Contacts of the helix formed by residues 67 - 78 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D GLU* 5.3 4.2 + - - +
64D ASP* 2.9 37.3 + - - +
66D PHE* 1.3 77.1 - - - +
68D THR* 1.3 62.5 + - - +
69D GLU 3.3 3.1 + - - -
70D ALA* 3.5 7.1 + - + +
71D ILE* 3.0 30.9 + - + +
113G TYR* 5.7 0.2 - - - -
114G LYS* 5.4 4.7 - - - +
117G GLY 3.5 4.5 - - - -
118G GLY* 3.4 4.7 - - - -
119G LYS* 3.2 39.6 + - - +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PRO 3.4 19.3 - - - +
66D PHE 2.9 5.9 + - - -
67D ASN* 1.3 73.1 - - - +
69D GLU* 1.3 60.1 + - - +
71D ILE* 4.1 5.0 - - - +
72D TRP* 3.0 31.4 + - - +
97D ASP* 4.1 8.8 - - - +
100D PHE* 3.6 21.7 - - + -
101D TRP* 3.9 15.9 - - - +
104D LYS* 2.9 32.3 + - - +
296D THR* 3.9 14.9 + - - -
117G GLY* 3.2 9.8 + - - -
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR* 1.3 78.8 - - - +
70D ALA* 1.3 57.2 + - - +
72D TRP* 3.6 4.4 - - - +
73D GLU* 3.0 29.6 + - - +
101D TRP* 6.0 1.0 - - - -
296D THR* 3.5 12.9 - - - +
300D LYS* 2.8 32.2 + - - -
116G LEU 3.8 2.4 - - - +
117G GLY* 3.1 29.0 + - - +
120G ASN* 3.8 10.3 - - - +
299G LYS* 2.7 29.1 + - - -
303G ASP* 4.5 0.9 - - - +
332G ALA 3.6 23.1 - - - +
333G ILE* 6.1 0.4 - - - +
334G PRO* 4.1 15.7 - - + +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLU* 6.0 0.9 - - - +
67D ASN* 3.5 13.0 + - + +
68D THR 3.5 0.2 - - - -
69D GLU* 1.3 77.5 - - - +
71D ILE* 1.3 60.0 + - + +
73D GLU* 3.4 3.9 + - - +
74D LYS* 2.8 29.5 + - - +
117G GLY 4.5 0.8 + - - -
119G LYS 3.4 24.9 - - - +
120G ASN* 3.5 20.0 + - - +
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Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 3.5 27.1 - - + -
63D GLU* 3.7 35.2 - - + +
64D ASP 3.4 23.3 - - - +
65D PRO* 4.5 1.6 - - + -
67D ASN* 3.0 26.2 + - + +
68D THR 4.1 2.5 - - - +
70D ALA* 1.3 74.8 - - + +
72D TRP* 1.3 66.2 + - - +
74D LYS* 3.2 9.0 + - + +
75D LEU* 2.9 30.0 + - + +
100D PHE* 3.7 35.7 - - + -
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Residues in contact with TRP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR 3.0 18.1 + - - +
69D GLU* 3.6 7.0 - - - +
71D ILE* 1.3 75.8 - - - +
73D GLU* 1.3 64.2 + - - +
75D LEU* 3.2 3.6 + - - +
76D PHE* 2.9 51.5 + + + -
90D PHE* 3.8 30.3 - + - -
93D ILE* 3.3 30.4 - - + +
97D ASP* 4.0 15.9 - - + +
270D ARG* 3.9 16.2 - - - -
271D TRP* 4.0 7.4 - + - -
293D GLY* 2.8 31.5 + - - -
296D THR* 4.0 14.6 - - + -
297D GLU* 3.3 41.2 - - + +
300D LYS* 5.6 2.5 - - - +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLU 3.0 18.1 + - - +
70D ALA* 3.9 5.6 - - - +
72D TRP* 1.3 82.3 - - + +
74D LYS* 1.3 52.0 + - - +
76D PHE* 3.3 12.0 + - - +
77D LYS* 2.8 78.6 + - + +
270D ARG* 5.5 0.5 + - - -
182E GLU* 4.1 4.2 - - - +
120G ASN* 4.9 0.4 - - - +
306G HIS* 3.0 31.9 + - - -
334G PRO* 3.8 25.2 - - + +
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 2.9 52.3 + - + +
60D LEU* 5.5 2.7 - - + -
63D GLU* 3.6 24.2 + - + +
70D ALA 2.8 19.5 + - - +
71D ILE* 3.2 9.8 + - + +
73D GLU* 1.3 77.0 - - - +
75D LEU* 1.3 61.0 + - + +
78D LYS* 2.8 54.6 + - + +
79D THR* 3.9 2.3 + - - +
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 4.1 34.4 + - + -
59D LEU* 4.0 24.7 - - + -
60D LEU* 4.3 23.6 - - + -
71D ILE* 2.9 34.0 + - + +
72D TRP* 3.8 2.5 - - - +
74D LYS* 1.3 77.7 - - + +
76D PHE* 1.3 56.0 + - - +
79D THR* 2.7 33.5 + - + +
82D GLY* 3.9 3.5 - - - -
93D ILE* 3.7 41.7 - - + +
96D PHE* 4.9 6.1 - - + -
100D PHE* 5.7 0.2 - - + -
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Residues in contact with PHE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TRP* 2.9 37.5 + + + +
73D GLU* 3.5 17.7 - - - +
75D LEU* 1.3 78.6 - - - +
77D LYS* 1.3 89.1 + - - +
79D THR* 4.1 0.7 + - - -
80D PHE 5.1 0.3 + - - +
82D GLY* 3.2 49.6 + - - -
83D GLN* 3.3 15.4 + - - +
90D PHE* 4.3 13.0 - + - -
93D ILE* 4.1 5.1 - - + +
271D TRP* 3.6 39.9 - + - -
243E THR* 4.1 13.9 - - + -
245E LEU* 3.7 18.6 - - + -
306G HIS* 4.9 1.1 - - - -
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D GLU* 2.8 55.2 + - + +
76D PHE* 1.3 101.2 - - + +
78D LYS* 1.3 74.8 + - + +
79D THR 3.6 1.7 + - - -
80D PHE* 4.6 3.3 + - - -
83D GLN* 3.4 34.1 - - + +
182E GLU* 2.7 36.1 + - - +
217E HIS* 5.7 4.7 - - - -
243E THR* 3.9 15.5 - - - -
306G HIS* 3.9 10.2 - - - -
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 4.8 6.6 - - + +
74D LYS* 2.8 43.8 + - + +
77D LYS* 1.3 85.1 + - + +
79D THR* 1.3 61.7 - - - +
80D PHE 3.4 2.4 + - - -
44E VAL* 4.6 6.4 - - - +
176E ARG* 4.0 21.5 - - - +
179E VAL 4.6 10.3 + - - -
180E PHE* 5.6 8.5 - - - -
217E HIS* 5.9 0.6 - - - -
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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