Contacts of the helix formed by residues 191 - 210 (chain B) in PDB entry 3NTV
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 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 3.3 7.7 - - - +
190B ARG* 1.3 79.3 - - - +
192B ARG* 1.3 57.7 + - - +
193B ASN* 3.2 14.9 + - - +
194B VAL* 3.2 33.4 + - - +
195B ARG* 3.0 25.4 + - - +
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Residues in contact with ARG 192 (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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190B ARG 3.7 3.0 + - - -
191B SER* 1.3 72.0 + - - +
193B ASN* 1.4 63.8 + - - +
195B ARG* 3.3 20.6 + - + +
196B GLN* 3.0 34.5 + - + +
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Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B SER* 3.2 10.1 + - - +
192B ARG* 1.4 81.0 - - - +
194B VAL* 1.3 62.5 + - + +
196B GLN* 3.1 37.4 + - + +
197B MSE 3.2 17.1 - - - +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TYR* 4.0 14.4 - - + +
182B PHE* 3.7 39.3 - - + -
189B VAL* 3.7 23.3 - - + -
191B SER* 3.2 20.9 + - - +
193B ASN* 1.3 76.2 - - + +
195B ARG* 1.4 59.4 - - - +
197B MSE 3.3 6.7 + - - +
198B VAL* 2.9 29.0 + - + +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 3.3 35.2 + - + +
189B VAL* 3.4 28.3 + - + +
190B ARG* 2.9 26.8 + - - +
191B SER 3.0 15.3 + - - +
192B ARG* 3.3 35.8 + - + +
194B VAL* 1.4 74.1 - - - +
196B GLN* 1.4 64.5 + - - +
198B VAL 3.4 0.2 + - - -
199B LYS* 3.1 21.5 + - - +
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Residues in contact with GLN 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 ARG* 3.0 19.6 + - + +
193B ASN* 3.1 36.6 + - - +
195B ARG* 1.4 74.9 - - - +
197B MSE 1.4 63.7 + - - +
199B LYS* 3.6 9.2 + - - +
200B LYS* 3.1 27.9 + - - +
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Residues in contact with MSE 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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151B ALA* 3.3 42.2 - - + +
179B TYR* 3.6 34.1 - - + +
193B ASN* 3.2 15.7 + - + +
194B VAL 3.3 9.2 + - - +
195B ARG 3.2 0.6 - - - -
196B GLN* 1.4 82.1 - - + +
198B VAL* 1.3 66.2 + - - +
200B LYS* 3.2 28.9 + - + -
201B VAL* 3.1 23.7 + - - +
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Residues in contact with VAL 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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179B TYR* 3.9 11.7 - - + -
182B PHE* 3.3 49.6 - - + +
183B VAL* 3.6 21.3 - - + +
186B ILE* 3.6 24.5 - - + -
189B VAL* 4.0 7.0 - - + -
194B VAL* 2.9 21.4 + - + +
195B ARG 3.4 0.2 + - - -
197B MSE 1.3 73.7 - - - +
199B LYS* 1.3 51.0 + - - +
201B VAL* 3.3 2.1 + - - +
202B GLN* 2.8 44.6 + - - +
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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
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186B ILE* 3.8 8.4 - - + +
195B ARG 3.1 17.0 + - - +
196B GLN* 3.6 9.4 - - - +
197B MSE 3.3 0.2 - - - -
198B VAL* 1.3 75.7 - - - +
200B LYS* 1.3 56.5 + - - +
202B GLN* 3.7 12.5 - - - +
203B ASP* 2.9 56.8 + - - +
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Residues in contact with LYS 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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150B ALA 3.8 12.1 - - - -
151B ALA 3.0 23.1 + - - -
153B ALA* 2.7 37.7 + - - +
154B GLN* 5.4 1.3 - - - -
155B SER* 4.3 8.1 - - - +
196B GLN 3.1 14.5 + - - +
197B MSE 3.2 30.7 + - + +
199B LYS* 1.3 74.1 - - - +
201B VAL* 1.3 57.8 + - - +
203B ASP* 3.3 8.5 + - - +
204B TYR* 2.9 28.3 + - - +
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Residues in contact with VAL 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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150B ALA* 3.8 23.3 - - + +
151B ALA* 3.8 22.7 - - + +
176B ASN 3.8 6.1 - - - +
177B VAL* 3.4 37.0 - - - +
179B TYR* 4.0 11.0 - - + -
183B VAL* 3.7 14.8 - - + -
197B MSE 3.1 17.9 + - + +
198B VAL 3.8 2.9 - - - +
200B LYS* 1.3 71.5 - - - +
202B GLN* 1.3 65.2 + - - +
204B TYR* 3.2 7.3 + - - +
205B ASN* 2.9 25.3 + - - +
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Residues in contact with GLN 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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28A TYR* 3.9 17.3 + - + +
32A LEU* 5.7 0.2 - - - +
183B VAL* 2.8 39.5 + - + +
184B SER 5.2 0.2 - - - -
185B ASP* 5.0 0.6 - - - +
186B ILE* 4.1 22.5 - - - +
198B VAL* 2.8 36.7 + - + +
199B LYS* 3.7 15.8 - - - +
201B VAL* 1.3 72.6 - - - +
203B ASP* 1.4 64.6 + - - +
205B ASN* 3.4 2.3 + - - +
206B GLU* 3.2 25.1 + - - +
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Residues in contact with ASP 203 (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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156B LYS* 4.4 15.0 + - - +
199B LYS* 2.9 50.9 + - - +
200B LYS* 3.6 8.0 - - - +
202B GLN* 1.4 75.4 - - - +
204B TYR* 1.3 61.0 + - - +
206B GLU* 3.5 15.4 + - - +
207B TRP* 3.0 30.7 + - - +
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Residues in contact with TYR 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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148B ILE* 4.4 7.3 - - + +
150B ALA* 4.0 10.3 - - + +
155B SER* 3.5 44.9 - - - +
156B LYS* 3.6 23.3 - - + +
159B PHE* 3.6 25.5 - + + -
174B THR* 2.8 42.7 + - + +
177B VAL* 4.6 0.2 - - + -
200B LYS 2.9 14.5 + - - +
201B VAL* 3.4 10.3 - - - +
203B ASP* 1.3 76.6 - - - +
205B ASN* 1.3 65.6 + - - +
207B TRP* 3.3 11.6 + + - +
208B LEU* 2.8 58.1 + - + +
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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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28A TYR* 3.1 32.7 + - - +
29A LEU* 5.4 0.2 - - - +
32A LEU* 3.9 13.2 - - + -
177B VAL* 2.9 51.5 + - - +
183B VAL* 4.2 0.4 - - - +
201B VAL* 2.9 21.3 + - - +
202B GLN 3.8 0.7 - - - +
203B ASP 3.4 0.2 - - - -
204B TYR* 1.3 82.6 - - - +
206B GLU* 1.3 57.7 + - - +
208B LEU* 3.4 2.8 + - - +
209B ILE* 3.0 31.7 + - - +
218B PHE* 3.6 19.3 - - + -
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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
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32A LEU* 4.2 10.7 - - + +
202B GLN 3.2 14.0 + - - +
203B ASP* 3.8 16.8 - - - +
205B ASN* 1.3 74.6 - - - +
207B TRP* 1.3 66.1 + - - +
209B ILE* 3.4 20.2 - - - +
210B LYS* 3.4 38.4 + - + +
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Residues in contact with TRP 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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156B LYS* 3.6 49.6 - - + +
159B PHE* 3.4 50.3 - + + -
160B GLU* 3.7 31.2 + - + -
203B ASP 3.0 18.3 + - - +
204B TYR* 3.6 11.2 - + - +
206B GLU* 1.3 74.9 - - - +
208B LEU* 1.3 80.1 + - + +
210B LYS* 3.2 14.7 + - - +
211B GLN* 3.2 48.9 + - + +
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Residues in contact with LEU 208 (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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159B PHE* 3.5 39.5 - - + -
174B THR* 4.4 2.9 - - - +
204B TYR* 2.8 44.8 + - + +
205B ASN 3.7 3.4 - - - +
207B TRP* 1.3 82.3 - - + +
209B ILE* 1.3 61.7 + - - +
211B GLN* 3.1 24.5 + - + +
214B TYR* 5.1 2.7 - - + +
216B THR* 3.8 24.1 + - + +
218B PHE* 4.2 7.0 - - + -
226B ALA* 4.1 14.6 - - + -
228B SER* 3.6 23.8 - - - +
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Residues in contact with ILE 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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32A LEU* 3.5 34.5 - - + +
33A HIS* 4.9 2.5 - - + -
35A HIS* 4.1 29.5 - - + +
36A GLN* 3.6 13.9 - - - +
205B ASN 3.0 16.3 + - - +
206B GLU* 3.4 17.0 - - - +
208B LEU* 1.3 76.0 - - - +
210B LYS* 1.3 59.7 + - + +
211B GLN 3.5 2.8 + - - +
214B TYR 5.4 2.3 - - - +
216B THR* 3.5 34.5 - - - +
218B PHE* 3.7 25.6 - - + -
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Residues in contact with LYS 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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35A HIS* 3.4 38.3 + - + +
206B GLU* 3.4 44.1 + - + +
207B TRP* 3.2 7.1 + - - +
208B LEU 3.1 1.0 - - - -
209B ILE* 1.3 81.0 - - + +
211B GLN* 1.4 64.5 + - - +
212B PRO* 3.1 11.8 - - - +
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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