Contacts of the strand formed by residues 78 - 81 (chain A) in PDB entry 2YYO
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 VAL 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLY* 3.2 0.9 - - - -
60A LEU* 2.9 42.4 + - + +
71A PRO* 5.0 0.2 - - - +
72A GLY* 4.1 1.7 + - - -
77A SER* 1.3 77.3 + - - +
79A ALA* 1.3 67.7 + - - +
87A LEU* 3.5 25.8 - - + -
88A TYR 3.3 8.3 - - - +
89A ASN* 3.8 9.0 - - + -
123A ILE* 3.5 31.0 - - + -
125A PHE* 3.9 15.9 - - + -
135A THR* 4.0 12.6 - - + -
137A MSE 3.9 10.8 - - - -
139A MSE 4.5 2.2 - - + -
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Residues in contact with ALA 79 (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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58A VAL 3.3 21.1 - - - +
59A GLY* 3.9 1.8 - - - +
71A PRO* 3.2 33.0 - - + +
72A GLY* 4.0 0.4 - - - -
78A VAL* 1.3 78.6 - - - +
80A TYR* 1.3 59.9 + - - +
81A HIS* 3.9 10.0 + - + +
86A LYS 3.7 0.7 - - - +
87A LEU* 3.4 5.4 - - - +
88A TYR* 2.8 39.9 + - - -
125A PHE* 3.9 8.3 - - - -
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Residues in contact with TYR 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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56A ILE 4.1 0.2 - - - +
57A ALA* 3.6 0.9 - - - -
58A VAL* 2.9 31.6 + - - +
79A ALA* 1.3 71.4 - - - +
81A HIS* 1.3 68.8 + - - +
82A ALA 3.9 0.7 + - - -
85A GLY* 3.5 22.2 - - - -
86A LYS 3.6 2.9 - - - -
87A LEU* 4.7 0.9 - - - +
97A PHE* 3.5 31.0 - + - -
98A GLY* 3.7 5.5 - - - -
99A SER 2.6 34.9 + - - -
101A CYS* 3.7 25.4 - - - -
107A ILE* 3.5 30.4 - - + +
125A PHE* 3.7 24.8 - + + -
126A THR 5.4 1.1 - - - -
127A LYS* 4.2 9.3 - - + +
132A VAL* 4.2 14.8 - - + +
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Residues in contact with HIS 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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55A THR 6.3 0.4 - - - -
56A ILE 3.7 4.3 - - - +
57A ALA* 3.4 20.9 - - + +
70A GLN* 3.9 10.0 - - + +
71A PRO 3.1 27.0 + - - -
73A TRP* 3.7 23.0 + + - -
79A ALA* 3.9 4.3 + - + -
80A TYR* 1.3 79.4 - - - +
82A ALA* 1.3 55.0 + - - +
83A ASP* 3.6 13.7 - - - +
84A ASP* 3.4 15.9 - - - +
85A GLY* 2.7 37.1 + - - -
86A LYS 3.0 6.3 + - - -
88A TYR* 3.4 41.7 - + + -
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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