Contacts of the helix formed by residues 197 - 210 (chain D) in PDB entry 3T79
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 CYS 197 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLN* 3.0 5.4 - - - +
188D VAL 4.0 0.2 - - - -
189D PRO* 3.4 15.9 - - - -
190D ASN* 3.1 46.2 - - + +
193D SER 3.0 2.2 + - - +
194D PRO* 2.9 20.2 + - + +
195D PHE 4.1 1.6 - - - +
196D THR* 1.3 76.0 - - - +
198D PRO* 1.3 59.6 - - - +
199D ILE* 3.4 17.3 - - - -
200D PHE* 3.6 12.3 - - + -
201D THR* 2.6 28.2 + - - -
344D VAL* 4.8 2.7 - - - -
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Residues in contact with PRO 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.4 16.5 - - + +
144D GLN* 2.9 31.3 - - + +
145D TRP* 4.5 1.6 - - - +
148D ASN* 3.6 29.4 - - - +
187D LEU* 4.3 21.8 - - + -
188D VAL 4.5 4.3 - - - +
190D ASN* 5.4 1.6 - - + +
196D THR 3.6 7.9 - - - +
197D CYS* 1.3 85.5 - - - -
199D ILE* 1.3 63.8 + - + +
201D THR* 2.7 23.1 + - - +
202D MET* 3.0 15.9 + - - +
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Residues in contact with ILE 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU* 3.8 34.5 - - + -
187D LEU* 3.9 8.3 - - + +
188D VAL* 3.2 20.6 - - - +
189D PRO* 3.2 36.1 - - + -
197D CYS* 3.3 7.1 - - - -
198D PRO* 1.3 82.1 - - + +
200D PHE* 1.3 59.6 + - - +
202D MET* 3.3 8.1 + - + +
203D ALA* 2.9 27.0 + - - +
340D LEU* 4.7 6.3 - - + -
341D LEU* 3.8 12.2 - - + +
344D VAL* 3.8 23.3 - - + -
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D TRP* 3.6 31.0 - + - -
194D PRO* 3.1 43.3 - - + +
195D PHE* 4.8 7.0 - + - -
197D CYS* 3.4 9.0 + - + +
198D PRO 3.4 0.2 - - - -
199D ILE* 1.3 79.1 - - - +
201D THR* 1.3 54.1 + - - +
203D ALA* 3.0 5.7 + - - +
204D VAL* 2.9 46.0 + - + +
344D VAL* 3.7 23.7 - - + +
345D LEU* 4.1 16.8 - - + -
348D SER* 3.5 40.4 - - - +
349D LEU* 4.3 0.7 - - + -
352D LEU* 4.2 20.2 - - + -
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Residues in contact with THR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D TRP* 3.1 36.6 - - + -
137D LEU* 4.3 7.1 - - + +
140D LEU* 3.1 31.6 - - + -
141D LEU* 4.5 12.1 - - - +
144D GLN* 2.9 7.0 + - - +
197D CYS 2.6 15.7 + - - +
198D PRO* 2.7 19.3 + - - +
200D PHE* 1.3 77.0 - - - +
202D MET* 1.3 56.1 + - - -
204D VAL* 4.2 0.7 - - - +
205D TYR* 2.9 30.7 + - - +
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Residues in contact with MET 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.9 16.3 - - + +
161D LEU* 6.1 0.7 - - - -
164D LEU* 5.5 10.1 - - - -
177D LEU* 3.3 35.4 - - + -
198D PRO 3.0 15.3 + - - +
199D ILE* 3.6 12.1 - - + +
200D PHE 3.3 0.2 - - - -
201D THR* 1.3 75.9 - - - +
203D ALA* 1.3 58.5 + - - +
205D TYR* 4.0 4.9 - - - -
206D TYR* 2.9 66.4 + - + +
233D ILE* 5.1 8.7 - - - -
337D VAL* 6.1 1.8 - - - -
341D LEU* 3.5 18.8 - - + -
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE 2.9 14.5 + - - +
200D PHE* 3.0 10.3 + - - +
202D MET* 1.3 73.4 - - - +
204D VAL* 1.3 68.4 + - - +
206D TYR 3.1 2.1 + - - -
207D TYR* 3.0 20.3 + - - +
326D PHE* 3.4 9.1 - - - -
341D LEU* 3.6 39.0 - - + +
344D VAL* 5.0 0.7 - - + -
345D LEU* 3.7 22.9 - - + +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D TRP* 4.1 10.8 - - + -
137D LEU* 3.3 25.4 - - + -
200D PHE* 2.9 37.6 + - + +
201D THR 4.2 1.3 - - - +
203D ALA* 1.3 77.7 - - - +
205D TYR* 1.3 67.1 + - - +
207D TYR* 3.2 6.6 + - - +
208D LEU* 3.0 32.9 + - + +
345D LEU* 3.8 23.1 - - + +
352D LEU* 4.5 7.9 - - + -
359D HIS* 4.0 11.7 - - + -
361D ILE* 4.1 9.4 - - + -
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Residues in contact with TYR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLN* 3.9 21.8 - - + -
137D LEU* 3.9 28.9 - - + +
138D LYS* 2.4 49.0 + - + +
141D LEU* 4.5 12.3 - - + -
201D THR 2.9 22.9 + - - +
202D MET 3.8 2.5 - - - +
204D VAL* 1.3 76.4 - - - +
206D TYR* 1.3 92.0 + + - +
208D LEU* 2.8 24.7 + - + +
209D ARG* 2.9 30.7 + - + +
233D ILE 3.9 10.3 - - - -
234D ILE* 4.0 8.5 - - + -
235D ARG 3.5 9.4 + - - -
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Residues in contact with TYR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D LEU* 3.7 23.9 - - + +
202D MET* 2.9 42.0 + - + +
203D ALA 3.1 3.1 + - - +
205D TYR* 1.3 93.8 - + - +
207D TYR* 1.3 68.4 + - - +
209D ARG* 2.7 40.4 + - - -
210D PHE* 2.8 33.3 + + + -
233D ILE* 2.4 37.4 + - - +
326D PHE* 4.0 13.5 - - + -
337D VAL* 6.2 1.8 - - + -
338D PHE* 4.8 5.6 - + + -
341D LEU* 3.4 23.1 - - + -
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Residues in contact with TYR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ALA 3.0 12.1 + - - +
204D VAL* 3.5 9.6 - - - +
206D TYR* 1.3 78.3 - - - +
208D LEU* 1.3 60.7 + - + +
211D HIS* 2.7 58.4 + + + +
212D GLY 3.0 27.5 + - - -
213D VAL* 5.5 1.3 - - + -
222D TYR* 4.6 1.8 - - - -
325D LEU* 3.5 39.8 - - + +
326D PHE* 3.5 19.5 - + + -
345D LEU* 4.4 7.4 - - + -
361D ILE* 3.7 31.9 - - + -
364D ASP* 3.1 12.4 + - + -
366D SER* 3.7 4.7 - - - -
367D LEU* 3.4 23.6 - - + +
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D THR* 5.8 0.2 - - - +
133D CYS* 5.3 0.9 - - + -
134D GLN* 4.4 35.6 + - + +
137D LEU* 4.9 3.1 - - + -
204D VAL* 3.0 36.6 + - + +
205D TYR* 2.8 12.1 + - + +
207D TYR* 1.3 77.1 - - + +
209D ARG* 1.3 59.5 + - - +
212D GLY* 4.0 13.5 - - - +
213D VAL* 4.2 20.0 - - + -
217D TYR* 5.8 4.2 - - - -
218D LYS 5.6 0.2 - - - +
220D ASP* 5.2 0.2 - - - +
359D HIS* 4.2 9.2 - - + -
360D ASP* 4.0 25.8 - - + +
361D ILE* 4.1 22.7 - - + +
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Residues in contact with ARG 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLN* 4.6 8.1 - - - +
161D LEU* 5.1 0.6 - - - +
205D TYR* 2.9 37.7 + - + +
206D TYR* 2.7 49.1 + - - +
208D LEU* 1.3 74.1 - - - +
210D PHE* 1.3 80.7 + - + +
212D GLY* 4.0 3.3 + - - -
218D LYS 4.6 0.2 - - - +
219D GLY 4.3 0.2 - - - -
220D ASP* 2.5 42.3 + - - +
231D ILE* 3.7 25.3 - - - +
232D PRO* 3.0 23.9 + - - +
233D ILE 3.3 12.9 + - - -
234D ILE* 4.0 0.4 - - - +
235D ARG* 3.6 32.3 - - + +
239D LEU* 4.6 2.6 + - - +
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Residues in contact with PHE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D LEU* 5.5 3.1 - - + -
206D TYR* 2.8 55.1 + + + +
209D ARG* 1.3 99.9 - - + +
211D HIS* 1.3 67.2 + - - +
212D GLY 3.1 0.9 - - - -
219D GLY* 3.4 1.7 - - - -
220D ASP* 3.2 24.2 + - + -
221D GLY* 3.2 29.2 + - - +
222D TYR* 3.2 31.6 - + + -
224D ILE* 3.6 22.7 - - + -
225D LEU* 3.9 17.7 - - + -
231D ILE* 4.3 11.2 - - + -
338D PHE* 4.4 11.0 - + - -
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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