Contacts of the helix formed by residues 82 - 97 (chain B) in PDB entry 3C51
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 HIS 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.7 13.4 - + - -
76B LEU* 3.5 48.0 - - + +
79B HIS* 3.6 11.8 + - + -
80B GLU 3.2 0.4 - - - -
81B GLN* 1.3 86.4 - - + +
83B GLY* 1.3 66.7 + - - +
84B PRO* 3.2 4.5 - - - -
85B ALA* 2.8 24.9 + - + +
86B LEU* 3.1 9.1 + - - -
154B LEU* 5.3 0.8 - - + +
158B PRO* 3.6 34.7 - - + +
161B GLU* 2.9 29.7 + - - -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU 4.0 4.5 + - - -
77B ARG* 5.6 3.1 - - - -
79B HIS 3.5 9.2 + - - -
80B GLU* 2.9 14.7 + - - -
82B HIS* 1.3 75.6 - - - +
84B PRO* 1.3 63.9 - - - +
86B LEU* 3.6 5.9 + - - +
87B GLN* 3.3 23.9 + - - +
121B LEU* 4.4 8.1 - - - -
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Residues in contact with PRO 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU 4.0 4.3 - - - +
81B GLN 3.5 14.1 - - - +
82B HIS 3.2 4.3 - - - -
83B GLY* 1.3 86.6 - - - +
85B ALA* 1.3 65.2 + - + +
87B GLN* 3.1 4.5 + - + +
88B LEU* 2.8 31.0 + - - +
121B LEU* 3.3 52.1 - - + +
122B PHE 4.4 8.5 - - - +
123B CYS* 4.3 11.0 - - - -
125B PHE* 5.8 2.2 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B HIS* 2.8 18.4 + - + +
84B PRO* 1.3 78.7 - - + +
86B LEU* 1.3 54.9 + - - +
88B LEU* 3.9 2.2 - - - +
89B TRP* 2.9 30.1 + - - +
123B CYS* 4.2 10.3 - - - -
125B PHE* 3.7 27.6 - - + -
150B VAL* 4.1 4.6 - - + +
153B HIS* 5.7 1.6 - - + -
154B LEU* 3.8 26.1 - - + +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.6 33.4 - - + +
76B LEU* 3.3 39.1 - - + +
77B ARG* 3.5 46.0 - - + +
82B HIS 3.1 8.8 + - - +
83B GLY* 3.8 9.0 - - - +
85B ALA* 1.3 77.0 - - - +
87B GLN* 1.3 55.7 + - + +
89B TRP* 3.2 11.0 + - + +
90B LYS* 2.7 43.5 + - + +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY 3.3 11.3 + - - +
84B PRO 3.1 7.4 + - - +
86B LEU* 1.3 80.2 - - + +
88B LEU* 1.3 60.8 + - - +
90B LYS* 4.3 15.0 + - - +
91B ASP* 2.9 63.6 + - - +
121B LEU* 4.5 21.2 - - + +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO 2.8 19.6 + - - +
85B ALA 3.9 2.5 - - - +
87B GLN* 1.3 71.6 - - - +
89B TRP* 1.3 63.7 + - - +
91B ASP* 3.9 3.3 - - - -
92B ILE* 3.1 43.5 + - + +
110B LEU* 4.6 17.0 - - + +
123B CYS* 3.4 27.8 - - + -
125B PHE* 5.0 0.2 - - + -
126B LEU* 4.1 15.0 - - + -
146B LEU* 4.3 12.3 - - + -
150B VAL* 3.5 29.6 - - + -
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Residues in contact with TRP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B CYS 4.2 15.5 - - - -
63B LEU* 3.6 25.9 - - + +
69B LYS* 4.3 11.0 - - + -
72B PHE* 4.1 23.3 - + - -
73B GLN* 3.3 43.7 - - + -
85B ALA 2.9 20.4 + - - +
86B LEU* 3.3 13.7 - - + +
88B LEU* 1.3 79.2 - - - +
90B LYS* 1.3 60.0 + - - +
92B ILE* 3.8 4.3 + - - +
93B GLU* 3.6 33.4 + - - +
147B LEU* 3.4 26.0 - - + +
150B VAL* 4.0 12.1 - - + -
151B LEU* 3.1 22.6 - - + +
154B LEU* 3.8 15.5 - - + -
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.7 31.4 - - - +
86B LEU* 2.7 27.5 + - + +
87B GLN* 3.9 17.6 + - - +
89B TRP* 1.3 74.9 - - - +
91B ASP* 1.3 62.3 - - - +
93B GLU* 3.2 11.9 + - - +
94B ASP* 3.0 27.5 + - - +
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLN* 2.9 45.3 + - - +
88B LEU* 4.1 3.8 - - - +
90B LYS* 1.3 73.2 - - - +
92B ILE* 1.3 60.6 + - - +
94B ASP* 3.3 18.1 - - - +
95B TYR* 2.9 28.3 + - - +
110B LEU* 3.9 23.8 - - + +
113B ALA* 5.2 10.2 - - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 3.1 42.3 + - + +
89B TRP 4.0 4.0 - - - +
91B ASP* 1.3 74.1 - - - +
93B GLU* 1.3 61.9 + - - +
95B TYR* 3.1 9.0 + - + +
96B ASP* 2.9 37.6 + - - +
110B LEU* 4.1 9.4 - - + -
143B PHE* 4.1 18.6 - - + +
146B LEU* 4.1 13.5 - - + -
147B LEU* 3.7 58.3 - - + +
150B VAL* 4.6 2.2 - - + -
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.8 27.9 + - - -
73B GLN* 4.3 8.9 + - - -
89B TRP* 3.6 36.7 + - + +
90B LYS* 3.2 12.3 + - - +
92B ILE* 1.3 79.6 - - - +
94B ASP* 1.3 62.8 + - - +
96B ASP* 3.1 17.2 + - - +
97B THR* 3.2 23.4 + - + +
147B LEU* 5.5 8.5 - - + -
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS 3.0 16.3 + - - +
91B ASP* 3.3 23.5 - - - +
93B GLU* 1.3 76.0 - - - +
95B TYR* 1.3 62.5 + - - +
97B THR* 3.6 10.3 + - - -
98B ALA* 3.3 19.8 + - - +
106B LYS* 3.4 34.8 + - - +
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP 2.9 20.0 + - - +
92B ILE* 3.1 9.6 + - + +
94B ASP* 1.3 79.2 - - - +
96B ASP* 1.3 75.6 + - - +
98B ALA* 3.1 20.3 + - - +
103B ARG* 3.6 72.0 + - + +
104B PRO* 5.4 1.4 - - - +
106B LYS* 4.5 7.4 - - + -
107B ALA* 3.5 31.1 - - + +
110B LEU* 4.7 4.7 - - + -
142B LEU* 4.6 7.9 + - - -
143B PHE* 3.4 46.3 - + + -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 2.9 25.0 + - - +
93B GLU* 3.1 11.0 + - - +
95B TYR* 1.3 89.7 - - - +
97B THR* 1.3 60.7 + - + +
98B ALA 3.3 0.4 - - - -
103B ARG* 3.7 10.4 + - - +
144B GLN* 3.1 34.7 + - - +
147B LEU* 4.5 8.3 - - - +
458B ARG* 3.5 33.9 + - + +
459B GLN* 5.7 0.5 - - - +
462B ALA* 5.6 1.2 - - - +
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B GLU* 3.2 19.1 + - + +
94B ASP* 3.6 10.2 + - - -
96B ASP* 1.3 80.1 - - + +
98B ALA* 1.3 58.6 + - - +
99B ASP 4.0 1.2 + - - -
458B ARG* 5.3 0.2 - - - -
459B GLN* 5.7 4.9 - - - +
462B ALA* 4.9 20.2 - - + -
464B MET* 5.4 7.9 - - - +
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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
------------------------------------------------------------
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