Contacts of the helix formed by residues 66 - 77 (chain A) in PDB entry 3OX3
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 ASN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.6 8.3 + - + +
65A PHE* 1.3 73.6 - - - +
67A TYR* 1.3 64.9 + - - +
68A GLY* 3.2 8.1 + - - -
69A VAL* 3.1 37.1 + - + +
70A GLU* 2.9 28.6 + - + +
11B HIS* 5.9 1.8 - - - -
193B GLU* 3.1 27.4 + - - +
232B FAD 3.6 15.8 + - - -
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Residues in contact with TYR 67 (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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50A ALA* 3.6 28.9 - - + -
51A THR 3.4 17.7 - - - -
54A ASP* 2.6 31.0 + - + +
65A PHE* 3.7 32.1 + + + -
66A ASN* 1.3 72.3 + - - +
68A GLY* 1.3 62.4 + - - +
70A GLU* 3.9 0.3 - - - +
71A THR* 2.8 60.7 + - + +
84A ILE* 4.3 1.7 - - - +
117A ASP 4.2 14.6 - - - -
118A ARG* 3.5 20.3 + - - +
121A CYS* 6.3 0.9 - - + -
11B HIS* 6.0 1.0 - - - -
12B GLN* 3.9 18.7 + - - +
104B TYR* 4.0 6.3 - - - +
232B FAD 3.9 18.4 - - + -
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.2 7.3 + - - -
67A TYR* 1.3 80.0 - - - +
69A VAL* 1.3 61.8 + - - +
71A THR* 3.3 5.8 + - - -
72A HIS* 3.1 25.5 + - - +
122A GLN* 5.2 0.2 - - - +
233A 4X4 3.3 33.3 - - - +
232B FAD 3.9 13.5 - - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.9 9.6 - - - +
66A ASN* 3.1 34.7 + - + +
68A GLY* 1.3 73.7 - - - +
70A GLU* 1.3 66.8 + - + +
72A HIS* 3.3 6.7 + - - +
73A GLU* 3.0 36.8 + - + +
233A 4X4 4.2 3.6 - - - -
193B GLU* 5.0 3.4 - - - +
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Residues in contact with GLU 70 (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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55A ILE* 3.8 22.7 - - + +
59A LEU* 3.5 16.9 - - - +
60A SER* 2.8 30.3 + - - -
61A ASN* 2.8 38.8 + - - +
64A VAL 4.6 1.2 - - - +
65A PHE* 3.6 19.9 - - + -
66A ASN* 2.9 24.2 + - + +
67A TYR 4.0 1.1 - - - +
69A VAL* 1.3 76.9 - - + +
71A THR* 1.3 57.5 + - - +
73A GLU* 3.5 5.0 + - - +
74A ALA* 2.9 29.1 + - - +
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Residues in contact with THR 71 (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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54A ASP* 4.6 2.0 - - + -
55A ILE* 4.0 12.6 - - + -
67A TYR* 2.8 65.2 + - + +
68A GLY* 3.3 7.4 + - - -
70A GLU* 1.3 73.2 - - - +
72A HIS* 1.3 62.5 + - - +
74A ALA* 3.8 1.4 - - - +
75A TYR* 2.9 29.8 + - - +
80A LEU* 3.8 22.6 - - + +
84A ILE* 5.8 0.4 - - + -
118A ARG 6.0 0.7 - - - +
121A CYS* 4.2 20.0 - - - +
122A GLN 5.3 0.7 + - - -
233A 4X4 5.5 0.2 - - - -
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Residues in contact with HIS 72 (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 GLY 3.1 19.9 + - - +
69A VAL* 3.6 7.3 - - - +
71A THR* 1.3 77.1 + - - +
73A GLU* 1.3 65.9 + - + +
75A TYR* 3.3 2.8 + - - +
76A LYS* 3.1 52.8 + - + +
122A GLN* 3.1 72.7 + - + +
123A GLY* 3.8 9.5 - - - -
127A ASP* 5.1 4.3 + - + +
233A 4X4 4.9 0.2 - - - -
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Residues in contact with GLU 73 (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 SER* 4.1 24.2 - - - +
69A VAL* 3.0 30.3 + - + +
70A GLU* 3.8 4.9 - - - +
72A HIS* 1.3 81.0 + - - +
74A ALA* 1.3 58.4 + - - +
76A LYS* 3.3 32.7 + - - +
77A GLN* 2.9 47.1 + - + +
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Residues in contact with ALA 74 (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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55A ILE* 3.9 18.2 - - + -
70A GLU 2.9 18.5 + - - +
71A THR 3.8 4.5 - - - +
73A GLU* 1.3 72.9 - - - +
75A TYR* 1.3 61.9 + - - +
77A GLN* 3.3 1.3 + - - -
78A ARG 2.9 9.0 + - - -
79A SER* 2.7 50.6 + - - +
80A LEU* 3.8 19.4 + - + -
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Residues in contact with TYR 75 (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 THR 2.9 17.8 + - - +
72A HIS 3.5 4.9 - - - +
73A GLU 3.3 0.2 - - - -
74A ALA* 1.3 76.7 - - - +
76A LYS* 1.3 70.7 + - + +
78A ARG* 3.2 16.9 + - - +
80A LEU* 3.8 12.5 - - + +
85A THR* 6.2 0.4 - - + -
88A GLN* 3.7 22.2 - - - -
92A ARG* 3.2 24.3 + - - -
121A CYS* 3.8 13.0 - - - -
122A GLN 4.1 1.6 - - - +
123A GLY* 3.2 36.4 + - - -
124A PHE* 3.6 28.9 - + + -
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Residues in contact with LYS 76 (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 HIS* 3.1 41.0 + - + +
73A GLU* 3.3 39.8 + - - +
75A TYR* 1.3 87.9 - - + +
77A GLN* 1.3 73.6 + - - +
78A ARG* 3.0 20.5 + - - +
123A GLY* 5.6 1.3 - - - -
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Residues in contact with GLN 77 (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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73A GLU* 2.9 34.6 + - + +
74A ALA* 4.2 1.8 - - - +
76A LYS* 1.3 94.6 + - - +
78A ARG* 1.3 91.4 + - - +
79A SER* 3.2 13.4 + - - -
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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