Contacts of the helix formed by residues 67 - 78 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 5.2 5.8 + - - +
64B ASP* 2.9 36.9 + - - +
66B PHE* 1.3 77.9 - - - +
68B THR* 1.3 61.6 + - - +
69B GLU 3.3 3.1 + - - -
70B ALA* 3.4 7.9 + - + +
71B ILE* 3.0 30.6 + - + +
113C TYR* 5.5 1.0 - - - -
114C LYS* 5.6 2.9 - - - +
117C GLY 3.5 4.7 - - - -
118C GLY* 3.4 4.5 - - - -
119C LYS* 3.1 40.5 + - - +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PRO 3.4 19.1 - - - +
66B PHE 3.0 3.8 + - - -
67B ASN* 1.3 74.6 - - - +
69B GLU* 1.3 59.6 + - - +
71B ILE* 4.0 5.8 - - - +
72B TRP* 3.0 31.4 + - - +
97B ASP* 4.1 5.8 - - - +
100B PHE* 3.6 24.2 - - + -
101B TRP* 3.9 15.3 - - - +
104B LYS* 2.8 31.9 + - - +
296B THR* 4.0 14.8 + - - -
117C GLY* 3.3 8.5 + - - -
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR* 1.3 79.0 - - - +
70B ALA* 1.3 56.6 + - - +
72B TRP* 3.6 4.6 - - - +
73B GLU* 3.0 30.7 + - - +
296B THR* 3.6 12.2 - - - +
300B LYS* 2.8 33.4 + - - -
116C LEU 3.9 2.2 - - - +
117C GLY* 3.1 28.4 + - - +
120C ASN* 3.8 9.6 - - - +
299C LYS* 2.6 26.3 + - - -
303C ASP* 4.6 1.5 - - - +
332C ALA 3.5 24.7 - - - +
333C ILE* 6.4 0.7 - - - -
334C PRO* 4.0 16.9 - - + +
3403C GOL 5.3 1.2 - - - -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 6.1 0.4 - - - +
67B ASN* 3.4 12.8 + - + +
68B THR 3.4 0.2 - - - -
69B GLU* 1.3 75.9 - - - +
71B ILE* 1.3 62.1 + - + +
73B GLU* 3.3 3.8 + - - +
74B LYS* 2.8 30.6 + - - +
117C GLY 4.5 0.4 + - - -
119C LYS 3.4 25.6 - - - +
120C ASN* 3.5 19.2 + - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 5.0 0.2 - - + -
60B LEU* 3.6 26.0 - - + -
63B GLU* 4.1 33.9 - - + +
64B ASP 3.5 22.9 - - - +
65B PRO* 4.5 2.0 - - + -
67B ASN* 3.0 25.5 + - + +
68B THR 4.0 2.7 - - - +
70B ALA* 1.3 75.2 - - + +
72B TRP* 1.3 64.9 + - - +
74B LYS* 3.2 9.6 + - + +
75B LEU* 2.9 31.1 + - + +
100B PHE* 3.6 37.7 - - + -
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Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR 3.0 18.2 + - - +
69B GLU* 3.6 6.5 - - - +
71B ILE* 1.3 79.3 - - - +
73B GLU* 1.3 61.3 + - - +
75B LEU* 3.3 3.0 + - - +
76B PHE* 2.9 52.6 + + + -
90B PHE* 3.7 33.9 - + - -
93B ILE* 3.3 30.1 - - + +
97B ASP* 4.0 16.8 - - + +
269B SER* 4.6 0.2 - - - -
270B ARG* 4.0 15.7 - - - -
271B TRP* 4.1 7.4 - + - -
293B GLY* 2.9 27.1 + - - -
296B THR* 4.1 14.1 - - + -
297B GLU* 3.4 40.9 - - + +
300B LYS* 5.7 2.5 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 4.3 4.0 - - - +
69B GLU 3.0 18.3 + - - +
70B ALA* 3.8 5.8 - - - +
72B TRP* 1.3 82.1 - - - +
74B LYS* 1.3 53.5 + - - +
76B PHE* 3.8 10.9 - - - -
77B LYS* 2.7 79.9 + - + +
270B ARG* 5.5 0.5 + - - -
120C ASN* 4.8 0.7 - - - +
306C HIS* 3.0 30.6 + - - -
334C PRO* 3.7 26.3 - - + +
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 2.8 46.2 + - + +
60B LEU* 5.5 2.9 - - + -
63B GLU* 2.8 30.8 + - - +
70B ALA 2.8 18.3 + - - +
71B ILE* 3.2 9.6 + - - +
73B GLU* 1.3 73.5 - - - +
75B LEU* 1.3 63.3 + - + +
77B LYS* 5.1 0.2 - - - -
78B LYS* 2.8 56.8 + - + +
79B THR* 3.9 1.6 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 4.0 39.9 + - + -
59B LEU* 4.0 24.7 - - + -
60B LEU* 4.3 23.8 - - + -
71B ILE* 2.9 33.6 + - + +
72B TRP 3.9 2.0 - - - +
74B LYS* 1.3 79.1 - - + +
76B PHE* 1.3 56.9 + - - +
79B THR* 2.6 33.8 + - + +
82B GLY* 3.9 3.8 - - - -
93B ILE* 3.8 37.7 - - + +
96B PHE* 4.8 5.6 - - + -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A THR* 4.1 17.9 - - + -
245A LEU* 3.8 15.3 - - + -
72B TRP* 2.9 39.0 + + + +
73B GLU* 3.5 18.2 - - - +
75B LEU* 1.3 78.4 - - - +
77B LYS* 1.3 89.8 + - - +
79B THR* 4.0 0.9 + - - -
80B PHE 5.1 0.5 + - - -
82B GLY* 3.2 47.8 + - - -
83B GLN* 3.3 15.0 + - - +
90B PHE* 4.3 11.2 - + - -
93B ILE* 4.0 4.2 - - + +
271B TRP* 3.5 38.6 - + - -
306C HIS* 4.7 1.1 - - - -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 2.6 38.3 + - - +
217A HIS* 5.8 3.6 - - - -
243A THR* 4.0 14.4 - - - -
73B GLU* 2.7 56.1 + - + +
76B PHE* 1.3 96.8 - - + +
78B LYS* 1.3 74.2 + - + +
79B THR 3.6 1.6 - - - -
80B PHE* 4.5 3.3 + - - -
83B GLN* 3.4 36.8 - - + +
306C HIS* 3.9 11.3 - - - -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.5 6.6 - - - +
176A ARG* 3.9 22.2 - - - +
179A VAL 4.8 7.9 + - - -
180A PHE* 5.7 7.7 - - - -
217A HIS* 6.0 0.8 - - - -
59B LEU* 4.7 7.1 - - + +
74B LYS* 2.8 41.2 + - + +
77B LYS* 1.3 85.3 + - + +
79B THR* 1.3 64.5 + - - +
80B PHE 3.4 2.0 - - - -
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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