Contacts of the helix formed by residues 74 - 82 (chain D) in PDB entry 2OQH
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 ALA 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D THR* 5.5 4.3 - - - -
71D SER* 3.1 28.1 + - - +
73D PHE* 1.3 74.1 - - - +
75D LEU* 1.3 64.6 + - - +
76D GLU 3.4 3.1 - - - +
77D ALA* 3.5 14.7 + - + +
78D PHE* 3.1 21.2 + - - +
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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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72D PRO 3.9 2.5 - - - +
73D PHE 2.8 11.6 + - - +
74D ALA* 1.3 69.9 - - - +
76D GLU* 1.3 65.9 + - + +
78D PHE* 3.5 25.3 - - + +
79D HIS* 2.9 37.1 + - + -
101D ASP* 3.5 20.2 - - - +
104D CYS* 4.0 22.0 - - + -
105D TRP* 3.1 38.6 - - + +
108D MSE 3.2 26.2 - - + -
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Residues in contact with GLU 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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74D ALA* 3.4 1.0 - - - -
75D LEU* 1.3 77.7 - - + +
77D ALA* 1.3 63.9 + - - +
79D HIS* 3.5 6.1 + - - +
80D ARG* 3.1 47.8 + - + +
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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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74D ALA* 3.5 19.7 + - + +
75D LEU 3.2 0.4 - - - -
76D GLU* 1.3 77.3 - - - +
78D PHE* 1.3 59.2 + - - +
80D ARG* 3.2 7.6 + - - +
81D LYS* 2.8 31.0 + - - +
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Residues in contact with PHE 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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63D MSE 4.4 12.8 - - + -
66D ASP* 6.0 1.3 - - + -
67D LEU* 3.7 35.7 - - + -
74D ALA 3.1 12.8 + - - +
75D LEU* 3.5 27.6 - - + +
77D ALA* 1.3 78.0 - - - +
79D HIS* 1.3 71.3 + + - +
81D LYS* 3.1 7.6 + - + +
82D GLN* 3.0 58.3 + - + +
97D ILE* 4.1 22.4 - - + -
100D VAL* 3.4 36.3 - - + -
101D ASP 4.5 2.9 - - - -
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Residues in contact with HIS 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 LEU* 2.9 37.5 + - + +
76D GLU* 3.9 6.3 - - - +
78D PHE* 1.3 82.2 - + - +
80D ARG* 1.3 67.4 + - + +
82D GLN* 3.2 6.7 + - - -
83D HIS* 3.2 20.6 + - - +
97D ILE* 3.4 23.0 - - + +
101D ASP* 2.8 26.7 + - - +
275D GLY* 3.0 30.3 - - - -
276D GLY* 4.6 1.3 - - - -
278D ALA* 6.1 3.9 - - + +
279D ALA* 6.2 2.2 - - + -
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Residues in contact with ARG 80 (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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76D GLU* 3.1 34.7 + - + +
77D ALA* 3.2 6.3 + - - +
79D HIS* 1.3 80.5 - - - +
81D LYS* 1.3 58.3 + - - +
82D GLN 3.2 0.3 + - - -
83D HIS* 2.9 36.9 + - - -
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Residues in contact with LYS 81 (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 ASP* 2.8 34.6 + - + +
77D ALA 2.8 13.6 + - - +
78D PHE* 3.1 12.3 + - - +
80D ARG* 1.3 77.2 - - - +
82D GLN* 1.3 76.7 + - - +
83D HIS* 3.7 5.9 + - - -
84D MSE 5.0 1.0 + - - +
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Residues in contact with GLN 82 (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 MSE 3.2 32.0 - - - +
66D ASP* 3.5 30.9 + - - +
78D PHE* 3.0 41.9 + - + +
79D HIS* 3.2 6.0 + - - +
80D ARG 3.1 0.4 - - - -
81D LYS* 1.3 99.5 + - - +
83D HIS* 1.3 62.0 + - - +
84D MSE 3.1 4.5 + - - -
85D VAL* 3.1 21.9 + - + +
86D PRO* 3.4 9.4 - - - +
97D ILE* 3.6 20.9 - - + +
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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