Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 2PY5
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 THR 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 4.0 8.0 - - - -
80A LYS* 3.1 29.8 - - + +
82A SER* 3.6 20.1 + - - -
85A GLY* 4.1 2.4 - - - -
86A LEU* 2.6 42.5 + - + +
87A PRO 3.6 10.1 - - - +
88A ASN* 1.3 86.6 - - - +
90A TYR* 1.3 57.9 + - - +
105A ILE* 3.8 0.5 - - - -
106A CYS* 2.8 32.8 + - - +
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Residues in contact with TYR 90 (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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71A ILE* 3.3 28.5 - - + +
74A LEU* 3.8 33.7 - - + -
75A GLU* 2.6 28.8 + - - -
79A PHE* 4.0 15.0 - - + -
80A LYS 3.0 23.3 + - - -
81A TRP* 3.3 26.2 - + + +
82A SER 2.9 25.6 + - - -
89A THR* 1.3 75.3 - - - +
91A ASN* 1.3 59.8 + - - +
92A THR* 3.9 21.5 - - + -
103A ILE* 4.2 4.3 - - + -
104A ASP 3.1 12.3 - - - +
105A ILE* 4.1 10.5 - - + -
106A CYS* 5.6 0.2 - - - -
404A PRO* 3.7 15.5 + - + +
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Residues in contact with ASN 91 (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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81A TRP* 3.8 10.6 - - - +
82A SER 3.4 17.6 - - - +
83A ALA* 3.7 23.4 + - - +
85A GLY* 5.6 4.7 - - - +
90A TYR* 1.3 72.6 - - - +
92A THR* 1.3 84.6 + - - +
93A ILE* 5.6 0.8 - - - +
102A MET* 4.1 6.9 - - - +
103A ILE* 3.4 2.1 - - - +
104A ASP* 2.8 42.4 + - + +
1D G 5.1 4.4 - - - +
2D G 3.7 21.0 + - - -
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Residues in contact with THR 92 (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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71A ILE* 4.1 16.8 - - + -
81A TRP* 3.0 21.3 + - + +
90A TYR* 3.9 25.1 - - + -
91A ASN* 1.3 95.4 + - - +
93A ILE* 1.3 66.6 + - - +
94A ILE* 3.9 19.4 + - + +
102A MET* 3.2 14.8 - - - +
103A ILE* 4.4 4.7 - - + -
402A LYS 4.1 5.7 + - - -
404A PRO* 3.7 9.8 - - + +
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Residues in contact with ILE 93 (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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91A ASN* 5.6 0.7 - - - +
92A THR* 1.3 77.4 - - - +
94A ILE* 1.3 62.6 + - - +
95A SER* 5.2 0.7 - - - +
101A TYR* 2.8 57.5 + - + -
102A MET* 3.0 34.6 + - + +
188A MET* 4.6 9.0 - - + -
2D G 3.7 48.5 - - + +
3D A 3.6 29.4 - - + +
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Residues in contact with ILE 94 (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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92A THR* 3.9 26.0 - - + +
93A ILE* 1.3 78.1 - - - +
95A SER* 1.3 70.2 + - - +
98A GLY* 4.3 1.3 - - - -
99A GLN 3.3 4.3 - - - +
100A TRP* 3.7 63.7 - - + +
102A MET 5.2 1.1 - - - +
401A GLY* 3.3 6.2 - - - -
402A LYS* 2.8 49.1 + - + +
404A PRO* 4.2 12.8 - - + -
414A PHE* 4.2 6.3 - - + -
5Y T 3.9 11.2 - - + +
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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