Contacts of the helix formed by residues 71 - 82 (chain B) in PDB entry 1Y8Q
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 SER 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B ASP 4.0 6.1 - - - -
51B THR* 4.3 4.3 - - - +
52B ILE* 4.4 0.4 - - - -
70B ARG* 1.3 73.2 - - - +
72B LYS* 1.3 64.0 + - - +
73B ALA* 3.3 4.0 + - - +
74B GLN* 3.0 30.7 + - - +
75B VAL* 2.9 27.6 + - - +
93B HIS* 3.6 40.5 - - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA* 3.9 11.9 - - + +
48B ASP* 3.6 15.0 - - - +
50B ASP* 3.2 27.0 + - + +
51B THR 3.7 12.1 - - - -
52B ILE* 3.8 16.6 - - + -
56B ASN* 3.1 22.2 + - - -
60B GLN* 3.0 16.7 + - - -
63B PHE* 3.3 18.3 - - + -
70B ARG 3.5 1.4 + - - -
71B SER* 1.3 70.8 + - - +
73B ALA* 1.3 63.9 + - - +
76B ALA* 2.9 27.5 + - - +
802B ATP 2.9 56.4 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.8 19.5 - - + +
48B ASP* 4.2 18.3 + - + +
50B ASP 4.9 0.2 + - - -
71B SER* 3.3 7.2 + - - +
72B LYS* 1.3 80.4 - - - +
74B GLN* 1.3 61.7 + - - +
76B ALA* 3.6 1.9 - - - +
77B LYS* 3.1 17.2 + - - +
91B ALA* 3.4 14.4 - - + +
92B TYR 3.4 38.1 - - - +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 4.0 11.2 - - - +
71B SER* 3.0 26.9 + - - +
73B ALA* 1.3 77.0 - - - +
75B VAL* 1.3 64.2 + - - +
77B LYS* 3.0 37.5 + - - +
78B GLU* 3.1 33.1 + - - +
91B ALA* 4.3 13.2 + - - +
93B HIS* 5.5 5.0 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.7 18.6 - - + -
62B LEU 3.6 13.0 - - - +
63B PHE* 3.8 6.5 - - + -
67B HIS* 3.5 36.3 - - + +
70B ARG* 3.6 39.0 - - + +
71B SER 2.9 22.6 + - - +
74B GLN* 1.3 72.1 - - - +
76B ALA* 1.3 57.4 + - - +
78B GLU* 3.3 10.1 + - + +
79B SER* 2.8 29.7 + - - +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 4.6 3.1 - - + -
30B CYS* 5.2 0.4 - - - -
33B LEU* 3.8 11.2 - - + -
46B LEU* 3.7 18.8 - - + -
62B LEU* 4.0 11.2 - - + +
63B PHE* 3.7 16.5 - - + -
72B LYS 2.9 21.7 + - - +
73B ALA 3.6 4.5 - - - +
75B VAL* 1.3 78.0 - - - +
77B LYS* 1.3 62.7 + - - +
79B SER* 4.0 1.2 - - - -
80B VAL* 3.1 30.4 + - - +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 5.5 0.4 - - - -
46B LEU* 4.8 1.5 - - + +
73B ALA 3.1 9.8 + - - +
74B GLN* 3.0 23.4 + - - +
76B ALA* 1.3 80.8 - - - +
78B GLU* 1.3 64.0 + - + +
80B VAL* 3.5 2.5 + - - +
81B LEU* 3.1 45.4 + - + +
89B ILE* 2.9 57.9 + - + +
90B VAL* 4.9 1.2 - - - +
91B ALA* 4.1 21.0 - - + +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 5.6 1.2 + - - -
70B ARG* 3.0 41.7 + - - -
74B GLN* 3.1 27.0 + - - +
75B VAL* 3.3 11.7 + - + +
77B LYS* 1.3 79.5 - - + +
79B SER* 1.3 63.0 + - - +
81B LEU* 3.3 21.5 + - + +
82B GLN* 3.4 15.7 + - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 3.8 8.4 + - - -
62B LEU* 2.7 45.0 + - - -
64B GLN* 4.4 3.2 + - - -
67B HIS* 4.3 6.9 - - - -
75B VAL* 2.8 23.6 + - - +
76B ALA 4.0 1.3 - - - -
78B GLU* 1.3 73.0 - - - +
80B VAL* 1.3 64.0 + - - +
82B GLN* 3.0 32.0 + - - +
83B PHE* 3.8 9.9 - - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.1 21.5 - - + +
34B LYS 5.0 0.2 - - - +
37B VAL* 3.6 28.9 - - + -
62B LEU* 3.9 22.9 - - + -
76B ALA 3.1 19.0 + - - +
77B LYS 3.7 3.8 - - - +
79B SER* 1.3 74.7 - - - +
81B LEU* 1.3 64.3 + - - +
82B GLN 3.0 1.7 + - - -
83B PHE* 3.1 30.4 + - + -
84B TYR* 3.2 8.7 + - - +
87B ALA* 4.6 3.6 - - + -
89B ILE* 3.5 24.2 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LYS* 3.1 41.4 + - + +
78B GLU* 3.6 14.1 - - + +
79B SER 3.3 0.4 - - - -
80B VAL* 1.3 77.6 - - - +
82B GLN* 1.3 56.8 + - - +
83B PHE 3.3 0.2 - - - -
84B TYR 3.8 4.0 - - - -
85B PRO* 3.0 45.3 - - + +
87B ALA* 3.4 38.6 - - + +
89B ILE* 4.7 5.2 - - + +
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.3 46.4 + - - +
84A THR* 5.2 2.6 + - - -
98A ARG* 3.2 27.0 + - - +
78B GLU 3.6 15.7 - - - +
79B SER* 3.0 17.6 + - - +
80B VAL 3.0 1.4 + - - -
81B LEU* 1.3 80.2 - - - +
83B PHE* 1.3 57.6 + - - +
84B TYR 3.5 0.2 - - - -
85B PRO* 4.7 6.0 - - - +
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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