Contacts of the helix formed by residues 67 - 78 (chain A) in PDB entry 2OX4
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU* 5.3 4.7 + - - +
64A ASP* 2.9 37.7 + - - +
66A PHE* 1.3 76.5 - - - +
68A THR* 1.3 64.0 + - - +
69A GLU 3.3 3.6 - - - -
70A ALA* 3.4 7.6 + - + +
71A ILE* 3.0 29.0 + - + +
113H TYR* 5.5 0.9 - - - -
114H LYS* 5.2 5.0 + - - +
117H GLY 3.6 4.9 - - - -
118H GLY* 3.4 5.0 - - - -
119H LYS* 3.1 41.3 + - - +
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Residues in contact with THR 68 (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 PRO 3.5 9.6 - - - +
66A PHE 3.0 3.4 + - - -
67A ASN* 1.3 75.6 - - - +
69A GLU* 1.3 63.9 + - - +
71A ILE* 4.1 5.8 - - - +
72A TRP* 3.0 25.5 + - - +
97A ASP* 4.0 9.1 - - - +
100A PHE* 3.6 23.0 - - + -
101A TRP* 3.9 17.0 - - - +
104A LYS* 2.8 40.4 + - - +
296A THR* 3.9 15.8 + - - -
117H GLY* 3.3 10.1 + - - -
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Residues in contact with GLU 69 (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 THR* 1.3 79.7 + - - +
70A ALA* 1.3 56.4 + - - +
72A TRP* 3.6 4.3 - - - +
73A GLU* 3.0 29.5 + - - +
101A TRP* 6.1 0.7 - - - -
296A THR* 3.4 16.1 - - - +
300A LYS* 2.8 29.2 + - - -
3414A GOL 5.4 0.5 + - - -
116H LEU 3.9 2.2 - - - +
117H GLY* 3.1 28.8 + - - +
120H ASN* 3.8 10.3 - - - +
299H LYS* 2.9 28.8 + - - -
303H ASP* 4.5 0.3 - - - +
332H ALA 3.4 24.0 - - - +
334H PRO* 4.0 16.2 - - + +
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Residues in contact with ALA 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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63A GLU* 6.2 0.4 - - - +
67A ASN* 3.4 13.9 + - + +
69A GLU* 1.3 76.5 - - - +
71A ILE* 1.3 61.6 + - + +
73A GLU* 3.5 3.8 + - - +
74A LYS* 2.8 29.8 + - - +
117H GLY 4.5 0.4 + - - -
119H LYS 3.4 24.5 - - - +
120H ASN* 3.6 18.9 + - - +
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Residues in contact with ILE 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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3A ILE* 5.0 0.2 - - + -
60A LEU* 3.5 25.8 - - + -
63A GLU* 4.0 34.3 - - + +
64A ASP 3.4 26.7 - - - +
65A PRO* 4.5 2.0 - - + -
67A ASN* 3.0 21.4 + - + +
68A THR 4.1 2.9 - - - +
70A ALA* 1.3 75.9 - - + +
72A TRP* 1.3 64.8 + - - +
74A LYS* 3.2 7.7 + - + +
75A LEU* 2.9 31.4 + - + +
100A PHE* 3.6 37.2 - - + -
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Residues in contact with TRP 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 THR 3.0 17.7 + - - +
69A GLU* 3.6 7.0 - - - +
71A ILE* 1.3 77.3 - - - +
73A GLU* 1.3 63.8 + - - +
75A LEU* 3.3 2.7 + - - +
76A PHE* 2.8 54.5 + + + +
90A PHE* 3.7 30.5 - + - -
93A ILE* 3.3 29.3 - - + +
97A ASP* 4.0 17.3 - - + -
270A ARG* 3.9 16.8 - - - -
271A TRP* 4.1 8.1 - + - -
293A GLY* 2.8 31.5 + - - -
296A THR* 4.1 14.1 - - + -
297A GLU* 3.3 42.5 - - + +
300A LYS* 5.6 2.7 - - - +
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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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69A GLU 3.0 17.5 + - - +
70A ALA* 3.8 6.1 - - - +
72A TRP* 1.3 83.4 - - - +
74A LYS* 1.3 50.6 + - - +
76A PHE* 3.3 12.5 + - - +
77A LYS* 2.8 79.6 + - + +
270A ARG* 5.5 0.7 + - - -
182B GLU* 4.3 3.8 - - - +
120H ASN* 4.9 0.2 - - - +
306H HIS* 2.9 31.8 + - - -
334H PRO* 3.7 25.9 - - + +
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Residues in contact with LYS 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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59A LEU* 2.8 46.2 + - + +
60A LEU* 5.3 4.3 - - + -
63A GLU* 2.7 30.6 + - + +
70A ALA 2.8 21.7 + - - +
71A ILE* 3.4 9.4 - - - +
73A GLU* 1.3 72.9 - - - +
75A LEU* 1.3 58.1 + - + +
78A LYS* 2.8 55.0 + - + +
79A THR* 3.9 1.9 + - - +
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Residues in contact with LEU 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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56A TYR* 4.0 39.7 + - + -
59A LEU* 3.9 25.8 - - + -
60A LEU* 4.4 22.9 - - + -
71A ILE* 2.9 36.1 + - + +
72A TRP* 3.8 4.0 - - - +
74A LYS* 1.3 74.6 - - + +
76A PHE* 1.3 56.0 + - - +
79A THR* 2.6 32.7 + - + +
82A GLY* 3.9 4.2 - - - -
93A ILE* 3.9 36.1 - - + +
96A PHE* 4.9 5.4 - - + -
100A PHE* 5.7 0.2 - - + -
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Residues in contact with PHE 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 TRP* 2.8 38.1 + + + +
73A GLU* 3.5 18.2 - - - +
75A LEU* 1.3 78.1 - - - +
77A LYS* 1.3 87.8 - - - +
78A LYS 3.7 0.2 - - - -
79A THR* 4.1 0.7 + - - -
80A PHE 5.1 0.3 - - - +
82A GLY* 3.3 33.4 + - - -
83A GLN* 3.2 32.5 + - + +
90A PHE* 4.2 10.8 - + - -
93A ILE* 4.1 3.7 - - + +
271A TRP* 3.5 37.2 - + - -
243B THR* 4.1 14.1 - - + -
245B LEU* 3.7 23.1 - - + -
306H HIS* 4.9 1.1 - - - -
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Residues in contact with LYS 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* 2.8 57.0 + - + +
76A PHE* 1.3 97.8 - - + +
78A LYS* 1.3 74.1 + - + +
79A THR 3.6 1.6 - - - -
80A PHE* 4.6 2.6 + - - -
83A GLN* 3.4 34.6 - - + +
182B GLU* 2.8 35.3 + - - +
216B GLY 5.5 0.2 - - - +
217B HIS* 5.8 4.2 - - - -
243B THR* 3.9 15.3 - - - -
306H HIS* 3.9 10.6 - - - -
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Residues in contact with LYS 78 (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 LEU* 4.8 6.6 - - + +
74A LYS* 2.8 43.8 + - + +
77A LYS* 1.3 83.6 + - + +
79A THR* 1.3 62.5 + - - +
80A PHE 3.4 2.6 + - - -
44B VAL* 4.5 6.4 - - - +
176B ARG* 3.8 24.3 - - - +
179B VAL 4.8 8.5 + - - -
180B PHE* 5.7 7.7 - - - -
217B HIS* 6.0 0.8 - - - -
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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