Contacts of the helix formed by residues 52 - 59 (chain X) in PDB entry 2YGD
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 PRO 52 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50X ARG* 3.2 16.4 - - - +
51X PRO* 1.4 82.0 - - + +
53X SER* 1.3 62.0 + - - +
54X PHE 3.3 0.4 - - - -
55X LEU* 3.1 25.4 + - + +
56X ARG* 3.5 18.4 + - - +
67X GLU* 3.6 17.0 - - - +
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Residues in contact with SER 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X PHE* 4.3 15.3 - - - -
51X PRO* 3.0 2.4 + - - -
52X PRO* 1.3 76.3 - - - +
54X PHE* 1.3 56.9 + - - +
56X ARG* 3.1 8.4 + - - +
57X ALA* 2.8 32.0 + - - +
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Residues in contact with PHE 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X PRO* 3.6 48.5 - - + -
14X PHE* 3.4 34.3 - + - -
23X LEU* 3.3 31.6 - - + -
27X PHE* 3.6 28.1 - + + -
49X LEU* 3.4 33.2 - - + +
51X PRO 3.4 5.8 + - - +
52X PRO 3.2 0.6 + - - -
53X SER* 1.3 76.6 - - - +
55X LEU* 1.3 63.3 + - + +
56X ARG 3.1 0.2 - - - -
57X ALA* 3.9 5.7 - - + +
58X PRO* 3.0 27.0 - - - +
70X LEU* 3.8 15.0 - - + -
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Residues in contact with LEU 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X PHE* 6.5 0.2 - - + -
49X LEU* 3.5 33.4 - - + +
50X ARG* 3.5 22.4 - - - +
51X PRO 3.8 0.9 - - - +
52X PRO* 3.1 24.0 + - + +
54X PHE* 1.3 87.7 - - + +
56X ARG* 1.3 77.3 + - - +
58X PRO* 4.2 1.6 - - - -
67X GLU* 3.9 6.1 - - - +
68X MET* 3.9 21.3 - - + -
69X ARG* 3.5 25.6 - - + +
70X LEU* 3.5 11.7 + - + +
71X GLU* 3.3 23.4 - - - +
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Residues in contact with ARG 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X PRO* 3.5 16.2 + - - +
53X SER* 3.1 11.8 + - - +
55X LEU* 1.3 112.6 + - - +
57X ALA* 1.3 63.8 + - - +
58X PRO* 3.4 2.2 - - - -
59X SER 3.2 3.8 + - - -
60X TRP* 3.1 40.7 + - + +
63X THR 4.4 4.7 - - - -
64X GLY* 3.4 34.0 + - - +
66X SER 3.9 8.0 + - - -
67X GLU* 2.7 31.7 + - - +
69X ARG* 3.7 9.7 - - - +
71X GLU* 3.6 14.1 + - - -
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Residues in contact with ALA 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X PRO* 5.1 9.0 - - + +
16X PRO* 6.0 4.9 - - + -
53X SER 2.8 21.3 + - - +
54X PHE* 3.9 6.5 - - + +
56X ARG* 1.3 71.7 - - - +
58X PRO* 1.4 66.1 - - + +
60X TRP* 3.4 25.5 - - - -
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Residues in contact with PRO 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X TRP* 4.1 11.7 - - + +
12X ARG* 3.1 31.4 + - + +
13X PRO* 4.0 33.0 - - + -
54X PHE 3.0 26.9 - - - +
56X ARG 3.5 4.3 - - - +
57X ALA* 1.4 82.0 - - + +
59X SER* 1.3 61.9 + - - +
60X TRP* 5.0 2.4 - - - -
70X LEU* 3.0 35.9 - - + +
71X GLU* 4.3 1.3 - - + -
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Residues in contact with SER 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X TRP* 4.2 10.6 - - - -
56X ARG* 3.2 5.9 + - - +
57X ALA 3.3 0.8 + - - -
58X PRO* 1.3 84.8 - - - +
60X TRP* 1.3 61.7 + - - +
61X PHE* 3.0 14.6 - - - +
62X ASP* 2.4 53.9 + - - +
63X THR 4.1 0.7 + - - -
64X GLY 5.3 0.2 + - - -
71X GLU* 3.6 20.8 - - - +
72X LYS 4.6 0.9 + - - -
74X ARG* 4.4 3.3 + - - -
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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