Contacts of the helix formed by residues 79 - 94 (chain A) in PDB entry 1OMW
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 ALA 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A CYS* 3.9 24.2 - - + +
76A LEU* 3.5 12.7 + - + -
77A GLU 3.0 2.0 + - - -
78A GLU* 1.3 79.0 - - + +
80A LYS* 1.3 63.8 + - - +
81A PRO* 3.4 1.6 - - - -
82A LEU* 3.4 13.2 + - - +
83A VAL* 3.3 22.2 + - - +
157A LEU* 4.8 2.2 - - + -
161A VAL* 3.8 30.1 - - + -
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Residues in contact with LYS 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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72A CYS 3.7 8.5 + - - +
73A LEU* 3.5 41.5 - - + +
76A LEU 3.8 5.8 + - - +
77A GLU* 3.5 25.4 + - - +
79A ALA* 1.3 74.5 - - - +
81A PRO* 1.3 69.2 - - + +
82A LEU 3.0 0.6 + - - -
83A VAL 3.1 0.9 + - - +
84A GLU* 2.8 57.7 + - - +
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Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 3.5 12.6 - - - +
78A GLU* 3.6 9.4 - - - +
79A ALA 3.5 3.6 - - - -
80A LYS* 1.3 97.0 - - + +
82A LEU* 1.3 57.8 + - + +
84A GLU* 4.3 10.1 - - + +
85A PHE* 3.1 24.7 + - - +
112A TYR* 4.0 5.0 - - + -
115A LYS* 5.2 8.7 - - - +
116A GLU* 3.5 32.9 - - + +
121A SER 5.9 0.2 - - - +
124A PHE* 6.0 0.2 - - - -
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Residues in contact with LEU 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 GLU* 4.2 17.9 - - - +
79A ALA* 3.4 8.7 + - - +
80A LYS 3.0 0.8 - - - -
81A PRO* 1.3 80.5 - - + +
83A VAL* 1.3 60.9 + - - +
85A PHE* 3.5 4.8 + - - +
86A TYR* 2.9 26.0 + - - +
123A PRO* 4.2 11.2 - - + -
124A PHE* 3.4 37.7 - - + -
153A ILE* 4.0 16.9 - - + +
156A ASN* 3.7 36.3 - - + +
157A LEU* 3.7 27.6 - - + -
161A VAL* 5.0 4.7 - - + -
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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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59A PHE* 6.1 1.3 - - + -
65A TYR* 4.4 5.2 - - + +
68A PHE* 5.0 2.9 - - + -
69A ARG* 3.9 25.8 - - + -
72A CYS* 3.5 35.0 - - + -
73A LEU* 4.3 14.4 - - + -
79A ALA 3.3 8.0 + - - +
80A LYS 3.1 5.6 + - - +
82A LEU* 1.3 73.2 - - - +
84A GLU* 1.3 68.7 + - - +
85A PHE 3.1 1.1 - - - -
86A TYR* 3.0 7.4 + - + +
87A GLU* 2.8 40.8 + - + +
157A LEU* 4.4 13.9 - - + -
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.7 20.7 - - + +
80A LYS* 2.8 48.7 + - - +
81A PRO* 4.3 5.6 - - + +
83A VAL* 1.3 76.5 - - - +
85A PHE* 1.3 62.2 + - - +
87A GLU* 3.3 6.8 + - - +
88A GLU* 3.1 26.2 + - - +
112A TYR* 3.7 27.7 + - + +
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Residues in contact with PHE 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 PRO 3.1 20.5 + - - +
82A LEU 3.7 4.3 - - - +
83A VAL 3.1 0.2 - - - -
84A GLU* 1.3 75.9 - - - +
86A TYR* 1.3 67.0 + - - +
88A GLU* 3.3 1.5 + - + +
89A ILE* 2.9 53.0 + - + +
108A ILE* 3.8 20.4 - - + -
112A TYR* 3.5 38.3 - + + -
113A ILE* 4.4 10.1 - - + -
116A GLU* 4.8 1.6 - - - -
122A HIS* 4.4 6.1 - + - -
124A PHE* 4.4 16.2 - + - -
146A PHE* 4.3 3.8 - + - -
149A TYR* 3.5 46.2 - + + -
153A ILE* 4.3 9.4 - - + -
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Residues in contact with TYR 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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59A PHE* 3.8 33.4 - + - -
65A TYR* 3.7 28.3 - + - -
82A LEU 2.9 16.5 + - - +
83A VAL* 3.2 13.7 - - + +
85A PHE* 1.3 78.7 - - - +
87A GLU* 1.3 62.0 + - - +
89A ILE* 3.5 5.3 + - - +
90A LYS* 3.1 58.8 + - + +
150A ILE* 4.2 31.3 - - + +
153A ILE* 4.2 24.8 - - + +
154A CYS* 4.9 6.5 - - - -
157A LEU* 5.7 1.1 - - + -
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Residues in contact with GLU 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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65A TYR* 2.9 31.3 + - - +
69A ARG* 2.8 41.5 + - - -
73A LEU* 4.4 5.5 - - - +
83A VAL* 2.8 28.4 + - + +
84A GLU* 4.0 6.0 - - - +
86A TYR* 1.3 75.3 - - + +
88A GLU* 1.3 58.4 + - - +
90A LYS* 3.4 8.2 + - + +
91A LYS* 3.2 47.4 + - - +
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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 GLU 3.1 16.3 + - - +
85A PHE* 3.8 3.8 - - + +
86A TYR 3.2 0.2 - - - -
87A GLU* 1.3 75.6 - - - +
89A ILE* 1.3 63.0 + - - +
90A LYS 3.1 0.9 - - - -
91A LYS* 3.5 20.2 + - - +
92A TYR* 3.1 21.8 + - - +
104A CYS* 5.1 4.4 - - - -
107A GLU* 5.3 7.8 - - - +
108A ILE* 3.6 29.2 - - + +
112A TYR* 3.9 28.9 + - + -
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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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85A PHE* 2.9 52.1 + - + +
86A TYR* 3.7 6.1 - - - +
88A GLU* 1.3 76.8 - - - +
90A LYS* 1.3 60.7 + - - +
92A TYR* 3.2 9.7 + - + +
93A GLU* 3.1 28.3 + - + +
108A ILE* 4.3 4.2 - - + +
143A PRO 5.8 0.2 - - - +
146A PHE* 3.4 39.3 - - + +
149A TYR* 4.2 7.0 - - + -
150A ILE* 4.3 25.8 - - + -
153A ILE* 4.0 20.0 - - + -
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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 TYR* 3.1 58.5 + - + +
87A GLU* 3.5 10.3 - - + +
88A GLU 3.1 0.6 - - - -
89A ILE* 1.3 77.7 - - - +
91A LYS* 1.3 62.7 + - - +
93A GLU* 2.6 55.3 + - - +
94A LYS* 3.5 25.7 + - - +
147A GLN* 5.2 1.4 - - - +
150A ILE* 3.8 18.1 - - - +
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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 GLU* 3.2 35.2 + - - +
88A GLU* 3.7 23.6 - - + +
90A LYS* 1.3 76.7 - - - +
92A TYR* 1.3 65.4 + - - +
93A GLU 3.1 1.0 + - - -
94A LYS* 3.2 20.6 + - + +
95A LEU* 3.4 16.1 + - + +
104A CYS* 6.2 1.6 - - - -
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Residues in contact with TYR 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 3.1 14.8 + - - +
89A ILE* 3.2 14.8 + - + +
91A LYS* 1.3 77.8 - - - +
93A GLU* 1.3 60.8 + - + +
95A LEU* 3.4 22.4 + - + +
101A ARG* 3.6 30.1 - - + +
104A CYS* 3.9 21.3 - - - -
105A SER* 3.6 25.1 - - - -
108A ILE* 4.1 7.2 - - + -
141A VAL* 3.2 26.2 + - - +
142A PRO 2.9 27.8 + - - -
143A PRO* 3.6 19.4 - - + +
145A LEU* 3.8 4.8 - - + +
146A PHE* 3.8 26.9 - + + -
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Residues in contact with GLU 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 ILE* 3.1 15.7 + - + +
90A LYS* 2.6 55.1 + - - +
91A LYS 3.1 0.6 - - - -
92A TYR* 1.3 78.1 - - + +
94A LYS* 1.3 61.5 + - + +
95A LEU 3.3 12.2 + - - +
143A PRO* 3.6 41.4 - - + +
144A ASP* 6.1 0.2 - - - -
147A GLN* 4.4 5.9 + - - -
150A ILE* 3.6 14.9 - - - +
459A GLN* 4.8 3.3 - - - +
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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* 3.5 26.2 - - - +
91A LYS* 3.2 13.4 + - + +
93A GLU* 1.3 76.1 - - + +
95A LEU* 1.3 62.7 + - - -
96A GLU* 3.9 12.8 + - - +
459A GLN* 4.5 5.7 + - - +
463A LEU* 5.0 5.8 - - + +
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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