Contacts of the helix formed by residues 55 - 61 (chain B) in PDB entry 1R2B
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 GLY 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B CYS 4.3 0.2 + - - -
54B SER* 1.3 70.8 + - - +
56B LEU* 1.3 67.3 + - - +
58B TYR* 2.9 5.7 + - - +
59B SER* 2.8 26.9 + - - -
112B LEU 3.4 4.8 + - - -
113B GLN* 3.6 28.0 + - - -
1426D HIS* 3.8 19.5 + - - -
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Residues in contact with LEU 56 (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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54B SER* 3.4 9.3 + - - +
55B GLY* 1.3 73.6 - - - +
57B PHE* 1.3 67.5 + - + +
59B SER* 2.9 9.1 + - - -
60B ILE* 2.8 42.5 + - + +
74B LEU* 4.8 4.3 - - + -
111B TYR* 3.6 55.0 - - + +
112B LEU* 3.4 20.2 + - + +
113B GLN* 3.3 25.8 - - - +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.7 44.6 - - + -
50B LEU* 3.6 50.0 - - + +
51B MET* 3.7 2.0 - - - +
54B SER* 3.4 21.5 + - - +
56B LEU* 1.3 81.5 - - + +
58B TYR* 1.3 63.2 + - - +
60B ILE* 3.8 20.6 - - + -
61B PHE* 3.0 46.3 + + + -
72B ILE* 4.7 1.8 - - + -
74B LEU* 4.5 8.3 - - + -
83B PHE* 4.2 14.4 - + - -
90B MET* 4.4 5.8 - - + -
112B LEU* 4.0 20.6 - - + -
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Residues in contact with TYR 58 (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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25A LEU* 4.1 12.3 - - + -
28A ARG* 2.9 41.5 + - - -
30A ILE* 3.8 7.2 - - + +
51B MET* 3.5 28.3 - - + +
54B SER 2.8 18.8 + - - +
55B GLY* 2.9 10.5 + - - +
57B PHE* 1.3 72.5 - - - +
59B SER* 1.3 67.7 + - - +
62B THR* 2.8 44.1 + - + -
1426D HIS* 3.9 13.5 - + + -
1428D ILE* 3.8 36.6 - - + -
1429D PRO* 6.1 1.3 - - + -
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Residues in contact with SER 59 (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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55B GLY 2.8 18.5 + - - -
56B LEU* 3.4 10.3 - - - -
58B TYR* 1.3 76.5 - - - +
60B ILE* 1.3 60.4 + - - +
62B THR* 2.6 29.3 - - - +
63B ASP* 3.0 14.6 + - - +
113B GLN* 4.8 6.1 + - - -
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Residues in contact with ILE 60 (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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56B LEU* 2.8 40.3 + - + +
57B PHE* 3.3 31.8 + - + +
59B SER* 1.3 73.4 - - - +
61B PHE* 1.3 68.4 + - + +
63B ASP* 3.1 22.9 + - - +
66B LYS* 3.3 40.6 - - + +
72B ILE* 3.7 39.9 - - + -
74B LEU* 5.3 2.0 - - + -
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Residues in contact with PHE 61 (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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30A ILE* 5.4 0.5 - - - +
31A LEU* 3.8 16.6 - - + +
34B VAL* 4.2 13.5 - - + -
36B ILE* 4.6 1.1 - - + -
47B LYS* 3.6 45.3 - - + -
50B LEU* 4.1 15.5 - - + -
51B MET* 3.7 31.8 - - + +
57B PHE* 3.0 51.2 + + + +
58B TYR 3.9 1.3 - - - -
60B ILE* 1.3 84.6 - - + +
62B THR* 1.3 57.1 + - - +
63B ASP 3.4 0.4 - - - -
66B LYS 4.1 6.7 - - - -
67B ARG* 3.3 31.2 - - - +
69B LEU 4.8 1.3 - - - -
72B ILE* 4.0 19.5 - - + -
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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