Contacts of the helix formed by residues 85 - 97 (chain F) 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 PHE 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C PHE* 3.8 34.1 - + - -
207D VAL* 4.1 16.4 - - + -
219D ILE* 3.4 25.3 - - + +
221D PRO* 3.4 41.7 - - + -
222D ASP* 3.5 28.9 - - - -
223D PRO* 4.0 2.0 - - + -
226D LYS* 3.9 25.4 - - + -
230D PHE* 3.7 3.9 - - - -
83F PHE 4.8 1.6 - - - -
84F THR* 1.3 96.9 + - + +
86F VAL* 1.3 67.8 + - - +
87F CYS 3.3 0.7 - - - -
88F PRO* 3.2 14.6 - - - +
89F THR* 3.5 2.8 - - - +
163F ARG* 5.7 0.2 - - - +
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D VAL* 3.6 30.7 - - + -
208D CYS 3.6 19.3 - - - +
209D PRO 4.7 0.2 - - - -
219D ILE* 4.6 2.0 - - + -
85F PHE* 1.3 73.7 - - + +
87F CYS* 1.3 67.3 + - - +
89F THR* 2.8 30.3 + - - +
90F GLU* 3.1 11.4 + - + +
163F ARG* 3.3 31.6 - - - +
182F LEU 4.2 3.1 - - - +
183F PRO 4.0 5.6 - - - +
185F GLY* 3.5 31.4 - - - -
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Residues in contact with CYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F TYR* 3.6 19.2 - - + +
80F PRO* 3.5 22.2 - - - -
81F LEU 3.6 18.8 - - - +
84F THR* 3.4 17.7 - - - +
86F VAL* 1.3 75.1 - - - +
88F PRO* 1.3 70.4 - - + +
90F GLU* 3.0 16.1 + - - +
91F ILE* 3.1 16.7 + - - +
122F TRP* 4.0 3.6 - - + -
163F ARG* 3.2 28.7 - - - +
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Residues in contact with PRO 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.6 18.4 - - + -
84F THR 3.4 22.4 - - - +
85F PHE 3.2 18.2 - - - +
87F CYS* 1.3 95.1 - - + +
89F THR* 1.3 55.5 + - - +
91F ILE* 3.3 0.3 + - - +
92F ILE* 2.9 38.3 + - + +
122F TRP* 3.4 28.7 - - + -
130F GLY 4.0 10.1 - - - +
131F GLY 4.6 4.3 - - - +
132F LEU* 3.8 12.1 - - + -
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Residues in contact with THR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D PRO* 3.4 11.7 - - + +
210D ALA* 2.9 24.4 + - - +
219D ILE* 3.8 7.2 - - + -
229D TYR* 3.6 35.7 - - + +
230D PHE* 4.1 6.3 - - + -
233D LEU* 6.0 0.2 - - + -
85F PHE 3.5 17.9 - - - +
86F VAL 2.8 15.7 + - - -
88F PRO* 1.3 76.5 - - - +
90F GLU* 1.3 57.4 + - - +
92F ILE* 4.1 5.9 - - - +
93F ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ALA* 3.8 20.9 - - + -
77F PHE* 4.6 12.3 - - + -
79F TYR* 4.3 1.6 - - - +
86F VAL* 3.8 20.4 - - + +
87F CYS* 3.0 8.7 + - - +
89F THR* 1.3 75.6 + - - +
91F ILE* 1.3 64.5 + - - +
93F ALA* 3.3 1.0 + - - +
94F PHE* 3.1 37.0 + - + -
163F ARG* 2.9 22.0 + - - -
185F GLY* 3.3 3.6 - - - -
186F ARG* 2.7 67.0 + - + +
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Residues in contact with ILE 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F PHE* 4.2 22.0 - - + -
79F TYR* 3.5 31.4 - - + +
87F CYS 3.1 13.2 + - - +
88F PRO 3.9 4.7 - - - +
90F GLU* 1.3 75.8 - - - +
92F ILE* 1.3 59.3 + - - +
94F PHE* 4.0 0.5 - - - -
95F GLY* 2.9 26.2 + - - -
110F ALA* 4.5 2.7 - - + -
122F TRP* 3.5 33.7 - - + -
132F LEU* 3.9 22.4 - - + -
135F ILE* 3.9 19.3 - - + +
137F ILE* 4.0 5.8 - - + +
139F LEU* 4.2 13.2 - - + -
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Residues in contact with ILE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 5.7 6.3 - - + -
234D ASN* 6.1 1.3 - - - +
88F PRO* 2.9 25.5 + - + +
89F THR* 4.1 5.2 - - - +
91F ILE* 1.3 74.2 - - + +
93F ALA* 1.3 62.3 + - - +
95F GLY* 4.4 1.1 - - - +
96F ASP* 2.8 50.8 + - - +
127F ARG* 3.4 43.3 - - + +
131F GLY 3.8 18.4 - - - +
132F LEU* 4.0 14.8 - - + +
135F ILE* 5.0 3.8 - - + -
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ALA* 3.8 15.9 - - + -
89F THR 2.9 21.3 + - - +
90F GLU 3.7 4.3 - - - +
92F ILE* 1.3 80.3 - - - +
94F PHE* 1.3 63.4 + - + +
96F ASP* 4.2 2.4 - - - +
97F ARG* 3.5 24.8 + - - +
188F VAL* 3.7 20.0 - - + +
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Residues in contact with PHE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F VAL* 4.4 6.1 - - + -
77F PHE* 3.8 24.5 - + + -
90F GLU* 3.1 30.8 + - + +
91F ILE 4.1 0.7 - - - +
93F ALA* 1.3 76.4 - - - +
95F GLY* 1.3 63.5 + - - +
97F ARG* 3.0 5.8 + - - -
98F LEU* 3.0 23.9 + - - +
101F PHE* 3.6 36.8 - + - -
108F VAL* 4.3 12.1 - - + -
137F ILE* 3.6 18.3 - - + +
165F LEU* 3.8 19.7 - - + -
186F ARG* 5.2 10.5 - - + -
187F SER 4.6 1.1 - - - -
188F VAL* 3.9 22.9 - - + -
191F THR* 3.5 31.2 - - + -
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Residues in contact with GLY 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE 2.9 16.1 + - - -
92F ILE 3.2 1.1 + - - -
94F PHE* 1.3 78.2 - - - +
96F ASP* 1.3 63.6 + - - +
97F ARG 3.1 1.0 + - - -
98F LEU* 3.2 18.3 + - - +
135F ILE* 3.8 15.9 - - - -
136F ARG* 5.4 6.2 + - - +
137F ILE* 3.3 18.5 - - - +
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Residues in contact with ASP 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ILE* 2.8 27.2 + - + +
93F ALA* 4.4 3.1 - - - +
95F GLY* 1.3 74.9 - - - +
97F ARG* 1.3 64.0 + - + +
98F LEU 3.5 0.4 - - - -
127F ARG* 2.8 43.6 + - - -
135F ILE* 5.8 0.5 - - - +
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Residues in contact with ARG 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ALA* 3.5 14.9 + - - +
94F PHE 3.0 5.9 + - - +
96F ASP* 1.3 83.3 - - + +
98F LEU* 1.3 64.9 + - - +
99F GLU 3.2 2.9 - - - -
100F GLU* 2.8 61.6 + - + +
101F PHE* 3.7 6.9 - - + -
188F VAL* 3.6 40.0 - - + +
189F ASP* 2.8 31.7 + - - +
192F LEU* 4.4 11.9 - - - +
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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