Contacts of the strand formed by residues 56 - 63 (chain C) in PDB entry 2PY9
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 GLU 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.3 24.4 - - + +
20C MSE 3.6 3.9 - - - +
21C HIS* 4.3 5.2 + - - -
22C GLY 4.2 0.2 - - - +
50C SER* 5.0 0.2 + - - -
54C CYS* 2.7 17.9 + - + +
55C PRO* 1.3 94.5 - - + +
57C ARG* 1.3 60.3 + - - +
58C ILE* 5.8 0.4 - - - +
17D ARG* 4.0 16.4 + - - -
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 3.5 4.4 - - - +
20C MSE 2.6 44.4 + - - +
22C GLY* 4.6 5.3 + - - -
25C VAL* 3.7 37.7 - - + +
49C ILE* 3.8 5.1 - - + +
50C SER* 2.6 35.6 + - - +
51C GLU 5.8 0.4 - - - +
52C GLY 2.9 27.6 + - - +
53C ASN* 5.0 1.6 - - - +
54C CYS* 3.8 22.7 - - + +
56C GLU* 1.3 77.0 - - - +
58C ILE* 1.3 64.3 + - - +
2F A 4.4 0.2 - - - -
4F C 2.8 50.1 + - - +
5F C 3.4 12.9 - - - +
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ARG* 3.8 22.2 - - + +
18C LEU 3.1 9.2 - - - +
19C LEU* 4.5 5.6 - - + -
48C ASN 3.7 1.0 - - - +
49C ILE* 3.6 2.5 - - - +
50C SER* 2.9 43.3 + - - +
56C GLU 5.8 0.2 - - - +
57C ARG* 1.3 78.2 - - - +
59C ILE* 1.3 62.2 + - - +
60C THR* 3.7 21.0 + - - +
19D LEU* 4.4 28.5 - - + -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE 3.8 0.5 - - - +
17C ARG* 3.7 0.7 - - - -
18C LEU* 2.7 49.9 + - + +
20C MSE 3.5 23.6 - - + -
25C VAL* 4.6 5.6 - - + -
28C ILE* 3.6 34.3 - - + -
47C ILE* 4.0 15.7 - - + -
48C ASN 3.3 4.5 - - - +
49C ILE* 4.1 25.4 - - + -
58C ILE* 1.3 75.8 - - - +
60C THR* 1.3 61.7 + - - +
61C LEU* 3.9 22.6 + - + -
75C ILE* 4.0 12.6 - - + -
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 3.7 28.7 - - + -
16C ILE 3.4 4.3 - - - +
17C ARG* 3.5 19.1 - - - +
46C ARG 3.2 6.2 - - - +
47C ILE* 3.2 3.3 - - - +
48C ASN* 2.7 49.4 + - + +
58C ILE* 3.7 9.2 - - - +
59C ILE* 1.3 72.1 - - - +
61C LEU* 1.3 66.8 + - - +
62C ALA* 4.9 3.8 - - + +
8F A 5.9 3.1 - - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C THR* 3.5 0.9 - - - +
16C ILE* 2.8 47.2 + - + +
18C LEU* 4.6 5.6 - - + -
45C ALA* 5.2 0.9 - - + -
46C ARG 3.4 2.9 - - - +
47C ILE* 4.0 17.5 - - + -
59C ILE* 3.9 23.3 - - + +
60C THR* 1.3 83.8 - - - +
62C ALA* 1.3 60.4 + - - +
68C ILE* 3.8 35.6 - - + +
71C ALA* 4.3 7.6 - - + -
72C PHE* 4.2 37.2 - - + +
75C ILE* 3.9 14.6 - - + -
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C THR* 6.3 0.4 - - - -
14C LEU 3.3 14.8 - - - +
15C THR* 4.1 15.9 - - + +
45C ALA* 3.4 6.1 - - - +
46C ARG* 2.6 67.7 + - + +
60C THR* 5.1 3.8 - - + -
61C LEU* 1.3 74.8 - - - +
63C GLY* 1.3 55.7 + - - +
68C ILE* 3.5 6.3 - - - -
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C THR* 3.5 17.0 - - - +
14C LEU 3.5 23.5 + - - +
44C GLY 5.4 0.2 - - - -
45C ALA* 5.0 0.4 - - - -
46C ARG* 4.4 11.3 - - - +
62C ALA* 1.3 76.5 - - - +
64C PRO* 1.3 81.7 - - - +
67C ALA* 4.9 1.8 - - - -
68C ILE* 4.1 2.5 - - - +
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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