Contacts of the helix formed by residues 195 - 211 (chain B) in PDB entry 2HNK
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 GLU 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B TRP* 6.0 0.2 - - - -
187B SER* 5.6 0.4 - - - -
193B HIS* 2.8 40.4 + - - +
194B GLN* 1.3 80.8 - - - +
196B PRO* 1.4 71.7 - - + +
197B SER* 2.9 18.9 + - - +
198B THR* 2.7 27.4 + - - -
199B VAL* 2.8 20.8 + - - +
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Residues in contact with PRO 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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158B GLU* 3.1 41.9 - - + +
194B GLN 3.6 4.7 - - - +
195B GLU* 1.4 84.5 - - + +
197B SER* 1.3 55.1 + - - +
199B VAL* 3.9 9.4 - - + +
200B GLY* 3.1 20.1 + - - -
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Residues in contact with SER 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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157B LYS* 3.9 23.2 - - - +
158B GLU* 4.2 6.2 + - - +
184B TRP* 3.3 26.4 + - - -
195B GLU* 2.9 14.6 + - - +
196B PRO* 1.3 74.3 - - - +
198B THR* 1.3 71.3 + - - -
199B VAL 3.1 0.7 - - - -
200B GLY* 2.9 13.9 + - - -
201B ILE* 3.0 15.9 + - - +
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B TRP* 3.2 21.8 + - - +
187B SER* 3.3 41.4 + - - +
188B VAL* 3.9 5.8 - - + +
193B HIS* 4.2 5.2 - - + +
195B GLU* 2.7 31.4 + - - +
197B SER* 1.3 77.3 + - - +
199B VAL* 1.3 57.1 + - - +
201B ILE* 3.4 3.3 + - - +
202B ARG* 3.0 46.9 + - - +
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Residues in contact with VAL 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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194B GLN* 3.7 38.1 - - + +
195B GLU 2.8 24.1 + - - +
196B PRO* 4.0 8.1 - - + +
198B THR* 1.3 70.2 - - - +
200B GLY* 1.3 61.3 + - - +
202B ARG* 3.6 11.2 + - - +
203B LYS* 3.0 30.9 + - + +
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Residues in contact with GLY 200 (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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157B LYS 3.9 11.4 - - - -
158B GLU* 4.1 5.6 - - - -
161B PRO* 3.3 27.4 - - - +
196B PRO 3.1 13.2 + - - -
197B SER 2.9 6.8 + - - -
199B VAL* 1.3 77.1 - - - +
201B ILE* 1.3 57.6 + - - +
203B LYS* 3.4 1.8 + - - +
204B PHE* 2.9 25.2 + - - +
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Residues in contact with ILE 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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157B LYS* 3.6 36.1 - - + +
160B TYR* 4.2 12.8 - - + -
181B ASN 3.3 23.6 - - - +
182B VAL* 3.6 27.4 - - + +
184B TRP* 3.5 28.0 - - + -
188B VAL* 3.7 12.8 - - + -
197B SER 3.0 10.8 + - - +
198B THR 3.8 4.0 - - - +
200B GLY* 1.3 74.1 - - - +
202B ARG* 1.3 65.9 + - - +
204B PHE* 3.3 7.7 + - - +
205B ASN* 2.9 26.1 + - - +
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Residues in contact with ARG 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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187B SER 2.6 27.1 + - - -
188B VAL* 2.6 35.3 + - + +
190B ASP 2.7 23.2 + - - -
191B LEU* 3.7 18.3 - - - +
193B HIS 2.8 25.4 + - - -
194B GLN* 3.4 15.8 + - - +
198B THR* 3.0 29.4 + - - +
199B VAL* 3.8 12.3 - - - +
201B ILE* 1.3 74.8 - - - +
203B LYS* 1.3 63.5 + - - +
205B ASN* 3.3 8.6 + - - +
206B GLU* 3.1 26.5 + - - +
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PRO* 3.9 21.3 - - + -
199B VAL* 3.0 22.2 + - + +
200B GLY* 3.6 6.7 - - - +
201B ILE 3.3 0.2 - - - -
202B ARG* 1.3 75.1 - - - +
204B PHE* 1.3 56.2 + - - +
206B GLU* 3.4 25.0 + - - +
207B LEU* 3.0 47.7 + - - +
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Residues in contact with PHE 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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153B LEU* 3.9 15.0 - - + -
160B TYR* 3.5 39.7 - + + -
161B PRO* 4.2 3.1 - - - +
164B TYR* 3.8 30.1 - + + -
177B LEU* 3.8 15.5 - - + -
179B ALA* 3.7 32.1 - - + -
182B VAL* 4.2 6.3 - - + -
200B GLY 2.9 14.3 + - - +
201B ILE* 3.4 9.0 - - + +
203B LYS* 1.3 75.4 - - - +
205B ASN* 1.3 78.5 + - - +
206B GLU 3.1 0.2 - - - -
207B LEU* 3.0 12.4 + - - +
208B VAL* 3.0 41.2 + - + +
226B SER* 5.0 4.9 - - - -
228B VAL* 5.0 0.9 - - + -
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Residues in contact with ASN 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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182B VAL* 2.9 41.9 + - - +
183B LEU* 5.7 0.4 - - - +
188B VAL* 4.7 5.9 - - - +
201B ILE* 2.9 23.2 + - - +
202B ARG* 3.3 8.6 + - - +
204B PHE* 1.3 91.7 - - - +
206B GLU* 1.3 57.1 - - - +
208B VAL* 4.1 6.2 - - - +
209B TYR* 3.3 25.6 + - - +
218B LEU* 4.7 14.0 - - + +
226B SER* 4.3 4.9 + - - -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 3.1 11.2 + - - +
203B LYS* 3.4 35.8 + - + +
204B PHE 3.1 0.2 - - - -
205B ASN* 1.3 76.9 - - - +
207B LEU* 1.3 59.6 + - - +
208B VAL 3.3 0.2 - - - -
209B TYR* 3.3 3.2 + - - +
210B ASN* 2.7 51.8 + - - +
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Residues in contact with LEU 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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161B PRO* 3.7 39.0 - - + +
164B TYR* 4.3 23.6 - - + -
165B PRO* 5.6 0.7 - - + -
203B LYS* 3.0 38.6 + - + +
204B PHE* 3.0 7.1 + - - +
206B GLU* 1.3 76.5 - - - +
208B VAL* 1.3 55.8 + - - +
210B ASN* 3.5 3.0 + - - +
211B ASP* 3.0 31.8 + - - +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 3.6 30.7 - - + -
204B PHE* 3.0 40.5 + - + +
205B ASN* 4.1 6.3 - - - +
207B LEU* 1.3 75.0 - - - +
209B TYR* 1.3 65.1 + - - +
211B ASP 3.2 10.0 + - - +
214B VAL* 3.5 13.9 - - + +
216B VAL* 3.6 26.9 - - + +
226B SER* 5.9 0.2 - - - -
228B VAL* 3.6 32.8 - - + -
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Residues in contact with TYR 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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205B ASN 3.3 17.8 + - - +
206B GLU* 3.3 5.4 + - - +
208B VAL* 1.3 80.2 - - - +
210B ASN* 1.3 79.5 + - - +
211B ASP 3.3 3.7 + - - +
216B VAL* 4.5 18.6 - - + +
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Residues in contact with ASN 210 (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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206B GLU* 2.7 43.5 + - - +
207B LEU* 3.7 3.1 - - - +
209B TYR* 1.3 94.9 - - - +
211B ASP* 1.3 61.2 + - - +
212B SER* 3.5 5.0 + - - -
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Residues in contact with ASP 211 (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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164B TYR* 2.6 31.6 + - - +
168B LEU* 3.3 19.1 - - - +
207B LEU 3.0 18.3 + - - +
208B VAL 3.2 7.3 + - - +
209B TYR 4.4 2.9 - - - +
210B ASN* 1.3 76.2 - - - +
212B SER* 1.3 59.4 + - - +
213B LEU* 3.1 31.9 + - - +
214B VAL* 3.3 25.8 - - + +
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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
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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