
217B MET* 1.3 76.9 - - - +
219B LEU* 1.3 63.0 + - - +
221B TYR* 3.3 4.5 + - - +
222B LEU* 3.0 41.3 + - + +
275B PHE* 3.6 27.1 - - + -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 5.7 2.7 - - + -
175B LEU* 3.8 29.2 - - + -
178B TYR* 3.8 33.4 - - + -
185B LEU* 4.1 14.6 - - + -
215B VAL* 2.9 26.5 + - + +
216B LEU* 3.8 13.5 - - + +
218B VAL* 1.3 77.0 - - - +
220B TYR* 1.3 62.6 + - - +
222B LEU* 3.1 3.4 + - - +
223B ILE* 2.9 32.4 + - + +
231B PHE* 3.8 29.6 - - + -
292B PHE* 3.9 13.5 - - + -
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU 2.9 21.1 + - - +
219B LEU* 1.3 70.7 - - - +
221B TYR* 1.3 57.9 - - - +
223B ILE* 4.8 1.8 - - - -
224B HIS* 2.9 42.7 + + + +
225B VAL* 3.6 21.0 + - + +
278B PHE* 4.2 13.2 - + - -
279B TYR* 3.5 19.3 - - - +
283B PHE* 5.0 5.0 - + - -
289B VAL 4.6 2.9 + - - -
290B VAL* 3.5 26.0 - - + -
291B THR 3.2 40.8 - - - -
292B PHE* 3.6 9.1 - + + -
296B ASP 4.9 0.3 + - - -
297B GLY* 2.4 37.6 + - - -
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Residues in contact with TYR 221 (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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188B MET* 4.4 2.0 - - + -
217B MET 3.1 13.0 + - - +
218B VAL 3.5 6.3 - - - +
219B LEU 3.2 0.2 - - - -
220B TYR* 1.3 81.2 - - - +
222B LEU* 1.3 79.3 + - + +
225B VAL* 3.2 39.9 + - + -
226B ILE* 3.1 62.4 + - + +
270B SER 4.8 1.2 + - - -
271B LEU 3.7 17.6 + - - -
274B GLY* 3.2 37.9 - - - -
275B PHE* 3.8 22.0 - - + -
278B PHE* 3.9 14.8 - - + -
279B TYR* 4.2 5.8 - - + -
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Residues in contact with LEU 222 (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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184B ARG 6.2 0.2 - - - -
185B LEU* 3.6 33.7 - - + -
188B MET* 3.9 19.7 - - + -
218B VAL* 3.0 28.8 + - + +
219B LEU* 3.1 4.0 + - - +
221B TYR* 1.3 95.8 - - + +
223B ILE* 1.3 60.4 + - - +
226B ILE* 3.6 6.9 - - + +
230B VAL* 3.0 53.1 + - + -
231B PHE* 3.4 25.1 + - + -
271B LEU* 4.3 10.3 - - + -
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Residues in contact with ILE 223 (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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178B TYR* 3.3 32.8 - - + +
219B LEU* 2.9 24.1 + - + +
222B LEU* 1.3 80.2 - - - +
224B HIS* 1.3 94.1 + - + +
225B VAL 3.8 0.2 - - - -
226B ILE 4.8 1.0 - - - +
227B LYS* 5.3 1.2 + - - -
229B PRO* 3.7 23.2 - - - +
231B PHE* 3.6 29.3 - - + +
232B PRO 4.0 0.7 - - - +
233B ASN* 3.9 21.1 - - + +
292B PHE* 4.1 21.5 - - + -
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Residues in contact with HIS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 2.9 30.8 + + + +
223B ILE* 1.3 102.8 + - + +
225B VAL* 1.3 61.7 + - - +
226B ILE 4.9 0.2 - - - -
227B LYS* 3.9 16.7 + - - +
233B ASN* 3.1 31.3 + - + -
236B LEU* 4.7 0.9 - - + -
291B THR 3.8 21.2 + - - -
292B PHE* 4.4 4.0 - + - -
294B ARG 3.1 24.1 + - - -
295B PRO* 3.7 17.8 + - + -
296B ASP 4.0 9.4 - - - +
297B GLY* 3.7 14.5 + - - -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 3.9 12.8 - - + -
221B TYR* 3.2 39.7 + - + +
224B HIS* 1.3 80.2 - - - +
226B ILE* 1.3 69.4 + - - +
227B LYS* 3.4 17.5 + - - +
278B PHE* 3.6 52.0 - - + -
282B LYS* 6.2 0.2 - - + -
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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
------------------------------------------------------------
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