Contacts of the helix formed by residues 85 - 97 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83E PHE 4.9 1.8 - - - -
84E THR* 1.3 95.7 + - - +
86E VAL* 1.3 66.1 + - + +
87E CYS 3.3 0.4 - - - -
88E PRO* 3.2 14.6 - - - +
89E THR* 3.6 1.4 - - - +
117I PHE* 3.8 34.3 - + - -
207J VAL* 4.1 17.3 - - + -
219J ILE* 3.4 25.2 - - + +
221J PRO* 3.3 39.7 - - + -
222J ASP* 3.3 30.1 - - - -
223J PRO* 4.0 2.5 - - + -
226J LYS* 3.8 26.9 - - + -
230J PHE* 3.6 5.6 - - - -
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PHE* 1.3 74.6 - - - +
87E CYS* 1.3 66.1 + - - +
89E THR* 2.7 32.1 + - - +
90E GLU* 3.2 8.9 + - - +
163E ARG* 3.4 29.3 - - - +
182E LEU 4.3 3.4 - - - +
183E PRO 4.2 6.1 - - - +
185E GLY* 3.5 22.2 - - - +
207J VAL* 3.6 29.8 - - + -
208J CYS 3.4 29.4 - - - +
209J PRO* 4.7 0.4 - - - -
219J ILE* 4.4 2.7 - - + -
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Residues in contact with CYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E TYR* 3.7 19.2 - - + +
80E PRO* 3.4 21.3 - - - -
81E LEU 3.5 18.8 - - - +
84E THR* 3.4 18.8 - - - -
86E VAL* 1.3 75.6 - - - +
88E PRO* 1.3 69.8 - - + +
90E GLU* 3.2 7.9 + - - +
91E ILE* 3.0 25.2 + - - +
122E TRP* 4.1 4.0 - - + -
163E ARG* 3.2 28.5 - - - +
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Residues in contact with PRO 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E THR 3.4 21.1 - - - +
85E PHE 3.2 19.3 - - - +
87E CYS* 1.3 94.1 - - + +
89E THR* 1.3 55.1 + - - +
91E ILE* 3.9 0.3 - - - +
92E ILE* 2.9 39.3 + - + +
122E TRP* 3.5 23.3 - - + -
130E GLY 4.0 9.4 - - - +
131E GLY 4.6 4.3 - - - +
132E LEU* 3.8 18.6 - - + -
230J PHE* 3.5 20.0 - - + -
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Residues in contact with THR 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PHE 3.6 17.7 - - - +
86E VAL 2.7 15.9 + - - -
88E PRO* 1.3 75.9 - - - +
90E GLU* 1.3 56.4 + - - +
92E ILE* 4.1 5.4 - - - +
93E ALA* 2.9 30.3 + - - +
209J PRO* 3.4 12.7 - - + +
210J ALA* 3.0 23.6 + - - +
219J ILE* 3.7 15.5 - - + -
229J TYR* 3.5 29.2 - - + +
230J PHE* 4.3 5.4 - - + -
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PHE* 4.5 11.4 - - + -
79E TYR* 4.5 1.3 - - + +
86E VAL* 3.2 22.5 + - + +
87E CYS* 3.2 7.0 + - - +
89E THR* 1.3 79.4 + - - +
91E ILE* 1.3 66.3 + - - +
93E ALA* 3.3 0.7 + - - +
94E PHE* 3.0 38.2 + - + -
163E ARG* 3.0 22.5 + - - -
185E GLY* 3.3 2.3 - - - -
186E ARG* 2.7 67.0 + - + +
210J ALA* 3.8 20.6 - - + -
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Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PHE* 4.1 22.4 - - + -
79E TYR* 3.5 35.9 - - + +
87E CYS 3.0 15.8 + - - +
88E PRO 3.9 3.1 - - - +
90E GLU* 1.3 75.6 - - - +
92E ILE* 1.3 59.6 + - - +
95E GLY* 2.9 25.5 + - - -
110E ALA* 4.5 2.7 - - + -
122E TRP* 3.5 28.5 - - + -
132E LEU* 3.9 17.3 - - + -
135E ILE* 3.0 32.0 - - + +
137E ILE* 4.0 6.3 - - + +
139E LEU* 4.3 8.3 - - + -
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Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PRO* 2.9 25.1 + - + +
89E THR* 4.1 5.2 - - - +
91E ILE* 1.3 76.0 - - + +
93E ALA* 1.3 60.5 + - - +
95E GLY* 4.4 1.1 - - - +
96E ASP* 2.8 38.3 + - + +
127E ARG* 3.4 57.0 - - + +
131E GLY 3.9 17.3 - - - +
132E LEU* 4.2 15.7 - - + +
135E ILE* 5.4 2.9 - - + -
230J PHE* 5.7 6.3 - - + -
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Residues in contact with ALA 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR 2.9 21.3 + - - +
90E GLU 3.3 3.8 + - - +
92E ILE* 1.3 78.2 - - - +
94E PHE* 1.3 61.5 + - - +
96E ASP* 4.3 2.5 - - - +
97E ARG* 3.5 27.5 + - - +
188E VAL* 3.7 21.5 - - + +
210J ALA* 3.8 16.6 - - + +
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Residues in contact with PHE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E VAL* 4.4 6.5 - - + -
77E PHE* 3.8 24.9 - + + -
90E GLU* 3.0 30.9 + - + +
91E ILE 4.0 0.9 - - - +
93E ALA* 1.3 76.1 - - - +
95E GLY* 1.3 65.1 + - - +
97E ARG 3.1 4.0 + - - -
98E LEU* 3.0 23.7 + - - +
101E PHE* 3.6 36.6 - + - -
108E VAL* 4.3 11.2 - - + -
137E ILE* 3.6 18.2 - - + +
165E LEU* 3.8 17.0 - - + -
186E ARG* 5.1 12.3 - - + -
187E SER 4.4 1.3 - - - -
188E VAL* 3.9 23.3 - - + -
191E THR* 3.5 30.5 - - + -
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Residues in contact with GLY 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ILE 2.9 17.1 + - - -
92E ILE* 3.8 1.1 - - - -
94E PHE* 1.3 75.3 - - - +
96E ASP* 1.3 64.4 + - - +
98E LEU* 3.4 19.6 + - - +
135E ILE* 4.7 10.3 - - - -
136E ARG* 5.0 9.4 + - - +
137E ILE* 3.3 21.3 - - - +
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Residues in contact with ASP 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ILE* 2.8 24.0 + - - +
93E ALA* 4.3 3.1 - - - +
95E GLY* 1.3 77.2 - - - +
97E ARG* 1.3 63.6 + - + +
98E LEU 3.4 1.5 + - - -
127E ARG* 2.9 44.1 + - - -
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Residues in contact with ARG 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ALA* 3.5 17.2 + - - +
94E PHE 3.1 6.6 + - - +
96E ASP* 1.3 82.5 - - + +
98E LEU* 1.3 64.8 + - - +
99E GLU 3.2 3.4 - - - -
100E GLU* 2.8 63.6 + - - +
101E PHE* 3.7 6.7 - - + -
188E VAL* 3.7 31.8 - - + +
189E ASP* 2.8 34.3 + - - +
192E LEU* 4.4 9.9 - - - +
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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