Contacts of the strand formed by residues 67 - 73 (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 TYR 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C PRO* 4.1 13.9 - - + -
171C GLU* 4.7 7.6 - - - +
172C ASN* 6.2 0.2 - - - -
175C LYS* 5.7 2.4 + - - -
271C PRO* 4.3 17.0 - - + -
55D THR* 3.8 20.4 - - + -
56D TYR 3.7 12.8 - - - -
57D TYR* 4.2 5.6 - - + -
62D HIS* 2.8 53.1 + + - -
65D ASN* 4.1 27.6 + - + -
66D ILE* 1.3 78.6 - - - +
68D PRO* 1.3 67.2 - - - +
69D PHE* 3.7 5.4 - - - +
82D TYR* 3.3 1.4 - - - -
83D ILE* 2.8 53.8 + - + +
87D HIS* 5.4 4.7 - + - -
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Residues in contact with PRO 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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7D LEU* 3.8 23.1 - - + -
11D ILE* 4.1 19.1 - - + -
23D TRP* 3.7 32.8 - - + -
55D THR* 3.4 3.6 - - - -
56D TYR* 2.9 41.8 + - + +
61D LEU* 4.0 7.9 - - + -
66D ILE* 3.5 9.9 - - + +
67D TYR* 1.3 89.7 - - - +
69D PHE* 1.3 58.7 + - - +
81D GLY 3.3 9.0 - - - +
82D TYR* 3.8 3.1 - - + -
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Residues in contact with PHE 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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272C LEU* 3.9 26.9 - - + -
7D LEU* 4.0 2.2 - - - +
54D TYR 2.9 15.7 - - - +
55D THR* 4.2 4.9 - - - +
56D TYR* 4.4 1.8 - - - -
67D TYR 3.7 7.0 - - - +
68D PRO* 1.3 75.3 - - - +
70D ILE* 1.3 70.5 + - - +
71D LEU* 3.8 28.3 - - + -
79D ALA* 4.3 2.0 - - + -
80D ILE* 3.6 3.3 - - - -
81D GLY* 2.9 52.1 + - - +
82D TYR* 3.3 33.2 - - - -
83D ILE* 3.9 3.1 - - + -
89D MET* 4.2 20.2 - - + -
90D ASP 4.0 2.7 - - - -
91D PHE* 3.9 28.0 - + - -
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Residues in contact with ILE 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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3D LEU* 4.2 15.0 - - + -
4D GLU* 4.2 25.1 - - + +
7D LEU* 4.0 14.8 - - + -
54D TYR* 2.9 41.1 + - + +
56D TYR* 3.8 24.7 - - + +
69D PHE* 1.3 79.5 - - - +
71D LEU* 1.3 66.3 + - - +
72D TYR* 3.5 30.1 - - + +
77D LEU* 3.6 14.8 - - + -
79D ALA 3.2 13.0 - - - +
80D ILE* 4.6 6.5 - - + -
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Residues in contact with LEU 71 (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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272C LEU* 3.9 13.5 - - + -
35D ILE* 4.3 11.0 - - + -
36D LEU* 3.9 27.6 - - + -
51D LEU* 4.5 11.7 - - + -
52D GLN 3.5 2.5 - - - +
53D THR* 3.5 32.1 - - + -
69D PHE* 3.8 20.0 - - + -
70D ILE* 1.3 83.7 - - - +
72D TYR* 1.3 58.5 + - - +
77D LEU* 3.6 6.1 - - - +
78D ILE* 2.6 38.8 + - + -
79D ALA* 2.8 35.2 + - + +
89D MET* 5.4 0.9 - - + -
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Residues in contact with TYR 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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3D LEU* 4.1 15.2 - - - +
51D LEU* 3.3 9.5 - - - +
52D GLN* 2.8 41.9 + - + +
54D TYR* 3.5 30.5 - + + -
70D ILE* 3.5 27.0 - - + +
71D LEU* 1.3 77.2 - - - +
73D TYR* 1.3 59.6 + - - +
74D GLN 3.7 14.6 - - - +
75D LYS* 3.9 13.9 - - - -
76D GLN 3.2 6.1 - - - -
77D LEU* 3.5 34.9 - - + +
78D ILE* 3.9 4.7 - - - +
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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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49D LYS* 3.7 43.5 - - + +
50D ILE* 3.5 21.8 - - + -
51D LEU* 4.0 6.3 - - + -
72D TYR* 1.3 72.5 - - - +
74D GLN* 1.3 87.4 + - + +
76D GLN* 2.7 47.7 + - + +
78D ILE* 3.5 19.9 - - + +
97D THR* 3.6 21.1 - - + -
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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