Contacts of the helix formed by residues 79 - 93 (chain A) in PDB entry 3ADB
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 TYR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ASN 3.2 0.9 - - - +
78A TYR* 1.3 112.6 - + + +
80A ASN* 1.3 64.8 + - - +
81A SER* 3.8 20.0 - - - +
82A MSE 3.1 39.9 + - + +
83A ARG* 3.4 15.5 + - - +
131A LYS* 5.4 5.7 + - - -
74C C 4.9 16.1 + - - +
75C C 3.6 45.9 + - - -
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Residues in contact with ASN 80 (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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79A TYR* 1.3 71.1 - - - +
81A SER* 1.3 69.1 + - - +
82A MSE 3.1 0.2 - - - -
83A ARG* 3.0 33.8 + - - +
84A ARG* 2.8 29.5 + - - +
138A LYS* 4.6 11.9 - - - +
139A TYR* 3.4 34.7 + - + -
141A TRP* 3.5 8.5 - - + -
142A ASP* 3.7 12.8 + - - +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.1 14.0 - - - +
80A ASN* 1.3 89.1 + - - +
82A MSE 1.3 67.5 + - - +
84A ARG* 3.7 9.5 - - - +
85A ASP* 3.1 28.7 + - - +
73C G 5.2 8.5 - - - -
74C C 4.2 23.4 + - - -
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Residues in contact with MSE 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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55A LYS* 6.2 3.1 - - - -
59A TYR* 4.1 9.7 + - - +
77A ASN* 3.9 20.0 - - - +
78A TYR* 3.8 13.9 - - + -
79A TYR* 3.1 39.9 + - + +
81A SER* 1.3 87.4 + - - +
83A ARG* 1.3 64.5 + - - +
85A ASP* 3.0 11.9 + - - +
86A LEU* 3.0 25.8 + - - +
75C C 3.0 43.1 - - - +
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Residues in contact with ARG 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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4A ILE* 3.8 7.8 - - + +
6A THR* 3.5 24.1 + - - -
77A ASN* 3.0 36.7 + - + -
78A TYR 3.6 12.9 + - - -
79A TYR 3.6 5.4 + - - +
80A ASN* 3.0 28.6 + - - +
82A MSE 1.3 76.3 - - - +
84A ARG* 1.3 60.5 + - - +
86A LEU* 3.3 11.1 + - - +
87A ILE* 2.9 30.8 + - - +
99A ILE* 4.0 20.2 - - + -
132A PHE* 4.6 3.8 - - - -
133A ASP 4.5 6.3 + - - -
134A GLU 4.7 0.8 + - - -
135A PRO* 3.8 21.6 - - - +
141A TRP* 4.7 0.9 - - + -
142A ASP* 2.6 45.5 + - - +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN* 2.8 17.8 + - - +
81A SER* 3.7 9.6 - - - +
83A ARG* 1.3 75.2 - - - +
85A ASP* 1.3 69.7 + - - +
87A ILE* 3.0 6.3 + - + +
88A ASN* 2.9 44.2 + - - +
139A TYR* 4.1 19.3 + - - -
141A TRP* 3.3 51.7 - - + +
68C C 3.9 15.5 + - - -
69C G 5.5 8.4 + - - -
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 4.3 11.1 + - - -
59A TYR* 3.4 33.8 + - + +
81A SER 3.1 15.1 + - - +
82A MSE 3.0 12.1 + - - +
84A ARG* 1.3 81.9 - - - +
86A LEU* 1.3 63.1 + - - +
88A ASN* 3.3 20.0 + - - +
89A ILE* 3.5 17.2 + - - +
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Residues in contact with LEU 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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2A LEU* 3.0 23.5 - - + +
4A ILE* 3.5 35.7 - - + -
59A TYR* 3.7 27.4 - - + -
62A ILE* 3.8 26.0 - - + -
73A VAL* 3.5 28.3 - - + -
77A ASN* 3.6 21.8 - - - +
82A MSE 3.0 14.3 + - - +
83A ARG* 3.7 2.7 - - - +
84A ARG 3.2 0.2 - - - -
85A ASP* 1.3 75.5 - - - +
87A ILE* 1.3 63.0 + - - +
89A ILE* 3.2 19.2 + - + +
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Residues in contact with ILE 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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2A LEU* 4.8 0.2 - - - -
4A ILE* 3.7 14.1 - - + -
83A ARG 2.9 21.3 + - - +
84A ARG* 3.0 8.2 + - + +
86A LEU* 1.3 77.4 - - - +
88A ASN* 1.3 61.4 + - - +
90A ALA* 2.8 11.2 + - - +
91A LYS* 2.8 25.6 + - + +
97A TYR* 3.6 49.6 - - + +
99A ILE* 4.4 7.6 - - + -
141A TRP* 3.6 36.1 - - + +
173A PHE* 4.2 8.7 - - + -
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Residues in contact with ASN 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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84A ARG* 2.9 42.3 + - - +
85A ASP* 3.7 14.4 + - - +
86A LEU 3.3 0.4 - - - -
87A ILE* 1.3 79.4 - - - +
89A ILE* 1.3 57.5 + - + +
91A LYS* 3.6 13.1 - - + +
92A LYS* 2.9 28.1 + - - +
69C G 3.6 24.2 + - - -
70C G 5.8 2.2 + - - -
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Residues in contact with ILE 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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2A LEU* 4.7 0.7 - - + -
59A TYR* 3.9 43.7 - - + +
62A ILE* 4.3 16.8 - - + -
63A ASP* 4.0 30.7 - - + +
66A LEU* 3.9 16.4 - - + -
85A ASP 3.5 14.6 + - - +
86A LEU* 3.2 13.9 + - + +
87A ILE 3.1 0.6 - - - -
88A ASN* 1.3 74.4 - - + +
90A ALA* 1.3 69.2 + - - +
92A LYS* 3.4 20.1 - - + +
93A TYR* 3.5 12.3 - - + -
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Residues in contact with ALA 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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2A LEU* 3.8 23.8 - - + -
66A LEU* 3.7 11.4 - - + -
86A LEU 3.4 1.4 + - - -
87A ILE 2.8 10.7 + - - +
89A ILE* 1.3 80.5 - - - +
91A LYS* 1.3 60.2 + - - +
93A TYR* 3.1 4.5 + - - +
94A ASN 3.0 3.8 + - - -
95A LYS* 2.8 44.0 + - - +
96A ASN 4.3 0.2 - - - +
97A TYR* 4.1 15.9 - - + -
173A PHE* 4.5 1.8 - - + -
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Residues in contact with LYS 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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87A ILE* 2.8 13.0 + - + +
88A ASN* 3.6 15.9 - - + +
90A ALA* 1.3 77.3 - - - +
92A LYS* 1.3 54.7 + - - +
94A ASN* 2.7 20.3 + - - -
173A PHE* 3.3 55.2 + - + +
174A TYR* 3.0 45.8 - - + +
176A LEU* 5.8 2.2 - - - +
68C C 3.0 19.6 + - - -
69C G 2.7 38.3 + - - +
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Residues in contact with LYS 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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63A ASP* 2.7 23.6 + - - +
67A LYS* 5.4 0.4 - - - +
88A ASN 2.9 18.3 + - - +
89A ILE* 3.4 10.5 - - + +
91A LYS* 1.3 77.1 - - - +
93A TYR* 1.3 97.8 + - + +
94A ASN 3.4 0.2 - - - -
174A TYR* 4.0 15.5 + - - -
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Residues in contact with TYR 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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63A ASP* 2.9 44.9 + - - -
66A LEU* 4.4 12.3 - - + +
67A LYS* 2.9 36.4 + - + -
89A ILE* 3.5 18.1 + - + -
90A ALA 3.1 2.8 + - - +
91A LYS 3.1 0.4 - - - -
92A LYS* 1.3 121.0 + - + +
94A ASN* 1.3 71.4 - - - +
95A LYS* 3.1 35.3 + - + -
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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