Contacts of the helix formed by residues 79 - 93 (chain A) in PDB entry 1W8I
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 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 TYR 3.6 4.2 + - - +
78A THR* 1.3 73.8 - - - +
80A ASP* 1.3 70.8 + - - +
81A GLU* 3.1 11.3 + - - +
82A VAL* 2.9 30.1 + - - +
83A GLU* 3.0 24.7 + - - +
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Residues in contact with ASP 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 ASP* 1.3 81.4 - - - +
81A GLU* 1.3 72.2 + - - +
83A GLU* 4.0 6.2 - - - +
84A ARG* 2.9 31.0 + - - +
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Residues in contact with GLU 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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79A ASP* 3.1 11.8 + - - +
80A ASP* 1.3 91.0 + - - +
82A VAL* 1.3 64.9 + - + +
84A ARG* 2.7 47.8 + - - +
85A LYS* 3.3 45.1 + - - +
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Residues in contact with VAL 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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78A THR* 3.9 19.7 - - + -
79A ASP* 2.9 23.4 + - - +
81A GLU* 1.3 76.8 - - + +
83A GLU* 1.3 57.0 + - - +
85A LYS* 3.3 5.9 + - - +
86A ALA* 2.9 24.3 + - - +
105A ILE* 4.3 9.2 - - + -
108A VAL* 3.9 15.9 - - + +
109A VAL* 3.8 30.1 - - + -
112A GLU* 3.5 24.0 - - - +
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Residues in contact with GLU 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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43A ASN* 5.3 0.7 + - - -
44A HIS* 2.7 30.8 + - - -
78A THR* 2.7 20.7 + - - +
79A ASP 3.0 21.1 + - - +
80A ASP* 4.0 5.8 - - - +
82A VAL* 1.3 73.6 - - - +
84A ARG* 1.3 60.7 + - - +
87A LEU* 2.8 32.1 + - + +
101A TYR* 2.7 42.4 + - - +
105A ILE* 3.7 9.0 - - + -
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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
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80A ASP* 2.9 20.7 + - - +
81A GLU* 2.7 39.2 + - - +
82A VAL 3.4 0.2 - - - -
83A GLU* 1.3 76.0 - - - +
85A LYS* 1.3 81.8 + - - +
87A LEU* 3.5 11.8 + - + +
88A GLU* 3.3 52.9 + - + +
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Residues in contact with LYS 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 GLU* 3.3 41.3 + - - +
82A VAL 3.6 6.1 - - - +
84A ARG* 1.3 92.0 - - - +
86A ALA* 1.3 63.8 + - - +
88A GLU* 3.2 18.0 + - - +
89A VAL* 3.1 24.1 + - + +
108A VAL* 3.9 14.8 - - + -
112A GLU* 3.0 32.8 + - - +
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Residues in contact with ALA 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 VAL 2.9 12.0 + - - +
83A GLU 3.3 3.1 + - - +
85A LYS* 1.3 75.1 - - - +
87A LEU* 1.3 57.9 + - - +
89A VAL* 3.2 1.6 + - - +
90A PHE* 2.8 26.9 + - - +
101A TYR* 4.2 4.5 - - + +
104A ALA* 3.4 15.2 - - + +
105A ILE* 3.4 51.4 - - + +
108A VAL* 3.6 10.2 - - + +
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Residues in contact with LEU 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 GLU* 2.8 19.3 + - + +
84A ARG* 3.5 11.4 - - + +
86A ALA* 1.3 77.2 - - - +
88A GLU* 1.3 56.7 + - + +
90A PHE* 3.3 9.4 + - + +
91A LYS* 2.8 31.9 + - - +
101A TYR* 3.6 28.6 - - + +
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Residues in contact with GLU 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* 3.4 36.7 + - + +
85A LYS* 3.2 23.7 + - - +
87A LEU* 1.3 75.9 - - + +
89A VAL* 1.3 64.2 + - + +
91A LYS* 3.4 8.7 + - - +
92A ALA* 3.0 24.7 + - - +
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Residues in contact with VAL 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 LYS* 3.1 14.7 + - + +
86A ALA* 3.2 7.4 + - - +
88A GLU* 1.3 76.5 - - + +
90A PHE* 1.3 63.5 + - - +
92A ALA* 3.2 6.6 + - - +
93A ARG* 3.1 30.5 + - + +
99A PHE* 3.8 20.9 - - + -
104A ALA* 4.2 7.6 - - + +
107A GLU* 3.7 24.0 - - + +
108A VAL* 4.2 15.7 - - + -
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Residues in contact with PHE 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 ALA 2.8 19.2 + - - +
87A LEU* 3.6 11.4 - - + +
89A VAL* 1.3 74.2 - - - +
91A LYS* 1.3 66.3 + - + +
93A ARG 3.2 3.9 + - - -
94A VAL* 3.0 45.7 + - + -
99A PHE* 3.9 19.7 - + - -
100A SER* 3.9 5.6 - - - -
101A TYR* 3.7 49.4 - + + -
104A ALA* 4.1 8.5 - - + +
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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 LEU 2.8 20.7 + - - +
88A GLU* 3.7 7.0 - - - +
90A PHE* 1.3 78.8 - - + +
92A ALA* 1.3 64.4 + - - +
93A ARG 3.2 0.9 + - - -
94A VAL* 3.2 26.6 + - + +
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Residues in contact with ALA 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 GLU 3.0 17.8 + - - +
89A VAL* 3.2 8.9 + - - +
91A LYS* 1.3 77.4 - - - +
93A ARG* 1.3 63.7 + - + +
94A VAL* 3.8 0.7 + - - +
95A TYR* 5.7 2.9 - - - -
96A GLU* 3.9 7.6 - - - +
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Residues in contact with ARG 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 VAL* 3.1 22.3 + - + +
90A PHE* 3.2 3.8 + - - +
91A LYS 3.1 0.8 - - - -
92A ALA* 1.3 85.2 - - + +
94A VAL* 1.3 61.6 + - - +
95A TYR 3.1 3.6 - - - -
96A GLU* 2.7 60.4 + - + +
99A PHE* 3.2 49.2 - - + +
107A GLU* 3.1 27.6 + - - -
123A ARG* 2.9 34.3 + - - +
125A SER* 4.2 8.3 - - - +
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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