Contacts of the helix formed by residues 80 - 97 (chain A) in PDB entry 2J6U
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 ARG 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLU* 2.8 32.8 + - - -
22A LEU* 3.5 32.3 - - - +
78A PRO* 3.8 15.0 - - + +
79A MET* 1.3 75.7 - - - +
81A LYS* 1.3 64.6 + - - +
82A GLU 3.4 2.5 - - - -
83A VAL* 3.3 24.5 + - + +
84A TYR* 3.0 39.2 + - + +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.4 32.1 - - + +
79A MET* 3.6 22.8 + - + +
80A ARG* 1.3 73.9 - - - +
82A GLU* 1.3 61.0 + - + +
84A TYR* 3.1 12.0 + - - +
85A GLN* 2.8 34.4 + - + +
107A ILE* 3.8 17.9 - - + -
245A ARG* 5.5 5.3 - - - +
278A LYS* 5.6 3.6 - - - +
6T G 4.7 24.5 + - - -
7T A 5.2 3.8 + - - -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG 3.4 0.6 - - - -
81A LYS* 1.3 80.6 - - + +
83A VAL* 1.3 67.5 + - + +
85A GLN* 3.2 9.1 + - - +
86A GLN* 3.0 35.2 + - - +
277A TYR* 4.5 16.3 - - - -
278A LYS* 5.9 3.0 - - + +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.5 10.3 - - + -
22A LEU* 3.9 28.5 - - + -
80A ARG* 3.3 35.6 + - + +
81A LYS 3.3 0.6 - - - -
82A GLU* 1.3 77.1 - - + +
84A TYR* 1.3 67.6 + - + +
86A GLN* 3.1 11.0 + - - +
87A VAL* 3.0 24.9 + - + +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.6 11.9 - - + -
15A TYR* 3.4 68.2 - + + -
18A VAL* 3.6 24.2 - - + -
19A GLU* 2.6 36.6 + - + +
33A VAL* 3.7 12.1 - - - +
78A PRO 3.7 1.2 + - - -
79A MET* 3.7 3.1 - - + -
80A ARG* 3.0 44.9 + - + -
81A LYS* 3.1 10.9 + - - +
83A VAL* 1.3 77.5 - - + +
85A GLN* 1.3 57.9 + - - +
87A VAL* 3.0 9.7 + - - +
88A SER* 2.8 28.6 + - - -
107A ILE* 4.5 1.6 - - + -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 2.8 19.2 + - + +
82A GLU* 3.3 13.9 - - - +
84A TYR* 1.3 76.7 - - - +
86A GLN* 1.3 61.0 + - + +
88A SER* 3.1 14.1 + - - -
89A SER* 2.9 40.7 + - - +
107A ILE* 3.7 28.2 - - + +
245A ARG* 4.6 15.8 + - - +
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.0 25.1 + - - +
83A VAL* 3.1 10.7 + - - +
85A GLN* 1.3 78.1 - - + +
87A VAL* 1.3 63.1 + - + +
89A SER* 3.5 7.1 + - - +
90A ARG* 3.3 39.4 + - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 4.2 7.6 - - + -
18A VAL* 4.0 36.3 - - + -
21A VAL* 6.5 1.1 - - + -
22A LEU* 5.2 6.5 - - + -
83A VAL* 3.0 19.8 + - + +
84A TYR 3.0 7.4 + - - +
86A GLN* 1.3 74.7 - - + +
88A SER* 1.3 66.5 + - - +
90A ARG* 3.5 31.0 + - - +
91A ILE* 3.2 31.3 + - + +
139A GLU* 4.7 5.8 - - + +
141A ILE* 4.5 9.9 - - + -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.1 5.9 - - - -
14A PHE* 3.8 13.2 - - - -
84A TYR 2.8 12.6 + - - -
85A GLN* 3.2 15.1 + - - -
87A VAL* 1.3 77.6 - - - +
89A SER* 1.3 56.9 + - - -
91A ILE* 3.0 6.4 + - - +
92A MET* 2.8 41.5 + - - +
107A ILE* 2.4 39.5 + - - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 2.9 30.7 + - - +
86A GLN* 3.8 8.2 - - - -
88A SER* 1.3 74.2 + - - +
90A ARG* 1.3 66.9 + - - +
92A MET* 3.1 11.2 + - - +
93A ASN* 2.9 31.4 + - - -
96A ARG* 5.5 0.2 + - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN* 3.3 33.1 + - - +
87A VAL* 3.9 24.9 - - - +
88A SER 3.3 0.4 - - - -
89A SER* 1.3 75.9 - - - +
91A ILE* 1.3 62.5 + - - +
93A ASN* 3.2 15.7 + - - +
94A LEU* 3.2 23.3 + - - +
139A GLU* 2.9 42.8 + - - +
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.7 34.8 - - + -
14A PHE* 4.7 0.4 - - + -
87A VAL* 3.2 20.0 - - + +
88A SER 3.0 7.2 + - - +
90A ARG* 1.3 74.6 - - - +
92A MET* 1.3 65.4 + - - +
94A LEU* 2.9 19.1 + - + +
95A LEU* 3.1 13.0 + - + +
135A ILE* 3.9 35.2 - - + -
139A GLU* 4.1 16.4 - - + -
141A ILE* 4.0 38.4 - - + -
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.9 16.8 - - + -
88A SER* 2.8 28.8 + - - +
89A SER* 3.1 11.4 + - - +
91A ILE* 1.3 75.6 - - - +
93A ASN* 1.3 57.3 + - - +
95A LEU* 3.3 16.0 + - - +
96A ARG* 2.9 33.5 + - - +
102A ILE* 4.0 4.5 - - + +
104A ILE* 3.8 35.0 - - + -
106A SER 3.6 16.2 - - - +
108A ASP 4.2 0.4 - - - -
109A GLU 3.3 36.1 - - - +
110A ALA* 3.9 17.9 - - - -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER* 2.9 26.0 + - - -
90A ARG* 3.3 13.5 - - - +
91A ILE 3.0 0.2 - - - -
92A MET* 1.3 74.5 - - - +
94A LEU* 1.3 68.1 + - + +
96A ARG* 3.0 42.3 + - - +
97A GLU* 3.4 14.4 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG 3.2 11.6 + - - +
91A ILE* 2.9 15.5 + - + +
93A ASN* 1.3 78.4 - - + +
95A LEU* 1.3 61.8 + - - +
97A GLU* 3.0 33.3 + - - +
98A TYR* 3.4 12.7 - - + -
131A ILE* 6.6 0.2 - - + -
134A LYS* 4.7 11.7 - - + -
135A ILE* 3.9 41.1 - - + +
138A LYS* 4.1 35.7 - - + -
139A GLU* 4.7 7.6 - - + -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.0 24.7 - - + -
11A PHE* 4.9 6.7 - - + -
91A ILE 3.1 11.7 + - - +
92A MET* 3.5 31.4 - - - +
94A LEU* 1.3 73.4 - - - +
96A ARG* 1.3 53.4 + - - +
97A GLU 2.8 5.7 + - - -
98A TYR* 2.7 35.9 + - - +
99A SER 3.7 3.8 + - - +
102A ILE* 4.2 9.2 - - + -
110A ALA* 4.2 15.7 - - + -
112A LEU* 3.9 20.4 - - + +
131A ILE* 3.3 33.7 - - + -
135A ILE* 4.0 12.6 - - + -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A SER 5.5 0.2 + - - -
92A MET* 2.9 20.6 + - - +
93A ASN* 3.0 36.1 + - - +
95A LEU* 1.3 73.8 - - - +
97A GLU* 1.3 57.5 + - + +
98A TYR 3.2 2.0 + - - -
99A SER 3.4 21.2 + - - +
100A GLU* 4.6 6.8 + - - +
102A ILE* 3.8 32.5 - - + +
104A ILE* 3.7 27.3 - - - +
242A THR* 5.8 5.5 + - - +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ASN* 3.5 15.6 - - - +
94A LEU* 3.0 24.2 + - - +
95A LEU 2.8 1.6 + - - -
96A ARG* 1.3 79.8 - - + +
98A TYR* 1.3 69.4 + - + +
99A SER 3.7 0.2 - - - -
100A GLU* 6.0 0.7 - - - -
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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