Contacts of the helix formed by residues 76 - 89 (chain A) in PDB entry 2O06
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 GLU 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A CYS* 4.3 7.0 - - + -
72A THR 3.0 22.2 + - - +
73A GLU* 3.8 14.1 - - - +
74A ARG 3.8 0.4 - - - -
75A ASP* 1.3 80.2 + - - +
77A PHE* 1.3 75.6 + - - +
78A SER 3.1 0.7 + - - -
79A TYR* 3.3 3.5 + - - +
80A GLN* 2.8 46.9 + - - +
109A ARG* 2.8 46.1 + - - -
139A GLY 5.4 0.2 - - - -
140A MET* 3.8 27.0 - - + +
238A ILE* 4.5 5.2 - - - -
277A LYS* 4.8 7.4 + - - -
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 5.0 4.0 - - - -
74A ARG 3.1 26.0 - - - -
75A ASP* 4.2 1.3 - - - -
76A GLU* 1.3 95.9 + - - +
78A SER* 1.3 68.6 + - - +
80A GLN* 4.3 3.1 - - - -
81A GLU* 2.9 49.0 + - + +
109A ARG* 4.4 4.3 - - - +
110A GLU* 5.5 0.2 - - - +
277A LYS* 3.6 48.7 - - + +
278A TYR* 3.8 10.5 - - + -
211B TRP* 3.5 33.2 - + - -
293B PHE* 3.8 26.2 - + + -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP 3.2 11.1 + - - -
76A GLU 3.1 1.0 + - - -
77A PHE* 1.3 80.2 - - - +
79A TYR* 1.3 64.2 + - - +
81A GLU* 4.1 0.5 - - - +
82A MET* 3.1 29.8 + - - +
236A CYS* 3.4 11.2 - - - -
237A THR 2.6 28.2 + - - -
238A ILE* 4.4 3.6 - - - -
278A TYR* 3.3 32.0 - - - -
211B TRP* 4.0 8.5 - - - -
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Residues in contact with TYR 79 (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 GLU 3.3 4.3 + - - +
78A SER* 1.3 79.7 + - - +
80A GLN* 1.3 78.8 + - - +
82A MET* 4.0 0.3 - - - +
83A ILE* 2.9 59.0 + - + +
173A ASP* 2.6 36.3 + - - -
174A SER 3.9 0.2 + - - -
206A GLN* 3.5 28.5 - - + +
236A CYS* 4.0 11.0 - - - -
238A ILE* 3.8 20.2 - - + +
241A TYR* 3.5 30.5 - + + +
246A ILE* 3.7 13.0 - - + -
248A PHE* 3.7 21.3 - + - -
601A PUT 3.5 9.3 + - - -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS* 5.0 3.9 - - - +
76A GLU* 2.8 62.7 + - - +
77A PHE 4.2 0.9 - - - +
79A TYR* 1.3 100.3 - - - +
81A GLU* 1.3 62.0 + - - +
83A ILE* 3.6 7.0 - - - +
84A ALA* 3.3 24.8 + - - +
104A ASP* 3.6 14.1 - - - +
106A GLY* 3.4 28.7 - - - -
107A VAL* 3.6 14.0 - - - +
109A ARG* 3.8 9.4 - - - +
110A GLU* 3.7 6.7 - - + +
140A MET* 3.7 11.6 - - - +
173A ASP* 3.9 2.8 - - - +
241A TYR* 5.4 1.0 + - - -
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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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77A PHE* 2.9 36.4 + - - +
78A SER 4.1 1.3 - - - +
80A GLN* 1.3 76.3 - - - +
82A MET* 1.3 58.7 + - - +
85A ASN* 2.9 41.1 + - - +
110A GLU* 3.6 28.5 - - - +
113A LYS* 5.2 0.9 + - - -
275A GLN 4.4 1.0 - - - +
276A LEU* 3.6 17.3 - - + +
277A LYS* 2.9 26.4 + - - +
278A TYR* 2.8 24.9 + - + -
279A TYR* 2.8 22.7 + - + +
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 3.1 22.5 + - - +
80A GLN 3.3 0.2 - - - -
81A GLU* 1.3 75.3 - - - +
83A ILE* 1.3 66.4 + - - +
85A ASN 4.5 0.2 - - - +
86A LEU* 3.0 51.2 + - + +
235A TYR 3.9 10.3 - - - +
236A CYS* 3.7 6.1 - - + -
248A PHE* 3.9 16.4 - - + -
278A TYR* 3.6 34.3 - - + -
279A TYR* 3.6 25.6 - - + -
283A VAL* 4.0 9.2 - - + +
284A HIS* 5.0 0.4 - - - -
287A ALA* 3.5 31.6 - - + -
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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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79A TYR* 2.9 53.2 + - + +
80A GLN* 3.6 3.1 - - - +
82A MET* 1.3 73.3 - - - +
84A ALA* 1.3 59.9 + - - +
87A PRO* 3.0 23.6 - - - +
107A VAL* 3.4 32.5 - - + -
171A ILE* 3.7 25.7 - - + +
172A THR 3.7 15.5 - - - +
173A ASP* 4.0 4.3 - - - -
204A CYS* 3.7 12.6 - - - -
205A CYS 4.6 0.4 - - - -
206A GLN 4.2 6.5 - - - +
248A PHE* 3.6 24.8 - - + -
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Residues in contact with ALA 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 GLN 3.3 16.3 + - - +
81A GLU 3.8 1.3 - - - +
82A MET 3.1 0.2 - - - -
83A ILE* 1.3 80.7 - - - +
85A ASN* 1.3 61.5 + - - +
87A PRO* 3.2 12.8 - - - +
88A LEU* 3.2 27.4 + - + +
107A VAL* 4.5 4.0 - - + +
110A GLU* 3.5 24.9 - - + -
111A VAL* 4.0 17.7 - - + +
171A ILE* 4.1 9.4 - - - -
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Residues in contact with ASN 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* 2.9 39.8 + - - +
84A ALA* 1.3 76.8 - - - +
86A LEU* 1.3 66.8 + - - +
88A LEU* 4.3 3.4 - - - -
89A CYS* 2.8 31.4 + - - +
110A GLU* 4.7 6.1 + - - +
114A HIS* 2.7 32.3 + - - -
266A LEU* 4.8 0.2 - - - +
274A MET* 3.6 11.4 - - - +
276A LEU* 4.2 16.8 - - - +
279A TYR* 3.6 34.3 + - + -
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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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82A MET* 3.0 47.1 + - + +
85A ASN* 1.3 79.0 - - - +
87A PRO* 1.4 65.9 - - + +
90A SER* 2.7 27.5 + - - -
204A CYS* 4.8 0.9 - - - -
234A ALA* 3.8 15.9 - - + -
248A PHE* 3.6 37.2 - - + -
250A LEU* 4.2 13.5 - - + -
279A TYR* 4.3 1.7 - - + -
284A HIS* 3.6 24.8 + - + +
288A PHE* 3.8 30.5 - - + -
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Residues in contact with PRO 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 ILE 3.0 25.6 - - - +
84A ALA 3.2 15.9 - - - +
86A LEU* 1.4 92.8 - - + +
88A LEU* 1.3 59.8 + - - +
90A SER* 3.0 15.0 + - - -
91A HIS* 3.3 9.0 + - - +
169A VAL* 3.8 18.4 - - + -
171A ILE* 4.0 11.2 - - + -
202A VAL* 3.7 20.6 - - + +
203A LEU 4.7 0.2 - - - -
204A CYS* 3.6 27.1 - - + +
250A LEU* 4.0 8.0 - - + -
259A PHE* 5.0 0.4 - - + -
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Residues in contact with LEU 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 ALA* 3.2 28.4 + - + +
85A ASN 4.3 0.7 - - - +
87A PRO* 1.3 79.7 - - + +
89A CYS* 1.3 59.0 + - - +
91A HIS 3.2 14.0 + - - +
94A PRO* 3.6 34.3 - - + +
97A VAL* 3.9 22.0 - - + -
111A VAL* 3.9 28.5 - - + -
114A HIS* 3.5 42.4 - - + +
117A VAL* 4.0 6.3 - - + -
169A VAL* 4.0 9.9 - - + -
171A ILE* 5.3 0.4 - - + -
264A GLN* 3.0 19.8 - - - +
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Residues in contact with CYS 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 ASN* 2.8 28.3 + - - +
86A LEU 4.0 0.2 - - - -
88A LEU* 1.3 72.6 - - - +
90A SER* 1.3 58.6 + - - +
91A HIS 3.4 1.1 - - - -
114A HIS* 3.9 21.8 - - - -
262A PRO* 3.7 4.0 - - + +
263A VAL* 3.2 7.1 + - - +
264A GLN* 3.0 53.2 + - - +
266A LEU* 4.1 11.7 - - - -
279A TYR* 3.3 29.2 - - - +
284A HIS* 4.3 3.4 - - + -
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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