Contacts of the strand formed by residues 79 - 83 (chain A) in PDB entry 2YNU
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 GLN 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL 3.8 0.7 - - - +
75A LEU* 3.5 4.8 - - - -
76A ASP* 2.9 49.8 + - + +
77A ASN* 5.4 2.2 - - + -
78A ASN* 1.3 83.4 - - - +
80A ALA* 1.3 60.1 + - - +
81A TYR* 4.2 16.4 + - + -
107A GLN* 3.4 11.9 + - + -
110A MET* 3.5 37.9 - - + +
184A ASN* 5.9 0.7 + - - -
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Residues in contact with ALA 80 (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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73A VAL* 4.1 11.9 - - + -
74A VAL 3.5 3.4 - - - -
75A LEU* 3.7 19.7 - - + -
78A ASN 4.1 0.2 - - - -
79A GLN* 1.3 75.2 - - - +
81A TYR* 1.3 63.0 + - - +
82A ILE* 5.7 0.4 - - + -
99A ALA* 4.8 3.4 - - + -
106A TYR* 4.1 14.1 - - + -
107A GLN 2.7 14.6 + - - +
109A VAL* 3.3 18.6 - - + +
110A MET 2.8 29.8 + - - -
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Residues in contact with TYR 81 (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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73A VAL* 3.4 3.5 - - - -
74A VAL* 2.8 43.0 + - - +
76A ASP* 4.7 6.0 + - + -
79A GLN* 4.2 20.1 + - + -
80A ALA* 1.3 75.1 - - - +
82A ILE* 1.3 64.8 + - - +
83A ILE 3.8 0.7 + - - -
110A MET* 3.8 33.1 - - + +
111A ALA* 3.6 24.0 - - + +
113A ILE* 6.4 0.4 - - + -
182A LEU* 4.5 11.7 - - + -
183A GLY* 3.2 33.3 - - - -
184A ASN* 5.5 2.4 + - - -
186A LEU* 3.6 25.4 - - + -
187A ILE* 3.6 27.8 - - + -
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Residues in contact with ILE 82 (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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55A HIS* 4.0 2.5 - - - +
72A LEU 3.5 3.4 - - - +
73A VAL* 4.7 12.1 - - + -
80A ALA* 5.5 0.4 - - + -
81A TYR* 1.3 75.5 - - - +
83A ILE* 1.3 60.9 + - - +
84A ASP 3.3 27.1 - - - +
85A THR* 4.4 4.7 - - + -
92A THR* 6.0 1.8 - - + -
95A LEU* 3.8 35.0 - - + +
96A LEU* 4.4 15.0 - - + +
109A VAL* 3.7 28.9 - - + -
111A ALA 3.0 9.5 + - - +
112A SER* 3.1 13.3 - - - -
113A ILE* 2.9 28.8 + - - +
128A LEU* 4.6 13.7 - - + -
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Residues in contact with ILE 83 (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 GLY* 3.1 1.6 - - - -
72A LEU* 2.8 49.8 + - + +
74A VAL* 4.0 24.0 - - + -
82A ILE* 1.3 73.2 - - - +
84A ASP* 1.3 70.4 + - - +
113A ILE* 3.7 19.5 - - + +
115A THR* 4.3 11.0 - - + -
187A ILE* 4.2 14.8 - - + -
203A ALA* 4.0 21.5 - - + -
205A LEU* 4.1 13.5 - - + -
218A PHE* 3.8 32.1 - - + -
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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