Contacts of the helix formed by residues 79 - 93 (chain A) in PDB entry 2WOE
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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71A SER* 4.0 1.9 + - - +
72A LEU* 5.4 0.2 - - - +
75A LYS* 3.9 30.3 + - + +
77A THR* 3.4 5.9 + - + -
78A LEU* 1.3 74.6 - - - +
80A VAL* 1.3 66.2 + - - +
81A ALA* 3.6 9.4 + - - +
82A ASP* 3.1 28.5 + - + +
83A ILE* 3.0 28.1 + - - +
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Residues in contact with VAL 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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78A LEU* 4.0 7.4 - - + +
79A ASP* 1.3 73.6 + - - +
81A ALA* 1.3 60.6 + - + +
83A ILE* 3.3 10.8 + - + +
84A CYS* 2.9 28.8 + - - -
115A THR* 3.7 30.3 - - + +
152A ALA* 3.9 34.8 - - + +
153A GLN 5.2 0.2 - - - +
156A ILE* 3.9 17.3 - - + -
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Residues in contact with ALA 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* 3.3 8.3 + - - +
80A VAL* 1.3 81.5 - - + +
82A ASP* 1.3 57.7 + - - +
84A CYS* 3.2 6.4 + - - +
85A GLU* 2.9 31.8 + - + +
109A TYR* 3.6 8.9 + - + +
115A THR* 4.1 19.7 - - + -
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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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71A SER* 2.6 28.2 + - - +
74A ALA* 5.0 2.3 - - - +
75A LYS* 3.4 30.7 + - - +
79A ASP* 3.1 29.8 + - + +
81A ALA* 1.3 76.1 - - - +
83A ILE* 1.3 64.8 + - - +
85A GLU* 3.1 13.0 + - - +
86A GLU* 2.9 33.1 + - - +
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Residues in contact with ILE 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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68A LEU* 3.5 29.2 - - + -
71A SER* 3.5 23.3 - - - +
72A LEU* 4.8 5.2 - - + -
78A LEU* 3.9 26.7 - - + -
79A ASP 3.0 22.3 + - - +
80A VAL* 3.5 12.1 - - + +
82A ASP* 1.3 75.8 - - - +
84A CYS* 1.3 57.9 + - - +
86A GLU* 3.3 4.4 + - - +
87A PHE* 2.9 49.5 + - + -
153A GLN* 4.3 9.0 - - + -
156A ILE* 3.4 19.7 - - + -
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Residues in contact with CYS 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 VAL 2.9 21.2 + - - -
81A ALA 3.2 9.2 + - - +
83A ILE* 1.3 75.2 - - - +
85A GLU* 1.3 57.7 + - - +
87A PHE* 3.3 8.7 + - - +
88A ALA* 2.8 29.5 + - - +
106A ILE* 5.0 1.0 - - - +
109A TYR* 3.5 42.1 - - + -
115A THR* 3.8 18.6 - - - -
156A ILE* 3.7 33.9 - - + -
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Residues in contact with GLU 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 ALA 2.9 19.6 + - - +
82A ASP* 3.4 16.4 - - - +
84A CYS* 1.3 76.1 - - - +
86A GLU* 1.3 57.8 + - + +
88A ALA* 3.2 9.2 + - - +
89A LEU* 2.8 43.1 + - + +
92A LYS* 5.6 2.9 + - - -
109A TYR* 2.5 29.6 + - - +
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Residues in contact with GLU 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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67A ALA* 3.5 30.0 - - + +
70A ARG* 3.5 38.7 + - - +
71A SER* 4.0 14.1 + - - +
74A ALA* 5.9 2.4 - - - +
82A ASP* 2.9 26.5 + - - +
83A ILE* 3.6 7.2 - - - +
85A GLU* 1.3 77.1 - - + +
87A PHE* 1.3 57.9 + - - +
89A LEU* 3.5 20.4 + - - +
90A TRP* 2.9 29.5 + - - +
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Residues in contact with PHE 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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64A MET* 3.7 38.4 - - + -
67A ALA* 3.9 10.8 - - + -
68A LEU* 4.0 12.3 - - + -
83A ILE* 2.9 34.8 + - + +
84A CYS* 3.6 5.6 - - - +
86A GLU* 1.3 76.0 - - - +
88A ALA* 1.3 58.1 + - - +
90A TRP* 3.3 11.1 + - + +
91A LEU* 2.8 28.8 + - - +
106A ILE* 4.0 20.8 - - + +
131A ARG* 3.5 41.3 - - - -
153A GLN* 4.1 4.9 - - - -
156A ILE* 3.8 37.7 - - + -
157A THR* 4.8 0.4 - - + -
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Residues in contact with ALA 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 CYS 2.8 14.5 + - - +
85A GLU* 3.2 18.4 + - - +
87A PHE* 1.3 74.1 - - - +
89A LEU* 1.3 59.8 + - + +
91A LEU* 3.2 2.8 + - - +
92A LYS* 2.9 45.5 + - - +
106A ILE* 3.7 12.5 - - + +
109A TYR* 4.7 4.5 - - + -
110A MET* 3.9 25.5 - - + +
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Residues in contact with LEU 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 GLU* 2.8 30.4 + - + +
86A GLU* 3.8 23.3 - - - +
88A ALA* 1.3 72.8 - - - +
90A TRP* 1.3 63.3 + - - +
92A LYS* 3.4 21.8 + - + +
93A SER* 3.1 21.1 + - - -
34B GLU* 6.1 0.9 - - - +
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Residues in contact with TRP 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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60A ASP* 3.6 26.9 - - + -
63A GLU* 2.9 44.2 + - + +
64A MET* 3.7 37.0 - - + -
67A ALA* 4.6 9.0 - - + -
70A ARG* 6.1 0.7 - - - +
86A GLU 2.9 18.7 + - - +
87A PHE* 3.4 11.2 - + - +
89A LEU* 1.3 76.9 - - - +
91A LEU* 1.3 77.7 + - + +
93A SER* 2.6 32.7 + - - -
95A PRO* 3.5 18.1 - - + +
97A ASN 3.7 7.2 - - - -
98A VAL* 3.8 31.2 - - + -
99A GLY 5.2 0.4 - - - -
102A CYS* 5.2 0.4 - - + -
106A ILE* 4.0 17.9 - - + -
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Residues in contact with LEU 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 PHE 2.8 16.3 + - - +
88A ALA 3.2 7.4 + - - +
90A TRP* 1.3 82.8 - - + +
92A LYS* 1.3 60.9 + - + +
93A SER 3.4 1.0 + - - -
94A ARG* 3.7 2.1 + - - +
95A PRO* 3.4 15.7 - - + +
98A VAL* 3.9 37.2 - - + -
103A ARG* 4.4 12.8 - - + +
106A ILE* 3.6 30.7 - - + -
107A ARG* 4.3 16.4 - - + -
110A MET* 4.1 14.8 - - + -
52B ARG* 6.2 0.4 - - - +
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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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85A GLU* 5.6 3.4 + - - -
88A ALA* 2.9 37.7 + - - +
89A LEU* 3.7 22.3 - - + +
90A TRP 3.1 0.2 - - - -
91A LEU* 1.3 74.1 - - + +
93A SER* 1.3 54.6 + - - +
94A ARG 3.2 8.2 + - - -
110A MET* 4.6 24.8 - - + +
30B MET* 5.3 2.4 - - - +
38B GLN* 3.3 17.3 + - - +
50B TRP* 5.5 12.1 - - + -
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Residues in contact with SER 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 GLU* 6.0 0.3 - - - -
89A LEU 3.1 10.8 + - - -
90A TRP* 2.6 33.0 + - - -
92A LYS* 1.3 76.5 - - - +
94A ARG* 1.3 67.6 + - - +
95A PRO* 4.0 5.9 - - - +
38B GLN* 3.4 24.4 - - - +
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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