Contacts of the helix formed by residues 184 - 199 (chain B) in PDB entry 4NKT
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 ARG 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 4.4 14.8 - - - +
182B ASP* 2.9 39.2 + - - +
183B ALA* 1.3 79.1 - - - +
185B LEU* 1.3 63.5 + - - +
187B PRO* 3.4 8.3 - - - +
188B MET* 3.3 24.4 + - - +
222B LEU* 6.1 0.4 - - - -
230B VAL* 3.8 14.2 - - + +
262B SER* 3.7 11.7 + - - -
264B ASN* 3.0 34.5 + - - -
265B TYR* 3.8 2.0 - - - +
266B SER* 2.8 43.8 + - - +
267B SER* 5.2 0.2 - - - +
268B LEU* 4.0 11.0 - - + +
271B LEU* 3.8 24.7 - - + +
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 5.1 2.5 - - + -
175B LEU* 4.6 1.8 - - + +
178B TYR* 3.6 19.3 - - + +
179B THR* 3.6 37.5 - - + +
182B ASP* 3.2 15.8 + - - +
184B ARG* 1.3 78.3 - - - +
186B LYS* 1.3 65.2 + - - +
188B MET* 3.2 3.8 + - + +
189B VAL* 2.9 42.4 + - + +
215B VAL* 6.2 0.9 - - + -
218B VAL* 3.8 8.7 - - + -
219B LEU* 4.0 15.9 - - + -
222B LEU* 3.6 29.2 - - + -
231B PHE* 3.9 11.4 - - + -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 3.3 34.1 + - + +
56B LYS* 4.8 7.6 - - - +
57B ILE* 5.7 8.2 + - - +
94B GLY* 3.4 26.9 + - - +
95B LEU* 3.8 15.3 - - + -
96B ALA 5.6 2.5 - - - +
179B THR* 5.2 10.1 - - - +
182B ASP 4.6 1.0 + - - -
183B ALA* 4.2 4.7 + - - +
185B LEU* 1.3 79.5 - - - +
187B PRO* 1.3 71.6 - - + +
189B VAL* 3.3 1.7 + - - +
190B LEU* 3.0 39.1 + - + +
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Residues in contact with PRO 187 (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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49B TYR* 4.0 18.8 - - + -
52B TYR* 3.6 40.6 - - + -
183B ALA 3.2 21.1 - - - +
184B ARG* 3.4 13.5 - - - +
186B LYS* 1.3 95.3 - - + +
188B MET* 1.3 60.8 + - - +
190B LEU* 3.3 0.9 + - - +
191B LEU* 2.9 31.9 + - - +
268B LEU* 3.8 17.9 - - + -
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Residues in contact with MET 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG 3.3 16.9 + - - +
185B LEU 3.2 4.3 + - - +
187B PRO* 1.3 78.3 - - - +
189B VAL* 1.3 59.4 + - - +
191B LEU* 3.4 4.4 + - - +
192B VAL* 3.0 35.2 + - + +
218B VAL* 4.0 17.7 - - + -
221B TYR* 4.3 3.6 - - + -
222B LEU* 4.0 36.6 - - + -
268B LEU* 3.7 14.5 - - + +
271B LEU* 3.6 30.7 - - + +
272B LEU* 3.9 16.1 - - + +
275B PHE* 3.6 35.7 - - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.0 28.9 - - + -
185B LEU* 2.9 43.2 + - + +
186B LYS 3.7 3.4 - - - +
188B MET* 1.3 74.7 - - - +
190B LEU* 1.3 65.3 + - - +
192B VAL* 3.3 6.5 + - - +
193B LYS* 2.9 44.0 + - + +
215B VAL* 3.8 23.1 - - + -
218B VAL* 4.0 16.2 - - + -
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Residues in contact with LEU 190 (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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52B TYR* 3.7 17.3 - - + -
55B ILE* 3.7 9.9 - - + +
56B LYS* 3.5 38.8 - - + +
94B GLY 5.1 0.2 - - - +
95B LEU* 3.4 41.1 - - + +
96B ALA 3.8 12.3 - - - +
97B LEU* 3.8 15.5 - - + +
186B LYS* 3.0 29.0 + - + +
187B PRO* 3.8 4.7 - - + +
189B VAL* 1.3 78.1 - - + +
191B LEU* 1.3 58.2 + - - +
193B LYS* 3.4 4.9 + - + +
194B HIS* 2.9 29.6 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B CYS* 3.6 43.1 - - + +
51B VAL* 3.6 31.4 - - + -
52B TYR* 4.0 6.7 - - + +
55B ILE* 3.9 9.6 - - + -
187B PRO 2.9 22.4 + - - +
188B MET 3.8 3.4 - - - +
190B LEU* 1.3 77.5 - - - +
192B VAL* 1.3 56.8 + - - +
194B HIS* 3.3 2.1 + - - +
195B TRP* 2.9 30.5 + - - +
268B LEU* 4.0 10.3 - - + -
272B LEU* 3.8 24.7 - - + -
276B PHE* 6.2 0.9 - - - -
374B PHE* 3.4 21.7 - - + -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET* 3.0 23.4 + - + +
189B VAL* 3.3 4.0 + - - +
191B LEU* 1.3 76.8 - - - +
193B LYS* 1.3 57.3 + - + +
195B TRP* 3.4 16.4 + - + +
196B ALA* 2.9 27.4 + - - +
214B TYR* 4.1 24.2 - - + -
218B VAL* 3.9 17.0 - - + -
272B LEU* 3.6 22.7 - - + -
275B PHE* 3.7 35.2 - - + -
276B PHE* 5.0 2.7 - - + -
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER* 3.6 5.1 - - - -
95B LEU* 2.7 28.0 + - - +
96B ALA* 4.6 1.0 - - - +
97B LEU* 4.2 20.9 - - + +
189B VAL* 2.9 37.6 + - + +
190B LEU* 3.7 5.8 - - - +
192B VAL* 1.3 75.5 - - + +
194B HIS* 1.3 57.7 + - - +
196B ALA* 3.4 6.4 + - - +
197B LYS* 3.1 38.0 + - + +
202B ASN* 4.6 0.8 - - - +
211B SER* 4.1 25.4 - - - +
214B TYR* 5.1 6.3 - - + -
215B VAL* 4.4 6.5 - - + -
401B 2KH 3.6 36.1 + - - -
402B BR 3.9 9.1 - - - +
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Residues in contact with HIS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.0 10.4 - - + +
55B ILE* 3.7 39.3 - - + +
97B LEU* 4.3 11.5 - - + +
190B LEU 2.9 18.2 + - - +
191B LEU 3.6 4.5 - - - +
193B LYS* 1.3 75.1 - - - +
195B TRP* 1.3 58.7 + - - +
197B LYS* 3.4 6.4 + - - +
198B ARG* 3.0 77.5 + - + +
374B PHE* 3.6 36.9 - + + +
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Residues in contact with TRP 195 (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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191B LEU 2.9 18.0 + - - +
192B VAL* 3.5 23.6 - - + +
194B HIS* 1.3 76.3 - - - +
196B ALA* 1.3 63.6 - - + +
198B ARG* 3.3 3.3 + - - +
199B LYS* 2.9 52.2 + - + +
201B ILE* 3.7 20.2 - - + -
214B TYR* 4.1 9.6 - + - -
276B PHE* 3.6 25.5 - + + -
353B GLU* 3.7 36.6 + - + +
354B PHE* 3.7 42.0 - + - -
357B ALA* 4.4 0.6 - - - +
373B LEU* 3.3 42.4 - - + +
374B PHE* 3.8 16.3 - - + -
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Residues in contact with ALA 196 (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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192B VAL 2.9 17.8 + - - +
193B LYS* 3.8 5.8 - - - +
194B HIS 3.3 0.2 - - - -
195B TRP* 1.3 82.0 - - + +
197B LYS* 1.3 59.7 + - - +
200B GLN 3.2 2.6 + - - -
201B ILE* 2.9 39.5 + - + +
202B ASN* 3.5 11.6 + - + -
214B TYR* 3.8 38.8 - - + -
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Residues in contact with LYS 197 (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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97B LEU* 4.1 23.3 - - + +
193B LYS* 3.1 22.5 + - - +
194B HIS* 3.9 6.7 - - - +
196B ALA* 1.3 73.9 - - - +
198B ARG* 1.3 70.3 + - + +
200B GLN* 3.1 22.1 + - - +
202B ASN* 3.0 25.5 + - - +
211B SER* 3.9 1.4 + - - -
376B GLU* 5.3 0.5 - - - +
401B 2KH 2.6 36.4 + - - -
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Residues in contact with ARG 198 (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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194B HIS* 3.0 55.9 + - + +
195B TRP* 3.7 5.6 - - - +
197B LYS* 1.3 81.1 - - + +
199B LYS* 1.3 60.5 + - + +
200B GLN* 3.4 2.8 + - - +
374B PHE* 3.2 34.7 + - - +
375B GLU 4.2 2.2 - - - +
376B GLU* 3.5 32.4 - - - +
377B ALA* 2.8 25.3 + - - -
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Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 2.9 37.5 + - - +
198B ARG* 1.3 76.3 - - + +
200B GLN* 1.3 72.2 + - - +
201B ILE* 3.3 15.6 + - + +
349B ARG* 4.8 4.3 - - - +
353B GLU* 3.5 40.6 - - + +
372B SER 3.0 22.2 + - - -
373B LEU* 3.1 22.9 + - - +
374B PHE 4.8 0.2 - - - -
375B GLU* 2.7 30.7 + - - +
376B GLU 4.7 1.4 + - - -
377B ALA 3.7 21.8 - - - +
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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