Contacts of the strand formed by residues 82 - 88 (chain A) in PDB entry 2GZY
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.1 6.1 - - - +
79A LYS 2.9 35.3 + - - +
80A ASP 3.7 2.8 - - - +
81A GLY* 1.3 79.2 - - - +
83A VAL* 1.3 69.0 + - + +
84A VAL* 3.7 11.4 - - + +
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Residues in contact with VAL 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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67A TYR* 4.3 19.9 - - + -
76A LEU* 3.8 21.3 - - + -
77A VAL 3.5 7.4 - - - +
78A LEU* 3.8 16.0 - - + +
82A GLU* 1.3 81.0 - - + +
84A VAL* 1.3 65.9 + - - +
85A GLU 3.5 22.7 - - - +
86A THR* 3.9 6.7 - - - +
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Residues in contact with VAL 84 (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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77A VAL* 2.8 36.2 + - + +
78A LEU 4.2 2.0 - - - +
79A LYS* 4.1 24.7 - - + -
82A GLU* 3.7 20.6 - - + +
83A VAL* 1.3 79.9 - - - +
85A GLU* 1.3 68.8 + - + +
103A HIS* 5.1 9.0 - - + -
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Residues in contact with GLU 85 (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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76A LEU* 3.5 0.9 - - - -
77A VAL* 2.9 48.4 + - + +
83A VAL* 3.5 6.2 - - - +
84A VAL* 1.3 81.5 - - + +
86A THR* 1.3 97.9 + - - +
87A SER* 4.2 4.9 + - - +
99A LEU* 3.9 24.7 - - + +
103A HIS* 5.5 4.3 - - + -
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Residues in contact with THR 86 (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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67A TYR* 5.7 2.9 - - + +
69A VAL* 5.0 4.9 - - + -
74A THR* 4.2 11.7 - - + -
75A LEU 3.4 7.9 - - - +
76A LEU* 3.5 27.8 - - + +
83A VAL* 3.9 6.9 - - - +
85A GLU* 1.3 93.0 + - - +
87A SER* 1.3 70.6 + - - +
88A VAL* 5.1 4.9 - - + -
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Residues in contact with SER 87 (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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74A THR* 3.4 4.3 - - - +
75A LEU* 2.8 42.7 + - - +
85A GLU* 4.2 6.9 + - - +
86A THR* 1.3 78.3 + - - +
88A VAL* 1.3 66.8 + - - +
91A LYS* 3.9 20.2 - - - -
99A LEU* 3.6 24.9 - - - +
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Residues in contact with VAL 88 (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 SER* 5.3 9.6 - - - -
72A ILE 5.4 3.1 - - - +
73A PRO 3.5 12.1 - - - +
74A THR* 3.9 19.7 - - + +
86A THR* 5.1 5.2 - - + -
87A SER* 1.3 81.9 - - - +
89A GLY* 1.3 63.9 + - - +
91A LYS* 2.8 23.5 + - - +
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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