Contacts of the helix formed by residues 48 - 54 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D VAL 4.8 0.4 - - - +
47D ASP* 1.3 84.2 - - + +
49D TYR* 1.3 61.9 + - - +
51D ARG* 2.9 22.0 + - - +
52D VAL 3.9 0.5 + - - -
242D ILE* 3.9 17.0 - - + -
245D TYR* 3.8 19.5 - - + -
316D MET* 3.5 25.4 - - + -
317D LEU* 4.2 5.6 - - + -
701D NAP 3.4 64.6 - - + +
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASP* 3.1 40.5 + - + -
48D PRO* 1.3 78.1 - - - +
50D MET* 1.3 64.4 + - + +
52D VAL* 3.0 12.9 + - + +
53D ALA* 2.8 35.8 + - + +
64D MET* 3.8 22.9 - - + +
65D GLY* 3.6 27.2 + - - -
66D GLN* 4.5 2.6 + - - +
124D MET* 4.1 19.7 - - + -
245D TYR* 5.2 0.4 - - - -
273D TYR* 4.8 9.3 + - - -
701D NAP 4.4 17.8 + + + +
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Residues in contact with MET 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PHE* 4.3 1.9 - - - -
45D THR* 3.5 17.9 - - + +
46D VAL* 3.8 3.4 - - - -
47D ASP* 3.0 48.7 + - - +
48D PRO 3.0 1.0 + - - -
49D TYR* 1.3 102.0 - - + +
51D ARG* 1.3 62.8 + - - +
53D ALA 4.0 0.4 - - - +
54D ALA* 3.1 26.0 + - - +
63D MET* 4.3 9.4 - - + +
64D MET* 3.5 29.7 - - - +
65D GLY* 3.7 7.2 - - - -
91D TRP* 3.6 27.8 - - - +
313D PHE* 3.7 12.6 - - + -
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PHE* 3.5 45.4 + - - +
15D GLY 2.8 31.9 + - - +
17D PRO* 4.0 11.2 - - - +
48D PRO 2.9 12.3 + - - +
50D MET* 1.3 78.8 - - - +
52D VAL* 1.3 61.0 + - - +
54D ALA* 4.2 2.8 + - - +
55D LYS* 4.7 18.1 - - - +
245D TYR* 3.4 37.2 + - + +
246D ASN* 2.7 31.4 + - - +
247D ARG 5.1 1.8 + - - -
313D PHE* 3.7 13.3 - - + -
317D LEU* 4.2 11.0 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PRO 4.5 0.4 - - - +
49D TYR* 3.0 11.5 + - + +
51D ARG* 1.3 75.7 - - - +
53D ALA* 1.3 65.5 + - + +
54D ALA 3.2 2.9 + - - -
55D LYS* 3.4 38.6 + - + +
56D ARG* 4.8 0.3 + - - +
245D TYR* 3.8 47.8 - - + +
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D TYR* 2.8 30.5 + - + +
52D VAL* 1.3 73.7 - - - +
54D ALA* 1.3 64.6 + - - +
56D ARG* 3.0 24.9 + - + +
57D LEU 4.0 0.9 + - - -
64D MET* 3.6 29.8 - - + +
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.0 7.9 - - + +
12D HIS* 3.4 10.7 - - - +
13D PHE* 3.4 32.3 - - + -
50D MET 3.1 21.6 + - - +
51D ARG 4.3 1.8 - - - +
52D VAL 3.2 0.6 - - - -
53D ALA* 1.3 76.7 - - - +
55D LYS* 1.3 56.8 + - - +
57D LEU* 3.0 34.2 + - + +
63D MET* 4.7 3.4 - - + -
64D MET* 3.9 9.6 - - - +
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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