Contacts of the strand formed by residues 60 - 65 (chain A) in PDB entry 3AYU
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 ILE 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TRP* 4.1 13.5 - - + +
15A ILE* 3.9 21.3 - - + -
16A THR 3.0 8.6 + - - +
17A TYR* 3.2 7.4 - - + +
18A ARG 3.0 24.9 + - - -
39A PHE* 3.7 30.5 - - + -
50A PHE* 4.4 0.2 - - + -
58A ALA* 4.2 0.9 - - - -
59A ASP* 1.3 76.8 - - - +
61A MET* 1.3 61.4 + - - +
62A ILE* 3.6 19.7 + - + +
94A GLY 3.4 25.1 - - - +
96A SER* 4.0 10.3 - - - +
122A PHE* 4.5 2.0 - - + -
125A ALA* 4.4 5.8 - - + -
126A MET* 3.9 21.3 - - + -
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Residues in contact with MET 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.8 18.6 - - - +
20A ILE* 3.4 31.9 - - + -
56A GLY 4.0 6.7 - - - +
57A GLU* 3.5 34.3 - - - +
58A ALA 3.4 35.4 - - - +
60A ILE* 1.3 70.1 - - - +
62A ILE* 1.3 60.5 + - - +
63A ASN* 4.2 0.8 + - - -
95A ASP* 3.2 29.2 + - - +
96A SER 3.1 22.9 + - - +
97A HIS* 4.2 4.9 - - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.7 32.3 - - + -
18A ARG 2.8 13.5 + - - +
19A ILE* 3.5 13.7 - - + +
20A ILE* 2.8 33.3 + - - +
21A GLY 4.0 0.2 + - - -
35A PHE* 3.6 37.0 - - + -
39A PHE* 3.9 6.3 - - + -
60A ILE* 3.9 15.0 - - + +
61A MET* 1.3 76.3 - - - +
63A ASN* 1.3 66.1 + - - +
64A PHE* 5.5 0.4 - - + -
96A SER* 3.3 10.1 - - - +
98A PHE* 3.9 8.1 - - + -
122A PHE* 3.8 26.7 - - + -
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Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.0 18.8 - - + +
21A GLY* 3.3 30.9 - - - +
61A MET 4.2 0.8 + - - -
62A ILE* 1.3 77.6 - - - +
64A PHE* 1.3 94.5 + - - +
96A SER 3.2 4.9 + - - -
97A HIS* 3.3 19.7 - - + +
98A PHE* 3.0 27.7 + - - -
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY 3.4 21.3 - - - -
22A TYR 3.7 20.2 - - - +
23A THR* 3.7 29.2 - - + -
31A VAL* 4.1 6.3 - - + -
35A PHE* 3.9 33.9 - + - -
63A ASN* 1.3 99.9 + - - +
65A GLY* 1.3 58.5 + - - +
69A HIS* 5.6 0.6 - - - +
97A HIS* 5.7 1.1 - - - -
98A PHE* 3.3 27.8 - - + +
100A ASP* 4.1 12.8 - - + +
104A TRP* 3.7 27.8 - + - -
114A LEU* 4.0 14.8 - - + -
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 1.3 76.6 - - - +
66A ARG* 1.3 64.1 + - - +
69A HIS* 4.1 20.6 - - - -
75A PHE* 3.9 9.2 - - - -
98A PHE 2.9 8.1 + - - +
99A ASP* 3.4 7.3 - - - -
100A ASP* 2.8 26.5 + - - +
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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