Contacts of the helix formed by residues 184 - 201 (chain B) in PDB entry 1NVD
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 PRO 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B THR 3.4 9.6 - - - +
183B LEU* 1.3 96.4 - - + +
185B VAL* 1.3 68.0 + - - +
186B ARG* 4.5 4.3 - - + +
187B GLU* 3.0 24.0 + - + +
188B PHE* 2.9 18.4 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU 3.5 2.9 + - - +
184B PRO* 1.3 70.4 - - - +
186B ARG* 1.3 64.2 + - - +
188B PHE* 3.1 4.1 + - - +
189B ILE* 2.9 35.2 + - + +
221B VAL* 3.5 44.6 - - + +
222B ARG* 3.9 38.6 - - + +
231B ARG* 5.3 2.0 - - - +
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Residues in contact with ARG 186 (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 PRO* 3.2 4.8 - - + +
185B VAL* 1.3 78.5 - - - +
187B GLU* 1.3 63.2 + - + +
189B ILE* 3.0 11.0 + - + +
190B ASN* 2.8 28.7 + - - +
284B GLN 2.8 28.7 + - - -
285B ILE* 4.0 1.2 - - - +
286B LEU* 3.8 23.3 - - + +
289B GLU* 3.1 38.9 + - - +
337B LEU* 3.8 26.1 - - - +
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 5.2 9.6 - - + +
141B LEU* 4.9 1.4 + - - +
142B LEU* 5.3 1.4 + - - +
183B LEU* 3.5 24.4 - - + +
184B PRO* 3.0 31.2 + - + +
186B ARG* 1.3 81.2 - - + +
188B PHE* 1.3 63.8 + - - +
190B ASN* 3.1 27.2 + - - +
191B GLY* 3.1 6.8 + - - -
286B LEU* 3.8 26.5 - - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.3 32.0 - - + +
180B LEU* 4.4 15.9 - - + -
183B LEU* 3.9 24.6 - - + +
184B PRO 2.9 13.1 + - - +
185B VAL* 3.1 9.8 + - - +
187B GLU* 1.3 75.2 - - - +
189B ILE* 1.3 68.3 + - + +
191B GLY 3.2 9.4 + - - -
192B MET* 3.3 16.9 + - + +
217B ILE* 3.7 16.4 - - + -
218B LEU* 6.3 0.2 - - + -
221B VAL* 3.4 34.3 - - + -
232B PHE* 3.6 24.0 - + - -
239B LEU* 3.7 28.3 - - + -
323B TYR* 6.0 0.2 - + - -
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Residues in contact with ILE 189 (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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185B VAL* 2.9 33.6 + - + +
186B ARG* 3.3 10.1 - - + +
188B PHE* 1.3 83.5 - - + +
190B ASN* 1.3 65.5 + - - +
192B MET* 3.1 21.4 + - + +
193B ALA 3.6 0.2 + - - -
218B LEU* 3.6 23.1 - - + -
221B VAL* 4.9 1.3 - - + -
222B ARG* 5.7 4.3 - - - +
289B GLU* 5.9 3.1 - - + +
323B TYR* 3.1 36.3 - - + +
324B GLY* 3.7 19.7 - - - +
325B LEU* 3.6 22.7 - - + +
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Residues in contact with ASN 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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142B LEU* 3.4 27.8 - - - +
186B ARG 2.8 12.3 + - - +
187B GLU* 3.1 25.5 + - - +
189B ILE* 1.3 76.4 - - - +
191B GLY* 1.3 63.6 + - - +
193B ALA* 3.1 22.3 + - - +
194B GLU 4.2 0.9 + - - -
286B LEU* 3.3 29.8 - - + +
287B HIS* 4.7 2.6 - - - +
288B GLY* 2.7 36.5 + - - +
289B GLU* 3.3 6.6 + - + +
325B LEU* 4.6 5.4 - - - -
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Residues in contact with GLY 191 (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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141B LEU* 4.0 8.1 - - - -
142B LEU* 3.6 35.2 - - - +
145B VAL* 4.0 1.9 - - - +
187B GLU 3.1 8.2 + - - -
188B PHE 3.2 4.2 + - - -
190B ASN* 1.3 77.5 - - - +
192B MET* 1.3 65.0 + - - +
194B GLU* 3.0 16.5 + - - +
195B VAL* 3.3 12.6 + - - +
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Residues in contact with MET 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.9 13.7 - - - -
188B PHE* 3.3 33.6 + - + +
189B ILE* 3.1 16.1 + - + +
191B GLY* 1.3 76.4 - - - +
193B ALA* 1.3 61.4 + - - +
195B VAL* 3.1 25.6 + - + +
196B ILE* 2.9 34.0 + - + +
210B LEU* 4.3 6.7 - - + -
217B ILE* 5.1 2.5 - - - -
239B LEU* 6.1 1.6 - - - -
242B ARG* 6.4 1.3 - - - -
323B TYR* 3.6 50.5 - - + -
325B LEU* 4.1 8.1 - - + -
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Residues in contact with ALA 193 (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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189B ILE 3.6 0.2 + - - -
190B ASN 3.1 13.6 + - - +
191B GLY 3.0 0.4 - - - -
192B MET* 1.3 78.9 - - - +
194B GLU* 1.3 59.0 + - - +
196B ILE* 4.0 1.2 - - - +
197B LYS* 3.2 12.8 + - - +
288B GLY* 3.0 34.3 - - - +
291B VAL* 4.8 2.9 - - + +
292B ALA* 4.7 0.4 - - + -
295B MET* 3.1 31.9 - - + +
325B LEU* 3.5 23.4 - - + +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.8 28.0 - - + +
145B VAL* 4.1 13.9 - - + -
146B ASP* 3.7 12.1 - - + +
190B ASN 5.0 1.1 - - - +
191B GLY 3.0 9.8 + - - +
193B ALA* 1.3 78.2 - - + +
195B VAL* 1.3 63.5 + - - +
197B LYS* 2.6 40.8 + - - +
198B THR* 2.8 31.2 + - - +
271B HIS* 3.5 4.0 + - - -
287B HIS* 3.3 11.6 + - - -
288B GLY* 4.8 0.9 - - - -
291B VAL* 4.1 6.4 - - - +
501B CRB 3.6 2.5 - - - -
601B ZN 2.4 31.2 - - - -
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Residues in contact with VAL 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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141B LEU* 4.8 3.1 - - + -
145B VAL* 3.8 27.4 - - + -
191B GLY 3.5 15.5 - - - +
192B MET* 3.1 26.8 + - + +
194B GLU* 1.3 78.2 - - - +
196B ILE* 1.3 61.4 + - - +
198B THR* 3.4 3.5 + - - -
199B ALA* 3.2 21.1 + - - +
210B LEU* 3.8 27.1 - - + -
242B ARG* 4.2 21.5 - - + +
243B ILE* 5.7 1.6 - - + -
246B SER* 4.1 11.6 - - - -
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Residues in contact with ILE 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 MET* 2.9 30.5 + - + +
193B ALA 4.0 3.4 - - - +
195B VAL* 1.3 73.5 - - - +
197B LYS* 1.3 65.3 + - - +
199B ALA* 3.3 2.3 + - - +
200B ALA* 2.9 22.6 + - + +
207B PHE* 3.6 25.9 - - + -
210B LEU* 4.0 11.9 - - + -
269B TRP* 5.8 0.2 - - + -
295B MET* 4.9 4.0 - - - -
316B ILE* 5.6 2.2 - - + +
319B CYS* 4.1 19.5 - - + +
320B LEU* 3.9 32.1 - - + -
323B TYR* 3.8 26.5 - - + -
325B LEU* 4.1 10.8 - - + -
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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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146B ASP* 4.3 5.9 + - - -
193B ALA 3.2 17.4 + - - +
194B GLU* 2.6 26.6 + - - +
195B VAL 3.3 0.2 - - - -
196B ILE* 1.3 79.1 - - - +
198B THR* 1.3 80.2 + - - +
200B ALA* 3.2 13.2 + - - +
201B ILE* 3.3 17.2 + - + +
266B LEU 5.2 0.4 - - - +
267B LEU* 2.8 35.3 + - - +
269B TRP* 3.4 43.2 - - + +
271B HIS* 3.5 9.8 - - + -
291B VAL* 5.2 0.2 - - + -
295B MET* 3.7 17.0 - - + -
501B CRB 2.8 20.0 + - - +
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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
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145B VAL 5.0 1.9 + - - -
146B ASP* 5.7 1.7 - - - +
194B GLU* 2.8 22.8 + - - +
195B VAL 3.7 4.5 - - - -
197B LYS* 1.3 85.9 + - - +
199B ALA* 1.3 55.3 + - - +
201B ILE* 3.3 20.0 - - + +
202B SER* 2.7 24.0 + - - +
245B ALA 4.8 0.4 - - - +
246B SER* 3.5 42.8 + - - +
249B HIS* 3.8 21.5 - - + -
250B LYS* 4.8 3.9 - - + +
267B LEU* 5.5 5.5 - - + +
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Residues in contact with ALA 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 3.2 7.1 + - - +
196B ILE 3.8 2.5 - - - +
197B LYS 3.2 0.2 - - - -
198B THR* 1.3 72.5 - - - +
200B ALA* 1.3 65.8 + - - +
201B ILE 3.0 2.9 - - - -
202B SER* 3.0 17.8 + - - -
203B SER 3.0 20.8 + - - +
206B GLU* 3.9 13.7 - - + -
207B PHE* 3.8 21.3 - - + +
210B LEU* 3.5 32.5 - - + -
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Residues in contact with ALA 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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196B ILE* 2.9 17.9 + - + +
197B LYS 3.5 1.1 - - - +
199B ALA* 1.3 76.5 - - - +
201B ILE* 1.3 58.0 + - - +
207B PHE* 4.0 21.7 - - + -
269B TRP* 3.4 33.2 - - + -
316B ILE* 4.7 4.3 - - + -
368B LEU* 3.5 16.2 - - + +
371B ILE* 3.8 3.2 - - + -
372B GLY 2.8 24.5 + - - +
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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
----------------------------------------------------------
197B LYS* 3.3 16.4 + - + +
198B THR* 3.3 18.6 - - - +
200B ALA* 1.3 79.0 - - - +
202B SER* 1.3 58.3 + - - +
249B HIS* 4.0 20.6 + - + +
253B VAL* 5.8 0.2 - - + -
266B LEU* 3.5 35.4 - - + +
267B LEU* 4.1 17.5 - - + -
269B TRP* 3.9 28.5 - - + -
366B VAL* 5.3 0.9 - - + -
368B LEU* 4.0 18.4 - - + -
372B GLY 3.7 5.1 - - - +
374B PRO* 3.5 29.4 - - + +
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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