Contacts of the helix formed by residues 53 - 61 (chain A) in PDB entry 1OY6
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY 3.2 4.8 + - - +
52A ALA* 1.3 78.1 - - - +
54A ALA* 1.3 63.8 + - - +
55A LYS* 3.2 33.7 + - - +
56A THR* 2.6 35.3 + - - -
57A VAL* 3.4 10.7 + - - +
83A ASP 4.2 1.6 - - - -
84A SER* 4.0 8.7 - - - +
726A GLN* 4.5 14.6 + - - +
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Residues in contact with ALA 54 (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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53A ASP* 1.3 75.8 + - - +
55A LYS* 1.3 60.2 + - + +
56A THR 3.5 0.2 - - - -
57A VAL* 3.5 3.6 - - - +
58A GLN* 3.2 24.6 + - - +
82A SER 3.6 17.0 - - - +
83A ASP 3.4 11.7 - - - -
84A SER* 3.6 10.5 - - - +
726A GLN* 4.9 1.5 - - - +
813A SER 3.3 26.7 - - - +
814A PRO* 3.6 17.0 - - + +
815A ARG* 4.0 1.3 - - - +
816A LEU* 3.5 5.1 - - + +
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Residues in contact with LYS 55 (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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53A ASP* 3.2 15.4 + - - +
54A ALA* 1.3 81.7 - - + +
56A THR* 1.3 66.5 + - - +
58A GLN* 3.4 9.4 + - - +
59A ASP* 3.0 25.4 - - - +
692A HIS* 4.4 14.6 - - - -
726A GLN* 3.6 11.2 - - - +
812A GLY* 3.4 28.9 - - - -
813A SER 3.4 27.2 - - - +
816A LEU* 3.9 19.2 - - + +
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Residues in contact with THR 56 (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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49A TYR* 3.8 27.8 - - + +
52A ALA* 4.1 9.5 - - + -
53A ASP* 2.6 30.7 + - - -
55A LYS* 1.3 78.3 - - - +
57A VAL* 1.3 58.5 + - - +
59A ASP* 3.2 7.6 - - - +
60A THR* 3.0 36.4 + - + +
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Residues in contact with VAL 57 (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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49A TYR* 3.9 13.2 - - + -
52A ALA* 3.7 16.8 - - + -
53A ASP 3.4 3.6 + - - +
54A ALA 3.5 11.7 - - - +
56A THR* 1.3 80.1 - - - +
58A GLN* 1.3 55.1 + - - +
59A ASP 3.3 0.3 + - - -
60A THR* 3.9 6.5 - - - -
61A VAL* 3.5 9.0 + - + +
62A THR* 2.6 38.4 + - - +
82A SER* 4.0 12.8 - - - -
83A ASP 3.3 25.1 - - - +
86A GLY* 3.6 31.0 - - - -
87A THR* 4.2 2.7 - - - +
88A VAL* 5.0 7.0 - - + +
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Residues in contact with GLN 58 (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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54A ALA 3.2 17.2 + - - +
55A LYS* 3.4 8.1 + - - +
56A THR 3.2 1.0 - - - -
57A VAL* 1.3 80.8 - - - +
59A ASP* 1.3 72.3 + - - +
62A THR* 3.3 18.2 - - - -
63A GLN* 3.1 33.6 + - - +
82A SER* 3.6 7.9 - - - +
816A LEU* 3.5 31.5 - - + +
818A ARG* 3.5 26.5 + - + -
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Residues in contact with ASP 59 (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 LYS* 3.0 21.3 - - - +
56A THR* 3.2 7.8 - - - +
58A GLN* 1.3 93.8 + - - +
60A THR* 1.3 58.0 + - - +
61A VAL 3.9 0.4 - - - -
63A GLN* 3.7 28.2 - - + +
64A VAL* 4.6 5.1 - - - +
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Residues in contact with THR 60 (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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49A TYR* 3.6 24.8 + - + -
56A THR* 3.0 29.1 + - + +
59A ASP* 1.3 79.8 - - - +
61A VAL* 1.3 77.5 + - + +
64A VAL* 3.5 15.2 - - - +
117A LEU 4.1 1.0 - - - +
118A LEU* 3.4 7.4 - - - +
119A PRO* 3.2 31.4 - - + +
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Residues in contact with VAL 61 (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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47A ALA* 3.8 29.4 - - + -
49A TYR* 4.2 4.7 - - + -
57A VAL* 3.5 13.4 + - + +
60A THR* 1.3 97.2 - - + +
62A THR* 1.3 68.7 + - - +
63A GLN 3.6 0.4 - - - -
64A VAL* 3.7 2.8 + - - +
65A ILE* 3.4 32.4 + - + +
88A VAL* 4.2 9.2 - - + -
118A LEU* 3.6 19.6 - - + +
119A PRO* 4.6 0.9 - - + -
122A VAL* 3.6 32.8 - - + -
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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