Contacts of the helix formed by residues 197 - 207 (chain B) in PDB entry 1LT8
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 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B GLU 4.8 2.5 - - - +
191B GLY* 4.2 2.0 - - - -
195B GLY 3.2 11.0 - - - +
196B VAL* 1.3 86.7 - - + +
198B PRO* 1.3 65.1 - - + +
199B GLY* 3.3 4.3 - - - +
200B GLU* 3.3 26.9 + - + +
201B ALA* 2.8 32.1 + - - +
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Residues in contact with PRO 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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187B ILE* 4.3 5.4 - - + -
188B GLY 3.5 17.3 - - - +
189B PRO* 3.4 31.0 - - + +
190B GLU 4.5 0.2 - - - -
191B GLY* 3.8 6.7 - - - +
197B PRO* 1.3 83.6 - - + +
199B GLY* 1.3 61.8 + - - +
201B ALA* 3.4 8.0 - - + +
202B ALA* 2.8 31.7 + - - +
227B THR* 4.0 10.1 - - + +
230B LEU* 3.8 23.8 - - + -
231B MET* 3.6 19.9 - - + +
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Residues in contact with GLY 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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197B PRO* 3.3 3.0 - - - +
198B PRO* 1.3 83.0 - - - +
200B GLU* 1.3 61.0 + - - +
202B ALA* 3.2 3.5 + - - +
203B VAL* 3.0 27.5 + - - +
230B LEU* 3.7 22.4 + - - +
231B MET* 3.9 2.7 - - - -
234B GLY* 3.8 15.9 - - - -
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Residues in contact with GLU 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 VAL* 3.6 16.5 - - + +
197B PRO* 3.3 29.2 + - + +
199B GLY* 1.3 74.2 - - - +
201B ALA* 1.3 63.7 + - - +
203B VAL* 3.1 12.0 + - + +
204B ARG* 2.9 56.6 + - + +
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Residues in contact with ALA 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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164B VAL* 3.4 39.1 - - + +
185B MET* 4.9 4.0 - - + -
187B ILE* 4.4 10.5 - - + -
196B VAL* 4.0 1.7 - - - +
197B PRO 2.8 19.3 + - - +
198B PRO* 3.4 10.5 - - + +
200B GLU* 1.3 77.7 - - - +
202B ALA* 1.3 62.8 + - - +
204B ARG 3.5 1.4 + - - -
205B LEU* 3.1 28.2 + - - +
231B MET* 4.7 4.5 - - + -
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Residues in contact with ALA 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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198B PRO 2.8 20.7 + - - +
199B GLY 3.5 4.5 - - - +
201B ALA* 1.3 69.9 - - - +
203B VAL* 1.3 66.7 + - - +
205B LEU* 2.9 22.9 + - - +
206B VAL* 3.0 17.3 + - - +
213B ILE* 3.9 11.4 - - + -
231B MET* 3.6 27.3 - - + +
235B LEU* 3.7 18.8 - - + -
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Residues in contact with VAL 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 GLY 3.0 21.4 + - - +
200B GLU* 3.2 14.1 - - + +
202B ALA* 1.3 77.2 - - - +
204B ARG* 1.3 57.6 + - + +
205B LEU 3.1 0.3 + - - -
206B VAL* 3.1 2.4 + - - +
207B LYS* 2.8 66.8 + - + +
234B GLY* 3.5 25.6 - - - +
235B LEU* 3.8 8.9 - - + +
238B ALA* 4.3 12.3 - - + -
240B LEU* 4.3 6.7 - - + +
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Residues in contact with ARG 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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164B VAL* 3.6 25.6 + - + +
165B GLU* 4.3 12.7 - - - +
168B VAL* 3.5 30.5 - - + +
196B VAL* 4.5 10.5 - - - +
200B GLU* 2.9 43.5 + - + +
201B ALA 4.0 4.3 - - - +
203B VAL* 1.3 80.2 - - + +
205B LEU* 1.3 60.1 + - - +
207B LYS* 4.0 10.3 - - + +
208B ALA* 3.3 22.0 + - - +
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Residues in contact with LEU 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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164B VAL* 4.6 2.2 - - + +
167B ALA* 4.0 33.9 - - + -
168B VAL* 4.4 9.9 - - + +
171B VAL* 4.1 6.3 - - + +
183B ALA* 4.1 32.5 - - + +
184B THR* 5.3 0.2 - - - -
185B MET* 3.9 28.0 - - + -
201B ALA 3.1 21.3 + - - +
202B ALA* 2.9 13.7 + - - +
204B ARG* 1.3 77.4 - - - +
206B VAL* 1.3 64.5 + - - +
208B ALA* 3.3 11.6 + - - +
210B ALA* 3.0 22.9 + - + +
213B ILE* 3.8 17.0 - - + -
214B GLY 5.3 1.3 - - - +
231B MET* 5.3 1.6 - - + -
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Residues in contact with VAL 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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202B ALA 3.0 13.2 + - - +
203B VAL 3.8 4.7 - - - +
205B LEU* 1.3 70.8 - - - +
207B LYS* 1.3 58.8 + - - +
208B ALA 2.9 4.7 - - - -
209B GLY* 2.8 19.9 + - - -
210B ALA 3.5 24.1 + - - +
213B ILE* 4.0 11.7 - - + -
235B LEU* 3.7 20.9 - - + -
240B LEU* 4.6 22.2 - - + -
241B LYS 4.0 16.4 - - - +
242B ALA* 3.9 15.0 - - + -
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Residues in contact with LYS 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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203B VAL* 2.8 38.8 + - + +
204B ARG* 4.3 9.2 - - + +
206B VAL* 1.3 76.7 - - - +
208B ALA* 1.3 56.8 + - - +
209B GLY 3.3 1.5 + - - -
238B ALA* 5.7 3.1 - - - +
240B LEU* 3.9 21.3 - - + -
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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