Contacts of the helix formed by residues 187 - 205 (chain H) in PDB entry 3TKR
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 187 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLU* 3.7 30.5 + - - -
193B ARG* 3.7 11.3 - - - +
211B GLY* 4.4 9.0 - - - +
94H PHE* 4.5 2.5 - - - -
186H ARG* 1.3 77.6 - - - +
188H VAL* 1.3 62.7 + - - +
189H ASP* 3.2 10.0 + - - +
190H GLU* 2.9 23.0 + - - +
191H THR* 2.8 27.2 + - - -
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Residues in contact with VAL 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 5.5 1.6 - - + -
211B GLY* 5.4 2.2 - - - +
93H ALA* 3.7 40.8 - - + +
94H PHE* 3.8 25.3 - - + +
97H ARG* 3.7 38.1 - - + +
101H PHE* 3.9 24.9 - - + -
186H ARG 4.2 0.8 + - - -
187H SER* 1.3 71.6 + - - +
189H ASP* 1.3 58.1 + - - +
191H THR* 3.2 2.6 + - - -
192H LEU* 2.9 31.9 + - + +
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Residues in contact with ASP 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLY* 6.2 0.2 - - - -
97H ARG* 2.8 39.4 + - - -
187H SER* 3.2 7.0 + - - +
188H VAL* 1.3 76.9 + - - +
190H GLU* 1.3 62.4 + - - +
192H LEU* 3.3 8.6 + - - +
193H ARG* 3.0 23.0 + - - +
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Residues in contact with GLU 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 6.2 0.2 - - - +
186B ARG* 5.3 0.5 - - - -
187B SER* 3.6 19.3 + - - -
190B GLU* 3.8 32.0 - - + +
187H SER* 2.9 19.3 + - - +
189H ASP* 1.3 76.8 - - - +
191H THR* 1.3 63.2 + - - +
193H ARG* 2.9 46.5 + - - +
194H LEU* 3.0 40.2 + - + +
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Residues in contact with THR 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H VAL* 3.7 40.4 - - + -
94H PHE* 3.6 20.8 - - + -
101H PHE* 4.0 3.1 - - + -
165H LEU* 3.7 13.8 - - + +
167H ILE* 4.3 11.0 - - + -
186H ARG* 5.6 0.5 - - - +
187H SER 2.8 22.2 + - - -
188H VAL 3.2 4.2 + - - -
190H GLU* 1.3 77.4 - - - +
192H LEU* 1.3 58.2 + - - +
194H LEU* 3.3 11.0 + - - +
195H VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ARG* 3.5 15.5 - - - +
100H GLU* 3.3 57.4 - - + +
101H PHE* 3.4 30.1 - - + -
104H ILE* 4.3 10.3 - - + -
188H VAL* 2.9 27.4 + - + +
189H ASP* 3.7 5.8 - - - +
191H THR* 1.3 73.7 - - - +
193H ARG* 1.3 65.7 + - - +
195H VAL* 3.2 2.7 + - - +
196H GLN* 2.9 41.7 + - - +
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Residues in contact with ARG 193 (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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184B VAL* 5.1 4.6 - - - +
185B GLY 3.2 26.1 + - - -
186B ARG* 3.6 3.6 - - - +
187B SER* 3.6 19.0 - - - -
189H ASP 3.0 13.8 + - - +
190H GLU* 2.9 46.1 + - - +
192H LEU* 1.3 74.9 - - - +
194H LEU* 1.3 69.2 + - - +
196H GLN* 3.4 12.2 + - - +
197H ALA* 2.9 30.6 + - - +
209H PRO 4.7 0.2 + - - -
211H GLY* 3.6 7.0 - - - -
212H TRP* 2.9 55.8 + - - +
213H LYS* 4.0 30.3 - - + +
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Residues in contact with LEU 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 6.0 0.9 - - + -
180B ASN* 3.7 28.9 - - - +
184B VAL* 3.9 12.3 - - + -
165H LEU* 6.2 0.7 - - + -
167H ILE* 3.6 19.3 - - + -
176H GLN* 3.8 32.3 - - + +
178H THR* 4.8 3.4 - - - +
190H GLU* 3.0 38.5 + - + +
191H THR* 3.6 4.5 - - - +
193H ARG* 1.3 91.7 - - - +
195H VAL* 1.3 65.3 + - - +
197H ALA* 3.2 3.6 + - - +
198H PHE* 3.0 34.7 + - + -
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Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TYR* 4.2 8.2 - - + -
75H VAL* 3.9 27.4 - - + -
101H PHE* 4.6 3.6 - - + -
104H ILE* 3.9 16.4 - - + -
106H THR* 3.4 28.7 - - + +
167H ILE* 4.1 21.1 - - + -
191H THR* 2.9 23.3 + - + +
192H LEU* 3.2 5.6 + - - +
194H LEU* 1.3 75.6 - - - +
196H GLN* 1.3 58.0 + - - +
198H PHE* 3.4 3.6 + - - +
199H GLN* 3.0 37.7 + - - +
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Residues in contact with GLN 196 (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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100H GLU 5.6 0.6 + - - -
104H ILE* 3.9 26.0 - - + +
192H LEU* 2.9 34.7 + - - +
193H ARG* 3.6 12.1 + - - +
195H VAL* 1.3 76.3 - - - +
197H ALA* 1.3 57.2 + - - +
199H GLN* 3.4 9.5 + - - +
200H TYR* 2.9 29.6 + - - +
212H TRP* 3.7 13.6 - - + -
214H PRO* 3.3 31.7 - - + +
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Residues in contact with ALA 197 (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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184B VAL* 3.6 30.5 - - + -
193H ARG* 2.9 21.6 + - - +
194H LEU* 3.2 3.3 + - - +
196H GLN* 1.3 77.5 - - - +
198H PHE* 1.3 57.1 + - - +
200H TYR* 3.2 1.7 + - - +
201H THR* 2.9 33.3 + - - +
208H CYS* 3.8 8.2 - - + -
212H TRP* 3.4 24.4 - - + -
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Residues in contact with PHE 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASN* 4.9 1.8 - - + -
181B ASP* 3.7 29.2 - - + -
183B PRO* 4.3 3.6 - - + -
184B VAL* 3.5 34.8 - - + -
73H TYR* 3.3 23.6 - - + +
167H ILE* 4.8 7.2 - - + -
175H ARG* 3.3 56.3 - - + -
176H GLN* 3.9 21.3 - - + -
194H LEU* 3.0 34.6 + - + +
195H VAL 4.0 0.2 - - - +
197H ALA* 1.3 74.0 - - - +
199H GLN* 1.3 60.5 + - - +
201H THR* 3.2 4.6 + - - -
202H ASP* 2.9 34.5 + - - -
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Residues in contact with GLN 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TYR* 3.6 32.1 - - + +
104H ILE* 2.8 44.6 + - - +
105H ASN* 4.4 6.5 + - - +
106H THR* 3.5 11.5 + - - -
195H VAL* 3.0 24.7 + - + +
196H GLN* 3.8 7.2 - - - +
198H PHE* 1.3 77.1 - - - +
200H TYR* 1.3 62.5 + - - +
202H ASP* 3.4 7.9 + - - +
203H LYS* 3.0 24.6 + - - +
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Residues in contact with TYR 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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196H GLN 2.9 17.4 + - - +
197H ALA* 3.2 4.7 + - - +
199H GLN* 1.3 78.1 - - - +
201H THR* 1.3 60.1 + - - +
203H LYS* 3.1 2.5 + - - -
204H HIS* 2.9 76.9 + + + +
206H GLU* 4.8 7.3 - - + -
208H CYS* 4.3 7.4 - - - -
212H TRP* 3.9 24.2 - + + -
216H SER 5.9 0.7 - - - -
218H THR* 3.5 40.6 + - + +
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Residues in contact with THR 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B PRO* 3.5 41.0 - - + +
184B VAL* 4.2 1.7 - - + +
175H ARG* 4.8 0.2 + - - -
197H ALA 2.9 18.5 + - - +
198H PHE* 3.2 14.7 + - - -
200H TYR* 1.3 72.5 - - - +
202H ASP* 1.3 72.5 + - - +
205H GLY* 3.1 21.8 + - - +
206H GLU 3.2 25.4 - - - +
207H VAL* 3.9 0.7 - - - -
208H CYS* 3.4 21.3 - - - -
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Residues in contact with ASP 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TYR* 2.6 32.2 + - - -
169H ASP* 4.5 1.8 - - - +
170H ASP* 4.2 7.1 - - - +
175H ARG* 3.0 27.3 + - - -
198H PHE 2.9 21.7 + - - +
199H GLN* 3.4 7.3 - - - +
201H THR* 1.3 80.8 + - - +
203H LYS* 1.3 61.8 + - - +
205H GLY 4.6 1.0 + - - -
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Residues in contact with LYS 203 (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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199H GLN 3.0 17.4 + - - +
200H TYR* 3.1 4.4 + - - +
202H ASP* 1.3 80.9 - - + +
204H HIS* 1.3 89.7 + - + +
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Residues in contact with HIS 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H TYR* 2.9 73.6 + + + +
203H LYS* 1.3 112.5 + - + +
205H GLY* 1.3 63.1 + - - +
206H GLU* 3.1 16.0 + - + +
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Residues in contact with GLY 205 (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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201H THR 3.1 17.6 + - - -
202H ASP 4.6 0.6 + - - -
203H LYS 3.7 1.2 - - - -
204H HIS* 1.3 77.2 - - - +
206H GLU* 1.3 61.5 + - - +
207H VAL* 5.1 1.3 - - - +
221H PRO* 3.5 22.7 - - - +
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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
------------------------------------------------------------
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