Contacts of the helix formed by residues 267 - 282 (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 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MET* 4.3 19.6 - - - +
41B HIS* 4.0 7.1 + - - +
42B LYS* 6.3 0.2 - - - -
45B THR* 3.0 28.8 + - - -
184B ARG* 5.2 0.4 - - - +
265B TYR 3.5 2.2 + - - -
266B SER* 1.3 77.6 - - - +
268B LEU* 1.3 65.1 + - - +
270B SER* 3.0 24.5 + - - -
271B LEU* 3.0 21.9 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 4.1 3.5 + - + +
48B CYS* 3.7 29.4 - - + -
49B TYR* 3.5 46.3 + - + +
184B ARG* 4.0 15.5 - - + +
187B PRO* 3.8 18.4 - - + -
188B MET* 3.8 38.6 - - + +
191B LEU* 4.0 4.9 - - + -
266B SER 4.0 0.4 + - - -
267B SER* 1.3 72.8 - - - +
269B GLY* 1.3 62.6 + - - +
271B LEU* 3.3 11.9 + - + +
272B LEU* 3.1 25.3 + - + +
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B HIS* 4.0 4.9 - - - -
44B PHE* 3.5 30.5 - - - -
45B THR* 2.9 25.9 + - - +
48B CYS* 4.6 2.7 - - - -
268B LEU* 1.3 76.1 - - - +
270B SER* 1.3 63.7 + - - +
272B LEU 3.5 0.5 + - - -
273B HIS* 3.0 25.1 + - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B MET* 5.3 0.9 - - - +
40B SER* 2.7 28.3 + - - -
41B HIS* 2.9 20.4 + - - +
221B TYR* 4.8 0.7 + - - -
266B SER* 3.9 18.3 - - - -
267B SER* 3.0 21.6 + - - -
269B GLY* 1.3 75.9 - - - +
271B LEU* 1.3 63.3 + - - +
273B HIS* 3.4 1.8 + - - +
274B GLY* 3.0 21.1 + - - -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 3.9 41.3 - - + +
188B MET* 3.6 23.4 - - + +
221B TYR* 3.7 6.8 - - - -
222B LEU* 4.3 15.3 - - + -
226B ILE* 3.6 29.6 - - + -
230B VAL* 3.9 15.7 - - + -
264B ASN* 4.0 0.4 - - - +
266B SER* 3.6 16.8 - - - -
267B SER 3.0 16.0 + - - +
268B LEU* 3.6 9.4 - - + +
270B SER* 1.3 77.6 - - - +
272B LEU* 1.3 57.7 + - - +
274B GLY 3.3 1.0 + - - -
275B PHE* 2.9 28.6 + - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 4.0 13.0 - - + -
48B CYS* 3.7 28.0 - - - -
188B MET* 3.8 24.2 - - + +
191B LEU* 3.8 25.4 - - + -
192B VAL* 3.6 31.4 - - + +
268B LEU* 3.1 15.8 + - + +
269B GLY 4.0 2.9 - - - +
271B LEU* 1.3 76.0 - - - +
273B HIS* 1.3 67.5 + - - +
275B PHE* 3.2 3.8 + - + +
276B PHE* 3.0 45.5 + - + -
373B LEU* 5.8 2.5 - - + -
374B PHE* 5.8 1.3 - - + -
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Residues in contact with HIS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B HIS* 2.8 33.9 + + + +
44B PHE* 4.3 1.0 - - - -
269B GLY 3.0 18.3 + - - +
270B SER 3.7 3.8 - - - +
271B LEU 3.3 0.2 - - - -
272B LEU* 1.3 78.6 - - - +
274B GLY* 1.3 62.1 + - - +
276B PHE* 3.4 1.0 + - - +
277B ARG* 3.1 42.5 + - + +
358B SER* 4.3 8.4 + - - -
361B LEU* 3.4 50.4 - - + +
362B ASN* 3.2 27.2 + - - -
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR* 3.2 22.4 - - - -
270B SER 3.0 13.6 + - - -
271B LEU 3.7 0.7 - - - -
273B HIS* 1.3 75.5 - - - +
275B PHE* 1.3 56.3 + - - +
277B ARG* 3.2 15.6 - - - +
278B PHE* 2.9 31.4 + - - +
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET* 3.6 14.1 - - + -
192B VAL* 3.6 33.2 - - + -
195B TRP* 4.7 0.4 - + - -
214B TYR* 4.9 1.3 - + - -
217B MET* 3.9 7.0 - - + -
218B VAL* 3.6 42.2 - - + -
221B TYR* 3.5 19.1 - - + -
271B LEU 2.9 13.7 + - - +
272B LEU* 3.2 11.0 + - + +
274B GLY* 1.3 73.3 - - - +
276B PHE* 1.3 81.6 + + - +
278B PHE* 3.5 0.3 + - - +
279B TYR* 3.3 52.7 + + - +
354B PHE* 3.5 29.8 - + - -
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Residues in contact with PHE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU 6.3 0.2 - - - -
192B VAL* 5.2 2.5 - - + -
195B TRP* 3.6 42.2 - + + -
272B LEU* 3.0 47.4 + - + +
273B HIS 3.8 3.8 - - - +
275B PHE* 1.3 85.0 - + - +
277B ARG* 1.3 57.6 + - - +
279B TYR 3.5 0.2 + - - -
280B ALA* 2.9 30.8 + - - +
354B PHE* 3.6 23.5 - + - +
357B ALA* 3.7 18.2 - - + -
358B SER* 3.2 15.2 + - - +
361B LEU* 3.9 19.1 - - + -
373B LEU* 4.1 35.0 - - + -
374B PHE* 6.1 0.4 - + - -
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Residues in contact with ARG 277 (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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273B HIS* 3.1 44.1 + - - +
274B GLY* 3.2 24.7 - - - +
276B PHE* 1.3 76.5 - - - +
278B PHE* 1.3 64.8 + - - +
280B ALA* 4.2 1.1 - - - -
281B TYR* 3.0 45.8 + - + +
282B LYS* 3.8 1.7 + - - +
358B SER* 3.4 15.4 + - - +
362B ASN* 3.5 24.4 + - - +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 4.2 8.5 - + - -
221B TYR* 3.9 12.1 - + + -
225B VAL* 3.6 44.6 - - + -
274B GLY 2.9 17.3 + - - +
275B PHE 3.9 3.6 - - - +
276B PHE 3.4 0.2 - - - -
277B ARG* 1.3 78.9 - - + +
279B TYR* 1.3 98.0 + + - +
282B LYS* 2.9 45.5 + - + -
283B PHE* 2.8 53.9 + + + -
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Residues in contact with TYR 279 (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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217B MET* 2.8 62.4 + - + -
220B TYR* 3.5 20.1 - - - +
221B TYR* 4.0 3.4 + - + -
275B PHE* 3.3 43.7 + + - -
278B PHE* 1.3 101.3 - + - +
280B ALA* 1.3 58.9 + - - +
283B PHE* 3.8 26.8 - + + +
290B VAL* 4.1 11.8 - - + +
351B ARG* 2.9 31.3 + - - -
354B PHE* 3.6 30.3 - + + +
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Residues in contact with ALA 280 (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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276B PHE 2.9 19.5 + - - +
277B ARG 3.8 2.7 - - - +
279B TYR* 1.3 78.4 - - - +
281B TYR* 1.3 75.9 + - + +
351B ARG* 3.4 21.1 + - - -
354B PHE* 3.7 22.4 - - - +
355B MET* 3.5 22.8 - - + +
358B SER* 3.4 17.0 - - - +
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Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ARG* 3.0 32.1 + - + +
280B ALA* 1.3 90.9 - - + +
282B LYS* 1.3 62.4 + - + +
283B PHE 4.0 2.9 - - - -
351B ARG* 5.1 3.4 + - - +
355B MET* 3.7 42.9 + - + +
358B SER* 3.7 21.3 - - - -
359B ARG* 4.5 11.8 + - - +
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Residues in contact with LYS 282 (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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277B ARG 3.8 1.3 + - - +
278B PHE* 2.9 36.8 + - + +
281B TYR* 1.3 81.2 - - + +
283B PHE* 1.3 67.6 + - - +
284B GLU* 3.5 17.2 + - - +
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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