Contacts of the helix formed by residues 48 - 54 (chain B) in PDB entry 2Y05
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 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL 4.8 0.4 - - - +
47B ASP* 1.3 84.9 - - + +
49B TYR* 1.3 63.7 + - - +
50B MET 3.0 1.4 + - - -
51B ARG* 3.0 20.1 + - - +
52B VAL 3.8 1.9 + - - -
242B ILE* 3.8 15.7 - - + -
245B TYR* 3.7 19.5 - - + -
316B MET* 3.6 21.8 - - + -
317B LEU* 4.4 6.5 - - + -
701B NAP 3.3 66.9 - - + +
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Residues in contact with TYR 49 (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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45B THR* 5.8 0.2 - - - +
47B ASP* 3.1 36.9 + - + +
48B PRO* 1.3 78.4 - - - +
50B MET* 1.3 60.5 + - + +
52B VAL* 3.1 11.7 + - + +
53B ALA* 2.7 45.4 + - + +
64B MET* 3.6 23.2 - - + +
65B GLY* 3.6 26.0 + - - -
66B GLN* 4.3 4.9 + - - +
124B MET* 4.3 19.5 - - + -
245B TYR* 5.2 0.9 - - - -
273B TYR* 4.7 10.1 + - - -
701B NAP 4.4 15.1 + + + +
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Residues in contact with MET 50 (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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13B PHE* 4.5 0.2 - - - -
45B THR* 3.5 23.6 - - + +
46B VAL* 3.9 2.9 - - - -
47B ASP* 3.3 39.7 - - - +
48B PRO 3.0 0.8 + - - -
49B TYR* 1.3 95.7 - - + +
51B ARG* 1.3 61.3 - - - +
54B ALA* 3.0 28.2 + - - +
63B MET* 4.2 5.9 - - + +
64B MET* 3.2 42.9 - - - +
65B GLY* 3.6 13.9 - - - -
91B TRP* 3.6 22.2 - - - +
313B PHE* 3.8 12.1 - - + -
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Residues in contact with ARG 51 (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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13B PHE* 3.5 41.0 + - - +
14B VAL* 4.6 0.2 - - - +
15B GLY 2.8 31.8 + - - +
17B PRO* 4.0 11.1 - - - +
48B PRO 3.0 12.3 + - - +
50B MET* 1.3 78.6 - - - +
52B VAL* 1.3 61.6 + - - +
54B ALA* 4.3 6.1 + - - +
55B LYS* 4.0 20.9 - - - +
245B TYR* 3.5 35.8 + - + +
246B ASN* 2.6 35.2 + - - +
247B ARG 4.8 3.2 + - - -
313B PHE* 3.6 15.1 - - + -
317B LEU* 4.2 10.1 - - + -
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Residues in contact with VAL 52 (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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48B PRO 4.5 0.9 - - - +
49B TYR* 3.1 10.9 + - + +
51B ARG* 1.3 77.4 - - - +
53B ALA* 1.3 65.8 + - - +
54B ALA 3.3 0.6 + - - -
55B LYS* 3.4 34.6 + - + +
56B ARG* 4.9 14.4 + - - +
245B TYR* 3.6 50.3 - - + +
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Residues in contact with ALA 53 (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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49B TYR* 2.7 31.9 + - + +
52B VAL* 1.3 71.1 - - - +
54B ALA* 1.3 56.6 + - - +
55B LYS 3.0 5.4 - - - -
56B ARG* 2.9 47.1 + - - +
57B LEU 4.1 0.3 + - - -
64B MET* 3.6 27.1 - - + +
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Residues in contact with ALA 54 (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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9B LEU* 3.9 6.0 - - + +
12B HIS* 3.2 15.8 - - - +
13B PHE* 3.4 33.7 - - + -
50B MET 3.0 19.5 + - - +
51B ARG 4.3 2.2 - - - +
52B VAL 3.3 0.6 - - - -
53B ALA* 1.3 75.2 - - - +
55B LYS* 1.3 61.7 + - + +
56B ARG 3.1 0.4 - - - -
57B LEU* 3.1 26.3 + - + +
63B MET* 4.5 5.6 - - + -
64B MET* 3.8 10.2 - - - +
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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