Contacts of the helix formed by residues 77 - 89 (chain A) in PDB entry 1Y8B
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 ASP 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LYS* 1.3 95.5 - - - +
78A LYS* 1.3 63.3 + - - +
79A ALA* 2.6 13.3 + - + +
80A ALA* 2.8 20.6 + - + +
81A TYR* 3.3 9.4 + - - +
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Residues in contact with LYS 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 PRO 5.0 1.8 + - - -
75A VAL* 3.8 40.1 - - + +
76A LYS 3.2 5.8 + - - +
77A ASP* 1.3 74.9 - - - +
79A ALA* 1.3 52.6 + - - +
81A TYR* 3.6 29.6 - - - +
82A LYS* 2.4 50.8 + - + +
573A LEU 5.3 0.2 - - - +
574A ASP* 3.4 37.5 - - + +
577A LEU* 3.4 34.5 + - + +
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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
----------------------------------------------------------
77A ASP* 2.6 10.6 + - + +
78A LYS* 1.3 76.9 - - - +
80A ALA* 1.3 59.6 + - - +
82A LYS* 4.7 5.2 - - - +
83A SER* 3.3 21.8 + - - -
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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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77A ASP* 2.8 20.9 + - + +
79A ALA* 1.3 74.8 - - + +
81A TYR* 1.3 55.4 + - - +
82A LYS 3.2 0.2 - - - -
83A SER* 2.6 16.9 + - - -
84A PHE* 2.6 43.4 - - + -
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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
----------------------------------------------------------
67A TRP 5.8 0.4 - - - -
68A HIS* 2.6 56.2 + + + -
71A ASN* 4.6 20.4 - - + -
73A GLY 5.6 5.8 - - - -
74A PRO 6.1 1.1 - - - -
77A ASP 3.3 7.8 + - - +
78A LYS* 3.3 31.1 + - - +
80A ALA* 1.3 79.7 - - - +
82A LYS* 1.3 61.6 + - - +
84A PHE* 3.9 12.5 + + - -
85A LEU* 3.4 31.1 + - + +
429A ARG* 6.4 0.2 - - - -
464A VAL* 4.2 0.7 - - - +
577A LEU* 4.4 11.0 - - + -
579A ILE* 3.6 28.9 - - + +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 2.4 48.9 + - + +
79A ALA* 4.4 3.8 - - - +
81A TYR* 1.3 70.5 - - - +
83A SER* 1.3 64.7 + - - +
85A LEU* 3.0 4.7 + - + +
86A ARG* 2.9 53.9 + - + +
573A LEU* 4.2 37.1 - - + +
574A ASP* 5.0 9.9 - - - +
577A LEU* 3.7 25.6 - - + -
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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 ALA 3.3 16.6 + - - -
80A ALA* 2.6 24.3 + - - -
82A LYS* 1.3 79.0 - - - +
84A PHE* 1.3 80.5 + - - -
86A ARG* 2.7 22.6 + - - +
87A GLU* 3.0 12.5 + - - +
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Residues in contact with PHE 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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64A LEU* 5.8 1.3 - - + -
67A TRP* 3.6 39.0 - + + +
71A ASN* 4.3 19.1 - - + -
80A ALA* 2.6 40.8 - - + -
81A TYR* 3.9 14.1 - + - +
82A LYS 3.4 0.4 - - - -
83A SER* 1.3 93.0 + - - +
85A LEU* 1.3 57.3 + - + +
87A GLU* 4.4 6.1 - - - +
88A LEU* 2.5 42.6 + - + +
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Residues in contact with LEU 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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64A LEU* 4.3 21.5 - - + -
68A HIS* 4.3 5.4 - - + +
81A TYR* 3.4 31.5 + - + +
82A LYS* 3.0 13.0 + - + +
83A SER 3.0 0.6 - - - -
84A PHE* 1.3 83.5 - - + +
86A ARG* 1.3 57.4 + - + +
89A GLY* 2.3 53.9 + - - +
91A LEU* 4.1 5.8 - - + +
429A ARG* 3.3 30.3 - - - +
433A LEU* 5.7 2.7 - - + -
577A LEU* 3.7 33.4 - - + -
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Residues in contact with ARG 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 LYS* 2.9 47.9 + - + +
83A SER* 2.7 15.5 + - - +
85A LEU* 1.3 74.3 - - + +
87A GLU* 1.3 60.3 + - - +
91A LEU* 3.2 53.3 + - + +
573A LEU* 6.0 3.7 - - - +
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Residues in contact with GLU 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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83A SER 3.0 10.9 + - - +
84A PHE* 3.8 8.5 - - - +
86A ARG* 1.3 79.8 - - - +
88A LEU* 1.3 60.3 + - + +
90A TYR* 5.2 0.8 - - - -
91A LEU 5.6 0.4 + - - -
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Residues in contact with LEU 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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60A ILE* 3.5 28.0 - - + +
63A ALA* 3.9 33.2 - - + -
64A LEU* 4.2 26.5 - - + +
67A TRP* 4.9 23.8 - - + +
84A PHE* 2.5 21.4 + - + +
87A GLU* 1.3 75.3 - - + +
89A GLY* 1.3 51.7 + - - +
90A TYR* 2.4 21.5 + - - -
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Residues in contact with GLY 89 (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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60A ILE* 5.1 2.2 - - - -
64A LEU* 5.6 4.2 - - - +
84A PHE 3.5 0.4 + - - -
85A LEU* 2.3 54.8 + - - +
88A LEU* 1.3 66.8 - - - +
90A TYR* 1.3 70.4 + - - +
91A LEU* 3.1 10.5 + - - +
429A ARG* 5.4 8.5 + - - -
433A LEU* 5.2 4.9 - - - +
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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