Contacts of the helix formed by residues 52 - 59 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U PHE* 4.1 12.6 - - + -
51U PRO* 1.4 89.0 - - + +
53U SER* 1.3 67.1 + - - +
54U PHE* 3.1 6.3 + - + -
55U LEU* 3.6 2.3 + - - +
56U ARG* 3.5 18.5 + - - +
152V VAL* 3.7 24.0 - - + -
154V GLY* 5.3 0.7 - - - -
156V GLU* 4.5 8.5 - - - +
159V ILE* 4.8 1.8 - - + -
161V ILE* 3.9 20.1 - - + +
168V ALA* 3.6 17.7 + - + +
169V VAL* 3.9 21.9 - - + +
171V ALA* 4.1 12.6 - - + -
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Residues in contact with SER 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U PRO 5.7 0.3 - - - +
17U PHE* 5.6 9.6 - - - -
51U PRO 3.6 0.2 - - - -
52U PRO* 1.3 73.9 - - - +
54U PHE* 1.3 66.0 + - - +
56U ARG* 3.9 9.5 - - - -
57U ALA* 3.2 23.4 + - - +
86U PRO* 4.8 5.2 - - - +
139U SER* 4.0 19.3 + - - -
156V GLU* 2.4 31.5 + - - +
161V ILE* 3.5 18.7 - - - +
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Residues in contact with PHE 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16U PRO* 3.3 40.7 - - + +
17U PHE* 4.5 8.7 - - + -
23U LEU* 3.6 42.8 - - + -
24U PHE* 4.6 8.5 - + - -
27U PHE* 4.8 3.8 - + - -
48U TYR 4.0 13.2 - - - -
49U LEU* 3.4 25.6 - - + +
51U PRO* 3.3 51.8 - - + +
52U PRO* 3.1 1.7 + - + -
53U SER* 1.3 86.0 - - - +
55U LEU* 1.3 60.3 + - - +
56U ARG 3.3 0.9 - - - -
57U ALA* 3.4 8.0 - - - +
58U PRO* 3.1 21.5 - - - +
156V GLU* 6.0 0.7 - - - -
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Residues in contact with LEU 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U LEU* 4.2 10.4 + - + +
51U PRO 3.7 1.8 + - - -
52U PRO 3.6 2.4 + - - +
54U PHE* 1.3 75.5 - - - +
56U ARG* 1.3 84.1 + - - +
57U ALA 3.2 0.4 - - - -
58U PRO* 3.2 22.3 - - + +
59U SER* 3.7 7.4 + - - -
47V PHE* 5.7 6.7 - - + +
68V MET* 3.6 48.7 - - + +
69V ARG 4.4 2.7 - - - +
167V PRO* 3.5 30.3 - - + +
168V ALA* 3.5 23.3 - - + +
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Residues in contact with ARG 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U PRO 3.5 5.5 + - - +
53U SER* 3.9 7.4 - - - +
54U PHE 3.3 0.6 - - - -
55U LEU* 1.3 104.7 - - - +
57U ALA* 1.3 56.3 + - - +
59U SER* 3.9 5.1 + - - -
60U TRP* 2.9 25.3 + - - -
62U ASP* 2.7 51.5 + - - -
137U LEU 4.3 1.3 - - - -
138U SER* 3.6 26.3 + - - +
139U SER* 4.1 7.3 + - - +
68V MET 4.8 0.2 + - - -
161V ILE* 2.7 47.0 + - + +
162V THR* 3.7 3.4 - - - +
163V ARG 4.4 1.6 - - - -
165V GLU* 2.8 52.6 + - - +
167V PRO 4.0 1.2 + - - -
169V VAL* 4.0 5.7 - - - +
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Residues in contact with ALA 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U ARG* 6.5 0.9 - - + -
16U PRO* 4.7 14.8 - - + +
53U SER 3.2 14.7 + - - +
54U PHE* 3.4 15.9 - - - +
55U LEU 3.2 0.2 - - - -
56U ARG* 1.3 73.5 - - - +
58U PRO* 1.4 65.5 - - + +
60U TRP* 3.3 37.8 + - + +
139U SER* 4.7 5.4 - - - +
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Residues in contact with PRO 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U TRP* 3.9 40.4 - - + -
12U ARG* 5.4 19.3 - - + +
49U LEU* 5.7 2.5 - - + -
54U PHE 3.1 25.4 - - - +
55U LEU* 3.2 18.8 - - + +
57U ALA* 1.4 76.6 - - + +
59U SER* 1.3 60.4 + - - +
60U TRP* 3.7 3.6 + - - +
68V MET* 5.9 0.9 - - + -
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Residues in contact with SER 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U LEU* 3.7 7.8 + - - -
56U ARG* 3.6 19.6 + - - -
57U ALA 3.3 0.4 - - - -
58U PRO* 1.3 82.9 - - - +
60U TRP* 1.3 54.2 + - - +
61U PHE* 2.8 7.4 + - - +
62U ASP* 2.4 56.5 + - - -
63U THR* 3.8 7.8 + - - +
163V ARG* 4.8 0.3 + - - -
165V GLU* 4.7 1.9 + - - -
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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