Contacts of the helix formed by residues 69 - 79 (chain D) in PDB entry 2ORE
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 ARG 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D ILE* 2.7 37.5 + - + +
68D MET* 1.3 86.0 - - + +
70D THR* 1.3 65.9 + - - +
71D ASP 3.3 2.4 + - - -
72D GLU* 3.0 42.5 + - + +
73D TYR* 3.0 21.1 + - - +
104D PRO* 6.3 0.4 - - - +
105D PHE* 3.3 42.6 - - + +
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Residues in contact with THR 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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66D VAL* 2.6 24.5 + - + +
67D LYS 3.7 8.7 + - - -
68D MET 3.6 1.2 - - - -
69D ARG* 1.3 74.7 - - - +
71D ASP* 1.3 64.4 + - - +
73D TYR* 3.5 3.6 - - - +
74D VAL* 3.0 33.1 + - + +
148D LEU* 4.9 1.3 - - + +
149D TYR* 3.5 30.7 - - + -
152D ALA* 3.3 29.8 - - + +
156D GLN* 5.0 1.6 + - - -
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Residues in contact with ASP 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ARG 3.4 0.6 - - - -
70D THR* 1.3 76.7 - - - +
72D GLU* 1.3 70.3 + - - +
73D TYR 3.0 0.5 + - - -
74D VAL* 3.2 12.0 + - - +
75D GLN* 3.2 12.8 + - - +
149D TYR* 3.1 32.9 + - - -
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Residues in contact with GLU 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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69D ARG* 3.0 50.7 + - + +
71D ASP* 1.3 79.0 - - - +
73D TYR* 1.3 64.8 + - - +
75D GLN* 3.5 9.7 + - - +
76D ALA* 3.3 17.2 + - - +
105D PHE* 3.7 16.9 - - + -
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Residues in contact with TYR 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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62D LEU* 3.3 12.8 - - + +
65D ILE* 4.0 22.2 - - + -
66D VAL* 4.1 14.8 - - + -
69D ARG 3.0 18.4 + - - +
70D THR* 3.5 4.5 - - - +
72D GLU* 1.3 73.2 - - - +
74D VAL* 1.3 65.2 + - + +
75D GLN 2.8 2.8 + - - -
76D ALA* 2.8 4.3 + - - +
77D ALA* 2.7 48.8 + - + +
105D PHE* 3.9 13.5 - + + -
108D ALA* 2.7 43.2 + - + -
109D VAL* 3.7 16.4 - - + -
112D LEU* 3.3 23.0 - - + +
148D LEU* 3.9 27.8 - - + -
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Residues in contact with VAL 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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70D THR* 3.0 24.4 + - + +
71D ASP 3.2 2.7 + - - +
73D TYR* 1.3 81.8 - - + +
75D GLN* 1.3 56.6 + - - +
77D ALA* 3.9 4.0 - - - -
78D ARG* 3.0 49.0 + - - +
143D PHE* 3.7 8.3 - - + -
145D GLU* 3.9 20.9 - - + +
148D LEU* 4.3 19.7 - - + -
149D TYR* 3.7 33.2 - - + +
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Residues in contact with GLN 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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71D ASP 3.2 8.4 + - - +
72D GLU* 3.6 11.7 - - - +
73D TYR 2.8 4.8 + - - -
74D VAL* 1.3 73.9 - - - +
76D ALA* 1.3 66.6 + - - +
78D ARG* 3.1 35.4 + - - +
79D GLU* 3.2 13.3 + - - +
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Residues in contact with ALA 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 GLU 3.3 8.8 + - - +
73D TYR 2.8 9.1 + - - +
75D GLN* 1.3 78.3 - - - +
77D ALA* 1.3 63.0 + - - +
79D GLU* 3.6 11.4 + - - +
80D LEU* 3.6 13.2 - - - +
105D PHE* 3.9 14.6 - - + -
106D ARG* 5.4 2.5 + - - +
109D VAL* 3.5 32.0 - - + +
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Residues in contact with ALA 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 TYR* 2.7 47.7 + - + +
74D VAL 3.9 3.8 - - - +
76D ALA* 1.3 72.2 - - - +
78D ARG* 1.3 64.9 + - - +
80D LEU* 3.1 15.6 + - - +
81D PHE* 3.6 14.4 - - - -
109D VAL* 3.9 13.4 - - + +
112D LEU* 4.1 7.2 - - + -
143D PHE* 3.7 18.8 - - + -
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Residues in contact with ARG 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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74D VAL* 3.0 37.1 + - - +
75D GLN* 3.4 30.4 - - - +
77D ALA* 1.3 79.7 - - - +
79D GLU* 1.3 62.0 + - - +
81D PHE* 3.0 20.7 + - + +
82D VAL* 4.4 2.9 + - - +
143D PHE* 3.5 25.3 - - + -
145D GLU* 3.1 30.1 + - - -
149D TYR* 4.6 5.1 + - - -
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Residues in contact with GLU 79 (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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75D GLN 3.2 10.6 + - - +
76D ALA* 3.6 14.6 - - - +
77D ALA 3.1 1.2 + - - -
78D ARG* 1.3 77.2 - - - +
80D LEU* 1.3 69.5 + - + +
82D VAL* 3.2 29.1 - - + +
85D THR* 4.7 1.6 - - - +
106D ARG* 4.9 6.8 + - - -
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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