Contacts of the helix formed by residues 85 - 97 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D PHE* 3.6 35.9 - + - -
207E VAL* 4.1 11.4 - - + -
219E ILE* 3.3 31.5 - - + +
221E PRO* 3.4 40.2 - - + -
222E ASP* 3.4 26.7 - - - -
223E PRO* 4.0 2.0 - - + -
226E LYS* 3.9 26.5 - - + -
230E PHE* 3.6 5.2 - - - -
83J PHE 4.9 1.6 - - - -
84J THR* 1.3 93.7 + - - +
86J VAL* 1.3 68.0 + - + +
87J CYS 3.3 0.7 - - - -
88J PRO* 3.1 14.8 - - - +
89J THR* 3.6 1.6 - - - +
163J ARG* 5.9 0.4 - - - +
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Residues in contact with VAL 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL* 3.6 31.0 - - + -
208E CYS 3.5 28.7 - - - +
209E PRO* 4.7 0.4 - - - -
219E ILE* 4.4 3.4 - - + -
85J PHE* 1.3 74.9 - - - +
87J CYS* 1.3 65.7 + - - +
89J THR* 2.6 29.1 + - - +
90J GLU* 3.2 10.4 + - + +
163J ARG* 3.4 32.1 - - - +
182J LEU 4.3 2.2 - - - +
183J PRO 4.1 5.8 - - - +
185J GLY* 3.6 21.5 - - - +
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Residues in contact with CYS 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J TYR* 3.7 19.4 - - + +
80J PRO* 3.4 22.7 - - - -
81J LEU 3.6 19.3 - - - +
84J THR* 3.4 17.9 - - - +
86J VAL* 1.3 75.6 - - - +
88J PRO* 1.3 69.5 - - + +
90J GLU* 3.1 8.2 + - - +
91J ILE* 3.1 24.7 + - - +
122J TRP* 4.1 4.0 - - + -
163J ARG* 3.3 28.3 - - - +
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Residues in contact with PRO 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E PHE* 3.6 19.5 - - + -
84J THR 3.4 22.7 - - - +
85J PHE 3.1 18.6 - - - +
87J CYS* 1.3 96.1 - - + +
89J THR* 1.3 55.4 + - - +
91J ILE* 3.8 0.6 - - + -
92J ILE* 2.8 38.4 + - + +
122J TRP* 3.5 22.2 - - + -
130J GLY 4.0 9.2 - - - +
131J GLY 4.6 3.6 - - - +
132J LEU* 3.8 19.7 - - + -
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Residues in contact with THR 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E PRO* 3.4 8.7 - - + +
210E ALA* 3.0 26.6 + - - +
219E ILE* 3.8 15.3 - - + -
229E TYR* 3.6 28.5 - - + +
230E PHE* 4.2 5.6 - - + -
85J PHE 3.6 17.3 - - - +
86J VAL* 2.6 16.0 + - - +
88J PRO* 1.3 76.3 - - - +
90J GLU* 1.3 57.9 + - - +
92J ILE* 4.1 4.8 - - - +
93J ALA* 2.9 31.5 + - - +
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Residues in contact with GLU 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ALA* 3.8 19.1 - - + -
77J PHE* 4.6 11.2 - - + -
79J TYR* 4.4 1.3 - - + +
86J VAL* 3.7 17.3 - - + +
87J CYS* 3.1 8.2 + - - +
89J THR* 1.3 80.2 + - - +
91J ILE* 1.3 64.9 + - - +
93J ALA* 3.8 0.2 - - - +
94J PHE* 3.1 38.2 + - + -
163J ARG* 3.0 28.4 + - - -
185J GLY* 3.4 3.1 - - - -
186J ARG* 2.8 66.9 + - + +
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Residues in contact with ILE 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J PHE* 4.2 17.7 - - + -
79J TYR* 3.6 34.3 - - + +
87J CYS 3.1 16.1 + - - +
88J PRO 3.8 3.4 - - - +
90J GLU* 1.3 78.1 - - - +
92J ILE* 1.3 56.6 + - - +
94J PHE* 4.0 1.7 - - - +
95J GLY* 2.9 26.5 + - - -
110J ALA* 4.7 2.2 - - + -
122J TRP* 3.4 34.5 - - + -
132J LEU* 4.0 22.0 - - + -
135J ILE* 3.9 22.2 - - + +
137J ILE* 4.1 4.5 - - + +
139J LEU* 4.2 10.1 - - + -
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Residues in contact with ILE 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E PHE* 5.8 5.4 - - + -
233E LEU* 6.2 6.5 - - + -
234E ASN* 6.2 0.7 - - - +
88J PRO* 2.8 25.2 + - + +
89J THR* 4.1 4.7 - - - +
91J ILE* 1.3 75.7 - - + +
93J ALA* 1.3 61.6 + - - +
95J GLY* 4.3 2.0 - - - +
96J ASP* 2.8 37.9 + - - +
127J ARG* 3.4 57.0 - - + +
131J GLY 3.9 18.2 - - - +
132J LEU* 4.2 15.0 - - + +
135J ILE* 5.0 3.8 - - + -
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Residues in contact with ALA 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ALA* 3.7 21.1 - - + +
89J THR 2.9 19.9 + - - +
90J GLU 3.8 2.2 - - - +
92J ILE* 1.3 80.2 - - - +
94J PHE* 1.3 64.1 + - - +
96J ASP* 4.2 1.9 - - - +
97J ARG* 3.5 26.7 + - - +
188J VAL* 3.8 17.4 - - + +
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Residues in contact with PHE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J VAL* 4.3 7.0 - - + -
77J PHE* 4.0 21.3 - + + -
90J GLU* 3.1 33.3 + - + +
91J ILE 4.1 0.7 - - - +
93J ALA* 1.3 76.1 - - - +
95J GLY* 1.3 63.5 + - - +
97J ARG 3.1 4.3 + - - -
98J LEU* 3.1 23.2 + - - +
101J PHE* 3.7 36.5 - + - -
108J VAL* 4.3 13.2 - - + -
137J ILE* 3.6 18.4 - - + +
165J LEU* 3.7 17.7 - - + -
186J ARG* 5.1 12.6 - - + -
187J SER 4.5 1.3 - - - -
188J VAL* 3.9 24.7 - - + -
191J THR* 3.7 29.8 - - + -
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Residues in contact with GLY 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J ILE 2.9 16.8 + - - -
92J ILE 3.1 1.1 + - - -
94J PHE* 1.3 77.8 - - - +
96J ASP* 1.3 63.9 + - - +
97J ARG 3.3 1.2 + - - -
98J LEU* 3.4 17.1 + - - +
135J ILE* 3.9 14.8 - - - -
136J ARG* 3.5 14.0 + - - +
137J ILE* 3.3 18.1 - - - +
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Residues in contact with ASP 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ILE* 2.8 26.1 + - - +
93J ALA* 4.5 2.7 - - - +
95J GLY* 1.3 74.3 - - - +
97J ARG* 1.3 65.0 + - + +
98J LEU 3.5 0.7 - - - -
127J ARG* 2.9 43.4 + - - -
135J ILE* 5.9 0.3 - - - +
136J ARG* 4.9 7.0 + - - +
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Residues in contact with ARG 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J ALA* 3.5 17.4 + - - +
94J PHE 3.1 6.4 + - - +
96J ASP* 1.3 84.3 - - + +
98J LEU* 1.3 64.2 + - - +
99J GLU 3.2 2.9 - - - -
100J GLU* 2.9 62.5 + - + +
101J PHE* 3.6 7.9 - - + -
188J VAL* 3.7 30.2 - - + +
189J ASP* 2.8 35.4 + - - -
192J LEU* 3.4 12.3 - - - +
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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