Contacts of the helix formed by residues 74 - 86 (chain A) in PDB entry 1RY2
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ASP* 1.3 74.5 + - - +
76A TYR 3.4 2.2 - - - -
77A GLN* 3.2 49.0 + - - +
78A ARG* 3.4 44.1 + - + +
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Residues in contact with ASP 75 (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 GLN* 1.3 81.0 + - - +
76A TYR* 1.3 65.1 + - - +
78A ARG* 3.3 6.2 + - - +
79A LEU* 3.0 46.4 + - + +
482A LEU* 6.3 0.9 - - + -
485A GLY* 5.3 13.6 + - - +
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Residues in contact with TYR 76 (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 GLN 3.4 0.6 - - - -
75A ASP* 1.3 78.7 - - - +
77A GLN* 1.3 81.0 + - + +
80A HIS* 3.1 52.4 + + + +
480A THR 6.0 0.7 - - - -
482A LEU* 4.3 21.0 - - + +
485A GLY* 4.7 12.1 + - - +
486A VAL* 4.6 12.6 - - + -
496A PHE* 3.2 37.7 - + + +
497A PRO* 3.0 34.9 + - - +
498A PHE* 5.4 1.3 - - - -
499A PHE* 3.9 24.2 - + - -
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Residues in contact with GLN 77 (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 GLN* 3.2 47.0 + - - +
76A TYR* 1.3 101.1 + - + +
78A ARG* 1.3 64.6 + - + +
80A HIS* 4.5 1.1 - - - +
81A LYS* 3.5 20.8 + - - +
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Residues in contact with ARG 78 (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 GLN* 3.6 39.3 - - + +
75A ASP* 3.3 6.4 + - - +
77A GLN* 1.3 76.1 - - + +
79A LEU* 1.3 57.8 + - + +
80A HIS 3.1 1.3 - - - -
81A LYS* 2.8 16.5 + - - +
82A GLU* 2.7 35.6 + - - +
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Residues in contact with LEU 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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75A ASP* 3.0 37.0 + - + +
78A ARG* 1.3 81.0 - - + +
80A HIS* 1.3 60.9 + - - +
82A GLU* 4.2 20.0 - - - +
83A SER* 3.2 23.7 + - - -
90A PHE* 3.6 14.9 - - + -
94A LYS* 5.3 4.0 - - - +
347A TYR* 4.0 30.7 - - + +
499A PHE* 3.4 27.5 - - + -
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Residues in contact with HIS 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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76A TYR* 3.1 39.7 + + + +
77A GLN* 4.5 1.6 - - - +
78A ARG 2.9 1.2 + - - -
79A LEU* 1.3 74.8 - - - +
81A LYS* 1.3 64.1 + - - +
83A SER* 2.7 17.0 + - - -
84A ILE* 2.9 35.7 - - + +
497A PRO* 3.3 23.7 + - + +
498A PHE 3.3 23.1 + - - -
499A PHE* 3.4 15.0 - - + -
501A ILE 3.0 27.6 + - - -
502A ASP* 5.0 5.4 - - - -
503A ALA 5.8 0.2 - - - -
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Residues in contact with LYS 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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77A GLN 3.5 18.1 + - - +
78A ARG* 2.8 12.1 + - - +
80A HIS* 1.3 75.3 + - - +
82A GLU* 1.3 64.9 + - - +
84A ILE* 4.4 6.5 - - + +
85A GLU* 2.9 63.3 + - + +
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Residues in contact with GLU 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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78A ARG 2.7 15.5 + - - +
79A LEU* 3.8 16.8 - - - +
81A LYS* 1.3 78.8 - - - +
83A SER* 1.3 57.6 + - - +
85A GLU* 4.8 3.1 - - - -
86A ASP* 3.0 47.5 + - + +
89A LYS* 5.3 5.0 - - + +
90A PHE* 2.9 39.3 - - + +
94A LYS* 4.7 4.9 + - - -
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Residues in contact with SER 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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79A LEU 3.2 11.0 + - - -
80A HIS* 2.7 23.9 + - - -
82A GLU* 1.3 80.3 - - - +
84A ILE* 1.3 58.7 + - - +
87A PRO* 3.5 21.0 - - - +
90A PHE* 3.4 37.0 - - - -
91A PHE* 3.9 1.6 - - - -
117A ARG* 5.4 0.5 - - - -
499A PHE* 3.6 1.3 - - - -
500A GLY* 2.9 35.8 + - - +
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Residues in contact with ILE 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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80A HIS* 2.9 49.9 + - + +
81A LYS* 3.2 7.3 + - + +
83A SER* 1.3 91.5 - - - +
85A GLU* 1.3 66.5 + - + +
86A ASP 3.4 0.2 - - - -
87A PRO* 3.6 2.0 - - - +
117A ARG* 2.8 55.4 - - - +
500A GLY* 3.5 22.9 - - - +
501A ILE 4.1 0.2 - - - +
502A ASP* 4.3 22.4 - - + +
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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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81A LYS* 2.9 59.6 + - + +
82A GLU* 4.8 2.5 - - - -
84A ILE* 1.3 80.0 - - + +
86A ASP* 1.3 65.2 + - + +
87A PRO* 3.5 3.9 - - - +
117A ARG* 5.3 1.1 - - - -
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Residues in contact with ASP 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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82A GLU* 3.0 26.7 + - + +
85A GLU* 1.3 88.5 - - + +
87A PRO* 1.3 65.6 - - - +
88A ALA* 3.2 4.1 - - - +
89A LYS* 2.8 42.9 + - - +
90A PHE 3.2 13.7 + - - -
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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