Contacts of the helix formed by residues 85 - 97 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D PHE 4.8 2.2 - - - -
84D THR* 1.3 94.7 + - + +
86D VAL* 1.3 68.2 + - - +
87D CYS 3.3 0.7 - - - -
88D PRO* 3.0 16.2 - - - +
89D THR* 3.5 2.4 - - - +
163D ARG* 5.8 0.2 - - - +
207F VAL* 4.1 17.9 - - + -
219F ILE* 3.3 24.6 - - + +
221F PRO* 3.4 40.6 - - + -
222F ASP* 3.5 27.8 - - - -
223F PRO* 4.1 2.0 - - + -
226F LYS* 3.8 26.5 - - + -
230F PHE* 3.6 4.1 - - - -
117J PHE* 3.8 33.9 - + - -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 1.3 78.7 - - - +
87D CYS* 1.3 65.6 + - - +
89D THR* 2.7 29.3 + - - +
90D GLU* 3.2 10.0 + - + -
163D ARG* 3.5 34.0 - - - +
182D LEU 4.4 3.1 - - - +
183D PRO 4.0 5.4 - - - +
185D GLY* 3.5 30.5 - - - +
207F VAL* 3.5 32.8 - - + -
208F CYS 3.5 19.3 - - - +
209F PRO* 4.5 0.7 - - + -
219F ILE* 4.3 2.5 - - + -
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Residues in contact with CYS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TYR* 3.6 20.0 - - + -
80D PRO* 3.5 21.8 - - - -
81D LEU 3.6 18.6 - - - +
84D THR* 3.5 18.4 - - - +
86D VAL* 1.3 75.0 - - - +
88D PRO* 1.3 70.2 - - + +
90D GLU* 3.1 15.9 + - - +
91D ILE* 3.1 17.0 + - - +
122D TRP* 4.0 4.5 - - + -
163D ARG* 3.2 28.7 - - - +
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Residues in contact with PRO 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D THR 3.4 21.5 - - - +
85D PHE 3.0 27.8 - - - +
87D CYS* 1.3 86.7 - - + +
89D THR* 1.3 54.2 + - - +
91D ILE* 3.3 0.5 + - - +
92D ILE* 2.8 39.7 + - + +
122D TRP* 3.5 21.3 - - + -
130D GLY 4.0 9.6 - - - +
131D GLY 4.4 4.5 - - - +
132D LEU* 3.8 18.4 - - + -
230F PHE* 3.5 19.7 - - + -
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE 3.5 18.2 - - - +
86D VAL 2.7 15.4 + - - -
88D PRO* 1.3 75.4 - - - +
90D GLU* 1.3 56.9 + - - +
92D ILE* 4.2 6.8 - - - +
93D ALA* 3.0 30.0 + - - +
209F PRO* 3.4 11.6 - - + +
210F ALA* 2.9 24.7 + - - +
219F ILE* 3.8 7.6 - - + -
229F TYR* 3.6 34.8 - - + +
230F PHE* 4.1 6.7 - - + -
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PHE* 4.5 10.8 - - + -
79D TYR* 4.4 1.2 - - - +
86D VAL* 3.7 17.0 - - + +
87D CYS* 3.1 8.9 + - - +
89D THR* 1.3 75.8 + - - +
91D ILE* 1.3 65.5 + - - +
93D ALA* 3.4 1.0 + - - +
94D PHE* 3.1 37.5 + - + -
163D ARG* 2.9 26.1 + - - -
185D GLY* 3.4 3.3 - - - -
186D ARG* 2.8 67.1 + - + +
210F ALA* 3.8 21.5 - - + -
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PHE* 4.2 17.0 - - + -
79D TYR* 3.5 35.4 - - + +
87D CYS 3.1 15.9 + - - +
88D PRO 3.8 3.4 - - - +
90D GLU* 1.3 76.4 - - - +
92D ILE* 1.3 57.3 + - - +
94D PHE* 4.0 1.4 - - - +
95D GLY* 2.9 27.0 + - - -
110D ALA* 4.5 1.8 - - + -
122D TRP* 3.5 34.1 - - + -
132D LEU* 3.9 12.8 - - + -
135D ILE* 3.5 23.1 - - + +
137D ILE* 4.1 13.3 - - + +
139D LEU* 4.1 11.7 - - + -
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PRO* 2.8 27.1 + - + +
89D THR* 4.2 6.3 - - - +
91D ILE* 1.3 76.6 - - - +
93D ALA* 1.3 57.9 + - - +
95D GLY 4.5 0.2 - - - +
96D ASP* 2.8 49.2 + - - +
127D ARG* 3.4 38.1 - - + +
131D GLY 3.7 22.7 - - - +
132D LEU* 4.0 15.7 - - + +
135D ILE* 4.6 6.5 - - + -
230F PHE* 5.6 5.8 - - + -
234F ASN* 6.2 0.4 - - - +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D THR 3.0 20.5 + - - +
90D GLU 3.8 3.6 - - - +
91D ILE 3.3 0.2 - - - -
92D ILE* 1.3 79.0 - - - +
94D PHE* 1.3 61.4 + - - +
96D ASP* 4.1 2.3 - - - +
97D ARG* 3.3 32.4 + - - +
188D VAL* 3.7 19.7 - - + +
210F ALA* 3.9 13.9 - - + +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 4.3 6.1 - - + -
77D PHE* 3.6 27.6 - + + -
90D GLU* 3.1 33.7 + - + +
91D ILE 4.0 2.2 - - - +
93D ALA* 1.3 73.5 - - - +
95D GLY* 1.3 65.4 + - - +
97D ARG* 3.1 5.2 + - - -
98D LEU* 3.0 24.9 + - - +
101D PHE* 3.6 37.7 - + - -
108D VAL* 4.1 22.7 - - + -
137D ILE* 4.6 4.5 - - + -
165D LEU* 3.7 18.6 - - + -
186D ARG* 5.2 9.6 - - + -
187D SER 4.6 1.6 - - - -
188D VAL* 3.9 22.9 - - + -
191D THR* 3.7 28.3 - - + -
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Residues in contact with GLY 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ILE 2.9 17.2 + - - -
92D ILE 3.8 0.4 - - - -
94D PHE* 1.3 76.8 - - - +
96D ASP* 1.3 63.5 + - - +
97D ARG 3.2 0.9 + - - -
98D LEU* 3.3 17.6 + - - +
135D ILE* 4.4 13.0 - - - -
136D ARG* 4.9 11.8 + - - +
137D ILE* 4.2 20.0 - - - +
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ILE* 2.8 28.5 + - - +
93D ALA* 4.3 4.0 - - - +
95D GLY* 1.3 73.4 - - - +
97D ARG* 1.3 62.5 + - + +
98D LEU 3.5 0.4 + - - -
127D ARG* 2.9 43.6 + - - -
135D ILE* 6.0 0.5 - - - +
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Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ALA* 3.3 20.0 + - - +
94D PHE 3.1 6.4 + - - +
96D ASP* 1.3 82.8 - - + +
98D LEU* 1.3 65.2 + - - +
99D GLU 3.2 3.1 - - - -
100D GLU* 2.9 62.4 + - - +
101D PHE* 3.8 5.9 - - - -
188D VAL* 3.6 30.4 - - + +
189D ASP* 2.8 43.6 + - - -
192D LEU* 3.5 8.9 - - - +
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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