Contacts of the strand formed by residues 101 - 106 (chain B) in PDB entry 2PY2
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 CYS 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TRP* 3.4 28.9 - - + -
63B TRP* 3.4 22.1 - - + -
66B GLY 3.7 3.4 - - - -
67B THR* 3.9 5.6 - - - -
69B CYS* 4.1 0.2 - - - -
100B CYS* 1.3 77.8 - - - +
102B ILE* 1.3 62.4 + - - +
103B GLN 3.6 0.5 + - - -
114B ASP* 3.3 2.5 - - - -
115B THR 2.8 33.4 + - - +
117B CYS* 2.0 46.4 - - - -
70C GLN* 3.8 10.1 - - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TRP* 3.4 7.9 - - - -
64B ILE* 3.1 51.5 + - + +
66B GLY* 2.9 35.6 + - - +
75B TRP* 3.7 25.8 - - + -
77B TRP* 4.5 3.1 - - + -
83B MET* 4.1 12.1 - - + -
88B TRP* 3.7 23.1 - - + -
101B CYS* 1.3 72.0 - - - +
103B GLN* 1.3 67.8 + - - +
112B TRP* 3.9 32.3 - - + -
113B ASN 4.0 2.7 - - - -
114B ASP* 4.5 0.7 - - + +
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PRO* 3.1 18.4 - - - +
62B SER 3.4 17.0 - - - +
63B TRP* 4.1 8.1 - - + -
101B CYS 3.6 0.6 + - - -
102B ILE* 1.3 76.1 - - - +
104B MET* 1.3 64.3 + - - +
106B VAL* 3.4 24.7 - - + +
112B TRP* 3.3 4.2 - - - -
113B ASN 3.0 30.0 + - - +
115B THR* 3.1 33.1 + - + +
119B HIS* 6.0 0.4 - - - -
121B HIS* 3.0 42.8 + - + -
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Residues in contact with MET 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ILE* 4.1 12.1 - - + -
48B SER* 4.6 1.8 - - - +
51B VAL* 3.8 16.6 - - + -
52B LYS* 3.6 37.0 - - + +
55B THR* 4.9 1.8 - - + -
61B PRO* 3.3 2.6 - - - +
62B SER* 2.7 39.8 + - - +
64B ILE* 3.7 28.4 - - + +
102B ILE 4.2 0.4 + - - -
103B GLN* 1.3 73.2 - - - +
105B ASN* 1.3 87.5 + - + +
106B VAL* 3.2 5.9 + - - +
111B CYS 3.8 3.6 - - - -
112B TRP* 3.8 22.7 - - + +
124B ILE* 4.1 15.9 - - - -
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 3.5 34.2 - - - +
55B THR* 3.0 27.0 + - - +
59B LEU* 3.4 24.4 - - - +
60B ILE 2.9 26.0 - - - +
61B PRO* 3.4 17.0 - - + +
104B MET* 1.3 87.0 - - - +
106B VAL* 1.3 61.2 + - - +
107B GLY 3.9 0.5 + - - -
110B LYS* 3.7 26.7 + - + +
111B CYS 3.4 5.9 + - - -
112B TRP* 5.0 0.2 - - - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PRO* 4.9 3.1 - - - -
89B CYS* 3.7 4.0 - - - -
103B GLN* 3.4 60.3 - - + +
104B MET 3.6 1.8 - - - +
105B ASN* 1.3 74.9 - - - +
107B GLY* 1.3 71.6 + - - +
110B LYS 3.2 11.1 + - - -
111B CYS* 2.9 26.0 + - - +
113B ASN* 3.9 29.4 - - + +
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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