Contacts of the helix formed by residues 190 - 205 (chain B) in PDB entry 3ROT
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 ASP 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A SER* 3.3 28.4 + - - -
33A GLN* 3.5 10.2 - - - +
59A ALA 5.6 0.9 - - - +
61A PRO* 5.3 3.5 - - - +
187B VAL 4.7 0.4 + - - -
188B GLY* 3.7 0.6 - - - -
189B THR* 1.3 77.8 + - - +
191B PRO* 1.3 60.0 - - - +
192B ASN* 3.6 13.1 + - - +
193B GLN* 2.8 70.1 + - - +
194B VAL* 3.0 12.5 + - - +
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Residues in contact with PRO 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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32A SER 3.9 18.6 - - - +
33A GLN* 4.0 24.2 - - - +
35A PRO* 6.2 0.4 - - + -
38A THR* 3.2 26.2 - - + -
189B THR 3.2 11.6 - - - +
190B ASP* 1.3 83.6 - - - +
192B ASN* 1.3 62.2 + - - +
194B VAL* 3.2 2.5 + - + +
195B GLN* 3.0 29.1 + - - +
221B PRO* 3.6 28.0 - - + +
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Residues in contact with ASN 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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32A SER* 5.4 1.3 + - - +
38A THR* 3.8 6.9 - - + +
41A PHE* 3.9 34.6 - - + +
45A LYS* 2.9 35.1 + - - +
57A ILE* 4.2 22.0 - - - +
190B ASP* 3.2 12.6 + - - +
191B PRO* 1.3 78.7 - - - +
193B GLN* 1.3 61.7 + - - +
195B GLN* 3.5 7.1 + - - +
196B SER* 3.1 29.5 + - - -
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Residues in contact with GLN 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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187B VAL 4.1 11.9 - - - +
188B GLY* 5.2 4.2 - - - -
189B THR 5.6 0.2 + - - -
190B ASP* 2.8 36.4 + - + +
192B ASN* 1.3 81.7 - - - +
194B VAL* 1.3 66.8 + - - +
196B SER* 3.3 6.9 + - - +
197B ARG* 2.9 35.2 + - + +
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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
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155B LEU* 4.9 1.8 - - + -
187B VAL* 3.5 40.8 - - + +
188B GLY 3.8 13.7 - - - +
189B THR 4.4 2.7 - - - -
190B ASP 3.0 16.9 + - - +
191B PRO 3.2 5.8 + - - +
193B GLN* 1.3 78.2 - - - +
195B GLN* 1.3 63.6 + - - +
197B ARG* 3.4 1.6 + - - +
198B VAL* 3.0 35.9 + - + +
217B GLN 4.6 4.5 - - - +
218B ALA* 3.8 24.5 - - + +
221B PRO* 3.8 16.6 - - + -
222B LEU* 4.9 3.1 - - + +
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Residues in contact with GLN 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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38A THR* 4.0 15.2 - - - +
42A GLN* 5.1 0.4 + - - +
45A LYS* 4.7 9.9 + - - +
191B PRO 3.0 19.7 + - - +
192B ASN* 3.8 7.6 - - - +
194B VAL* 1.3 76.8 - - - +
196B SER* 1.3 57.6 + - - +
198B VAL* 3.4 1.7 + - - +
199B LYS* 2.9 37.7 + - + +
221B PRO* 2.9 36.5 + - + +
224B GLN* 3.3 24.8 + - - +
225B MSE 3.6 25.0 - - - +
232B TYR* 3.4 27.9 - - - -
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Residues in contact with SER 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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45A LYS* 4.7 11.6 - - - +
192B ASN* 3.1 17.0 + - - -
193B GLN* 3.3 13.5 + - - +
194B VAL 3.4 0.2 - - - -
195B GLN* 1.3 73.4 - - - +
197B ARG* 1.3 64.2 + - - +
199B LYS* 3.8 9.3 - - - +
200B SER* 2.8 37.0 + - - -
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Residues in contact with ARG 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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185B LEU* 3.4 51.3 - - + +
186B ASP* 3.0 38.0 + - - +
187B VAL* 4.3 11.0 - - + +
193B GLN* 2.9 28.5 + - + +
194B VAL 3.8 3.6 - - - +
196B SER* 1.3 80.9 + - - +
198B VAL* 1.3 57.2 + - - +
200B SER* 3.6 7.1 - - - -
201B TYR* 3.1 20.6 + - - +
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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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153B LEU* 4.6 3.4 - - + -
155B LEU* 3.8 36.6 - - + -
185B LEU* 4.8 1.3 - - - -
187B VAL* 4.6 2.2 - - + -
194B VAL* 3.0 25.3 + - + +
195B GLN 3.7 3.6 - - - +
197B ARG* 1.3 75.2 - - - +
199B LYS* 1.3 65.4 + - - +
201B TYR* 3.2 5.3 + - - +
202B PHE* 3.0 35.5 + - + -
211B ILE* 4.8 1.8 - - + -
222B LEU* 4.5 7.6 - - + -
225B MSE 4.1 12.1 - - + -
234B PHE* 3.8 27.4 - - + -
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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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42A GLN* 3.5 28.9 + - - +
45A LYS* 5.4 3.7 - - - +
49A GLU* 4.8 8.3 + - - -
195B GLN* 2.9 30.6 + - + +
196B SER* 3.9 7.0 - - - +
198B VAL* 1.3 74.8 - - - +
200B SER* 1.3 61.4 - - - +
202B PHE* 3.5 1.6 + - - +
203B LYS* 3.2 30.1 + - + +
225B MSE 3.7 22.7 - - - -
232B TYR 2.8 30.0 + - - +
233B ASP* 4.1 15.0 + - - +
234B PHE* 4.1 16.2 - - + -
236B TYR* 4.9 1.5 + - - -
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Residues in contact with SER 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 SER* 2.8 25.6 + - - -
197B ARG* 3.6 7.9 - - - -
199B LYS* 1.3 77.9 - - - +
201B TYR* 1.3 62.1 + - - +
203B LYS* 3.4 11.6 + - - +
204B ILE* 3.4 27.4 + - - +
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Residues in contact with TYR 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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151B ARG* 3.3 19.5 + - - -
152B ALA 4.3 2.8 + - - -
153B LEU* 3.6 46.9 - - + -
183B GLU* 3.3 41.0 + - + +
185B LEU* 4.4 17.7 - - + -
197B ARG 3.1 11.9 + - - +
198B VAL 3.2 7.8 + - - +
200B SER* 1.3 79.5 - - - +
202B PHE* 1.3 61.9 + + - +
204B ILE* 3.2 6.1 + - - -
205B HIS* 2.8 46.9 + + + -
208B THR* 3.3 26.5 - - + -
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Residues in contact with PHE 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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153B LEU* 3.9 16.8 - - + -
198B VAL* 3.0 23.0 + - + +
199B LYS 4.1 2.5 - - - +
200B SER 3.4 0.2 - - - -
201B TYR* 1.3 80.7 - + - +
203B LYS* 1.3 59.6 + - - +
204B ILE 3.2 0.2 - - - -
205B HIS 3.9 7.6 - - - -
206B PRO* 2.8 35.8 - - + +
208B THR* 3.6 42.4 - - + -
211B ILE* 3.5 34.8 - - + -
234B PHE* 3.8 13.0 - + + -
236B TYR* 3.3 57.3 + + + +
238B PRO* 4.0 7.6 - - + -
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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
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199B LYS* 3.2 20.8 + - + +
200B SER* 3.8 8.5 - - - +
201B TYR 3.2 0.4 - - - -
202B PHE* 1.3 77.1 - - - +
204B ILE* 1.3 63.9 + - + +
206B PRO* 3.6 10.4 - - - +
236B TYR* 4.1 13.0 - - - +
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B SER* 3.4 19.1 - - - +
201B TYR* 3.2 5.5 + - + +
203B LYS* 1.3 81.6 - - + +
205B HIS* 1.3 85.1 + - + +
206B PRO* 3.3 8.4 - - - +
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Residues in contact with HIS 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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151B ARG* 2.9 44.5 + - - +
183B GLU* 3.9 14.5 + - - -
201B TYR* 2.8 29.2 + + + +
202B PHE* 3.2 8.8 - - - +
204B ILE* 1.3 106.0 - - + +
206B PRO* 1.3 57.3 - - - +
207B GLU* 2.8 14.0 + - + +
208B THR* 2.9 28.9 + - - +
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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