Contacts of the helix formed by residues 58 - 65 (chain D) in PDB entry 5AYR
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 SER 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C PRO* 5.0 6.5 - - - -
21D GLU* 2.7 32.2 + - - -
22D LYS 3.5 16.6 - - - -
23D TRP* 3.9 7.5 + - - -
24D GLU* 6.0 1.3 - - - -
57D TYR* 1.3 79.6 - - - +
59D ASP* 1.3 64.2 + - - +
61D LEU* 3.2 23.6 + - - +
62D HIS* 3.0 30.6 + - - -
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Residues in contact with ASP 59 (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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165C PRO* 4.1 23.7 - - - +
21D GLU* 3.1 9.4 + - - +
58D SER* 1.3 76.5 - - - +
60D THR* 1.3 62.2 + - + +
62D HIS* 3.3 7.0 + - - +
63D GLU* 2.9 46.1 + - - +
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Residues in contact with THR 60 (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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17D LEU* 3.7 28.1 - - - +
18D PRO* 3.7 20.8 - - + +
21D GLU* 2.7 33.1 + - - +
58D SER* 3.7 0.5 + - - -
59D ASP* 1.3 77.3 - - + +
61D LEU* 1.3 55.5 + - - +
63D GLU* 3.3 17.8 + - - +
64D SER* 2.6 39.2 + - - -
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Residues in contact with LEU 61 (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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11D ILE* 4.3 1.8 - - + -
17D LEU* 3.6 25.4 - - + -
23D TRP* 3.4 44.2 - - + +
56D TYR 3.8 9.0 - - - +
57D TYR* 3.7 25.8 - - + -
58D SER* 3.2 15.9 + - - +
60D THR* 1.3 77.4 + - - +
62D HIS* 1.3 65.7 + - - +
64D SER* 3.4 2.5 + - - -
65D ASN* 2.9 19.1 + - - -
66D ILE* 3.1 47.7 + - + +
67D TYR* 4.6 1.7 - - + -
68D PRO* 4.0 6.5 - - + -
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Residues in contact with HIS 62 (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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165C PRO* 4.3 10.8 - - + -
166C PRO* 2.8 29.6 + - + -
168C PRO* 4.0 8.3 - - + -
171C GLU* 3.6 28.0 - - + +
57D TYR* 3.4 27.4 - + + -
58D SER 3.0 23.6 + - - +
59D ASP* 3.5 7.2 - - - +
61D LEU* 1.3 76.2 - - - +
63D GLU* 1.3 59.2 + - + +
65D ASN* 2.9 31.2 + - - +
67D TYR* 2.8 32.7 + + - -
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Residues in contact with GLU 63 (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 ASP* 2.9 33.9 + - - +
60D THR* 3.5 19.5 - - - +
61D LEU 3.2 0.2 - - - -
62D HIS* 1.3 79.1 - - + +
64D SER* 1.3 58.8 + - - +
65D ASN* 3.7 7.3 + - - -
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Residues in contact with SER 64 (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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15D PHE* 6.1 2.7 - - - -
17D LEU* 4.0 16.3 - - - +
60D THR* 2.6 24.8 + - - -
61D LEU* 4.2 1.6 + - - -
63D GLU* 1.3 74.6 - - - +
65D ASN* 1.3 70.7 + - - +
66D ILE* 3.3 18.6 + - - +
85D GLU* 3.6 19.1 - - - +
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Residues in contact with ASN 65 (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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175C LYS* 4.8 13.0 + - - -
61D LEU 2.9 9.2 + - - -
62D HIS 2.9 18.7 + - - +
63D GLU 4.1 7.1 + - - -
64D SER* 1.3 78.4 + - - +
66D ILE* 1.3 56.9 + - - +
67D TYR* 4.1 22.3 + - + -
83D ILE 3.6 1.6 - - - +
84D ASP 3.2 6.6 - - - +
85D GLU* 3.2 39.3 + - - +
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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