Contacts of the helix formed by residues 197 - 211 (chain H) in PDB entry 1TKK
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 ARG 197 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264D LEU* 6.2 4.0 - - - -
291D GLU* 4.5 25.2 + - - -
319D ARG* 5.3 13.3 - - - +
196H TRP* 1.3 75.6 - - - +
198H PRO* 1.3 71.6 - - + +
199H LYS 3.5 1.8 - - - +
200H GLU* 3.1 41.1 + - + +
201H ALA* 2.8 26.3 + - - +
222H VAL* 4.1 1.1 - - - -
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Residues in contact with PRO 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ASP* 6.2 0.2 - - - +
196H TRP 4.5 0.2 - - - +
197H ARG* 1.3 88.0 - - + +
199H LYS* 1.3 65.7 + - + +
201H ALA* 3.1 3.8 + - - +
202H VAL* 3.0 27.9 + - - +
222H VAL* 3.7 18.6 - - + -
226H ASP* 3.7 22.4 - - - +
229H GLY* 3.7 28.0 - - - +
232H LYS* 4.5 16.6 - - + +
233H VAL* 3.7 4.3 - - + +
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Residues in contact with LYS 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D THR* 2.6 29.7 + - - +
237D THR* 3.3 23.0 + - - -
238D ASP* 3.6 18.9 - - + +
239D THR 3.0 17.9 + - - +
240D PRO* 3.7 32.3 - - + -
263D ASP* 2.8 33.3 + - - +
197H ARG* 3.5 1.6 - - - +
198H PRO* 1.3 81.9 - - + +
200H GLU* 1.3 62.6 + - - +
202H VAL* 3.3 9.6 + - + +
203H THR* 3.1 29.4 + - - -
232H LYS* 4.7 16.6 - - + +
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Residues in contact with GLU 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ASP 5.7 0.5 - - - +
167H ASP* 5.7 0.3 - - - -
168H ILE* 3.7 38.9 + - + +
195H GLY 4.5 1.7 - - - +
196H TRP* 3.5 10.4 - - - -
197H ARG* 3.1 58.6 + - + +
199H LYS* 1.3 79.4 - - - +
201H ALA* 1.3 61.1 + - - +
203H THR* 3.5 5.6 + - - -
204H ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H TRP* 3.5 35.4 - - + +
197H ARG 2.8 15.2 + - - +
198H PRO* 3.1 8.9 + - + +
200H GLU* 1.3 70.8 - - - +
202H VAL* 1.3 60.4 + - - +
204H ALA* 3.7 1.7 - - - +
205H ILE* 2.8 38.9 + - + +
221H PRO* 4.1 7.6 - - + -
222H VAL* 4.9 0.4 - - + -
233H VAL* 3.9 19.3 - - + -
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Residues in contact with VAL 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ASP* 3.8 17.9 - - - +
198H PRO 3.0 20.9 + - - +
199H LYS* 3.6 11.0 - - + +
201H ALA* 1.3 76.8 - - - +
203H THR* 1.3 63.3 + - - +
205H ILE* 3.9 1.0 - - - +
206H ARG* 3.0 51.5 + - + +
232H LYS* 4.2 7.6 - - + +
233H VAL* 4.0 17.3 - - + +
236H ALA* 3.4 34.1 - - + -
237H THR* 4.4 8.7 - - + +
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Residues in contact with THR 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ASP* 4.2 17.7 + - - +
199H LYS 3.1 15.8 + - - -
200H GLU* 3.9 5.6 - - - -
202H VAL* 1.3 79.8 - - - +
204H ALA* 1.3 58.4 + - - +
206H ARG* 3.9 7.0 - - - +
207H LYS* 3.1 51.4 + - - +
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Residues in contact with ALA 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ILE* 3.3 41.7 - - + -
172H ILE* 4.3 7.4 - - + +
196H TRP* 5.1 1.6 - - + -
200H GLU 3.1 15.4 + - - +
201H ALA* 3.9 3.8 - - - +
202H VAL 3.3 0.2 - - - -
203H THR* 1.3 77.1 - - - +
205H ILE* 1.3 58.5 + - - +
207H LYS* 3.3 9.3 + - - +
208H MET* 3.1 41.1 + - + +
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Residues in contact with ILE 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196H TRP* 4.2 19.7 - - + -
201H ALA* 2.8 26.7 + - + +
204H ALA* 1.3 69.6 - - - +
206H ARG* 1.3 59.3 + - - +
208H MET* 3.4 11.3 + - + +
209H GLU* 3.0 27.5 + - - +
215H ILE* 6.1 1.1 - - + -
218H VAL* 4.1 17.3 - - + -
221H PRO* 5.1 0.2 - - + -
233H VAL* 3.6 29.6 - - + -
237H THR* 3.5 23.1 - - + -
239H THR* 3.4 30.1 - - + +
241H ILE* 4.0 13.2 - - + -
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Residues in contact with ARG 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ASP* 3.0 29.3 + - - -
202H VAL* 3.0 31.6 + - + +
203H THR* 3.9 6.5 - - - +
205H ILE* 1.3 73.2 - - - +
207H LYS* 1.3 60.4 + - - +
209H GLU* 3.4 18.2 + - - +
210H ASP* 2.9 46.9 + - - +
236H ALA* 2.9 35.2 + - - +
237H THR* 4.7 7.1 - - + +
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Residues in contact with LYS 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ILE* 6.1 3.2 - - - +
172H ILE* 4.0 24.3 - - + +
203H THR* 3.1 43.6 + - - +
204H ALA* 3.5 7.4 - - - +
205H ILE 3.3 0.4 - - - -
206H ARG* 1.3 78.8 - - - +
208H MET* 1.3 55.2 + - - +
210H ASP* 3.9 5.5 - - - +
211H ALA* 3.2 28.2 + - - +
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Residues in contact with MET 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H VAL* 6.5 0.2 - - + -
168H ILE* 4.9 0.4 - - + -
171H ASP* 5.5 1.8 - - + -
172H ILE* 4.1 21.8 - - + +
175H ILE* 4.2 15.3 - - + -
190H LEU* 3.6 26.5 - - + -
196H TRP* 3.9 28.9 - - + -
204H ALA* 3.1 33.2 + - + +
205H ILE* 3.7 13.5 - - + +
206H ARG 3.2 0.2 - - - -
207H LYS* 1.3 75.0 - - - +
209H GLU* 1.3 64.7 + - - +
211H ALA 3.3 5.0 + - - -
213H LEU* 3.1 50.4 + - + +
214H GLY 5.4 0.2 - - - -
215H ILE* 4.1 17.3 - - + -
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Residues in contact with GLU 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H ILE* 3.0 20.3 + - - +
206H ARG* 3.5 23.6 - - - +
208H MET* 1.3 75.1 - - - +
210H ASP* 1.3 63.9 + - - +
212H GLY* 3.2 16.6 + - - -
213H LEU 5.1 1.3 - - - +
214H GLY 5.6 2.4 + - - +
215H ILE* 5.5 5.3 - - + +
237H THR* 3.6 6.5 - - - -
238H ASP* 3.0 40.1 + - - +
239H THR* 2.7 28.1 + - - +
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Residues in contact with ASP 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H ARG* 2.9 34.8 + - - +
207H LYS* 3.9 5.9 - - - +
209H GLU* 1.3 82.9 - - - +
211H ALA* 1.3 56.9 + - - +
212H GLY 3.2 4.8 + - - -
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Residues in contact with ALA 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H ILE* 6.5 0.4 - - + -
176H GLN* 4.6 10.1 - - - +
207H LYS 3.2 18.0 + - - +
208H MET* 3.3 4.7 + - - +
209H GLU 3.3 0.4 - - - -
210H ASP* 1.3 74.7 - - - +
212H GLY* 1.3 63.2 + - - +
213H LEU* 3.2 24.1 + - + +
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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