Contacts of the helix formed by residues 80 - 95 (chain A) in PDB entry 1X3W
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 ASP 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A THR 5.3 0.2 - - - +
79A LEU* 1.3 73.0 - - - +
81A LEU* 1.3 55.3 + - - +
82A ASP* 3.2 14.0 + - - +
83A LEU* 2.9 40.1 + - + +
84A ILE* 3.0 29.8 + - - +
115A TYR* 3.3 23.6 + - + +
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Residues in contact with LEU 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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76A LEU* 3.0 57.9 - - + +
77A GLU* 4.7 2.7 - - - +
79A LEU* 3.8 12.3 - - + +
80A ASP* 1.3 69.6 - - - +
82A ASP* 1.3 62.6 + - - +
84A ILE* 4.1 8.5 - - - -
85A TYR* 2.8 52.0 + - + +
205A PHE* 3.9 19.1 - - + -
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Residues in contact with ASP 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 ASP* 3.2 9.4 - - - +
81A LEU* 1.3 77.8 - - - +
83A LEU* 1.3 57.8 + - - +
85A TYR* 4.3 1.4 - - - +
86A LYS* 3.0 55.1 + - - +
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Residues in contact with LEU 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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80A ASP* 2.9 32.5 + - + +
82A ASP* 1.3 71.3 + - - +
84A ILE* 1.3 68.4 + - - +
86A LYS* 3.4 13.4 - - + +
87A ASN* 2.9 58.4 + - - +
114A ARG* 4.7 3.1 - - - +
115A TYR* 3.8 29.8 - - + -
119A ASP* 3.9 14.8 - - - +
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Residues in contact with ILE 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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79A LEU* 4.5 10.8 - - + -
80A ASP 3.0 26.2 + - - +
81A LEU* 3.2 8.7 + - - +
83A LEU* 1.3 75.3 - - - +
85A TYR* 1.3 63.5 + - + +
87A ASN* 3.0 10.3 + - - +
88A VAL* 2.9 41.1 + - + +
108A LEU* 4.2 16.2 - - + -
111A GLU* 4.4 9.3 - - + +
112A LEU* 3.8 29.6 - - + -
114A ARG* 5.9 0.2 - - - +
115A TYR* 3.8 39.5 - - + -
205A PHE* 4.6 7.0 - - + -
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Residues in contact with TYR 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 LEU* 2.8 45.0 + - + +
82A ASP* 4.5 1.6 - - - +
84A ILE* 1.3 71.8 - - + +
86A LYS* 1.3 67.2 + - - +
88A VAL* 3.0 3.5 + - + -
89A ASP* 2.8 36.3 + - - +
104A TYR* 3.4 28.0 - + - -
108A LEU* 4.2 18.9 - - + +
205A PHE* 3.3 37.0 - + - -
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Residues in contact with LYS 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 ASP* 3.0 47.9 + - - +
83A LEU* 3.4 16.0 - - + +
85A TYR* 1.3 75.5 - - - +
87A ASN* 1.3 62.7 + - - +
89A ASP* 4.0 5.0 - - - +
90A LYS* 3.1 26.5 + - + +
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Residues in contact with ASN 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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83A LEU* 2.9 40.8 + - - +
84A ILE 3.0 6.3 + - - +
86A LYS* 1.3 81.8 - - - +
88A VAL* 1.3 66.7 + - - +
89A ASP 3.2 0.4 - - - -
90A LYS* 3.1 20.8 + - - +
91A GLU* 2.9 26.6 + - - +
111A GLU* 3.1 33.5 + - + +
114A ARG* 3.5 7.5 - - - +
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Residues in contact with VAL 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 ILE* 2.9 28.0 + - + +
85A TYR* 3.0 6.9 + - + +
87A ASN* 1.3 73.7 - - - +
89A ASP* 1.3 53.5 + - - +
91A GLU* 3.1 6.2 + - - +
92A PHE* 2.7 36.1 + - - +
104A TYR* 3.7 28.9 - - + +
107A TYR* 3.6 13.4 - - + -
108A LEU* 3.5 34.8 - - + +
111A GLU* 3.8 23.6 - - + -
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Residues in contact with ASP 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 TYR* 2.8 25.2 + - - +
86A LYS* 4.0 5.1 - - - +
88A VAL* 1.3 73.6 - - - +
90A LYS* 1.3 66.3 + - - +
92A PHE* 3.7 6.0 - - - +
93A ALA* 2.9 28.6 + - - +
104A TYR* 3.1 28.9 + - - -
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Residues in contact with LYS 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 LYS* 3.1 16.9 + - + +
87A ASN* 3.1 23.2 + - - +
89A ASP* 1.3 78.6 - - - +
91A GLU* 1.3 69.8 + - - +
93A ALA* 3.7 4.6 + - - +
94A LYS* 3.3 29.8 + - + +
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Residues in contact with GLU 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 ASN* 2.9 17.2 + - - +
88A VAL* 3.8 4.5 - - - +
90A LYS* 1.3 85.6 - - - +
92A PHE* 1.3 66.1 + - - +
94A LYS* 3.2 49.5 + - + +
95A ASP 3.9 1.0 + - - -
107A TYR* 3.1 31.4 - - + -
111A GLU* 6.3 1.8 - - + -
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Residues in contact with PHE 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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88A VAL 2.7 21.6 + - - +
89A ASP* 3.7 7.6 - - - +
91A GLU* 1.3 72.8 - - - +
93A ALA* 1.3 59.9 + - - +
95A ASP 3.5 1.0 - - - +
96A GLY* 3.0 39.7 + - - -
100A GLY* 6.2 1.6 - - - -
101A GLU 4.7 8.7 - - - -
103A ILE* 3.5 31.4 - - + -
104A TYR* 3.6 48.7 - + + -
107A TYR* 3.7 14.8 - + + -
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Residues in contact with ALA 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 ASP 2.9 17.2 + - - +
90A LYS* 3.9 5.2 - - - +
92A PHE* 1.3 79.6 - - - +
94A LYS* 1.3 66.3 + - - +
95A ASP 3.6 4.2 + - - +
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Residues in contact with LYS 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 LYS* 3.3 25.4 + - + +
91A GLU* 3.2 43.6 + - + +
92A PHE 3.2 0.4 - - - -
93A ALA* 1.3 80.4 - - - +
95A ASP* 1.3 61.7 + - + +
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Residues in contact with ASP 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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91A GLU 3.9 1.2 + - - -
92A PHE 3.5 4.6 + - - +
93A ALA 4.3 2.9 - - - +
94A LYS* 1.3 81.5 - - + +
96A GLY* 1.3 73.9 + - - +
97A HIS* 3.2 30.2 + - - +
107A TYR* 4.3 5.1 + - + +
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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