Contacts of the helix formed by residues 55 - 60 (chain B) in PDB entry 1AOC
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 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B HIS 4.0 5.4 - - - +
54B HIS* 1.3 92.8 - - + +
56B VAL* 1.3 69.8 + - + +
58B ARG* 4.2 5.8 - - + +
59B GLU* 3.3 21.7 + - - +
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Residues in contact with VAL 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 HIS* 3.2 22.5 + - + -
55B PRO* 1.3 78.9 - - + +
57B PHE* 1.3 64.8 + - + +
59B GLU* 3.2 4.3 + - - -
60B CYS* 3.0 24.2 + - - -
150B VAL* 4.3 8.7 - - + -
159B PHE* 3.3 27.6 - - + +
160B LEU* 3.9 15.0 - - + +
161B CYS* 3.4 35.4 - - - +
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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
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34B VAL* 4.7 5.8 - - + -
37B VAL* 4.3 9.0 - - + -
51B PHE* 3.1 48.9 - + + +
52B SER* 5.1 0.4 - - - -
54B HIS* 3.2 33.5 + + + +
56B VAL* 1.3 76.5 - - + +
58B ARG* 1.3 60.6 + - - +
61B GLY* 2.8 31.5 + - - +
62B LYS* 5.1 1.0 - - - +
111B VAL* 5.3 0.2 - - + -
118B PHE* 3.7 47.1 - + + -
150B VAL* 4.0 18.6 - - + -
159B PHE* 3.8 43.3 - + + -
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Residues in contact with ARG 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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48B PHE* 2.8 41.9 - - - -
51B PHE 4.1 0.8 + - - -
52B SER* 3.0 42.7 + - - +
54B HIS 2.8 22.0 + - - +
55B PRO* 4.2 5.8 - - + +
56B VAL 3.4 0.4 - - - -
57B PHE* 1.3 71.7 - - - +
59B GLU* 1.3 56.6 + - - +
62B LYS* 3.0 32.2 + - - +
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Residues in contact with GLU 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 PRO 3.3 11.3 + - - +
56B VAL* 3.2 8.5 + - - +
57B PHE 3.1 0.6 - - - -
58B ARG* 1.3 78.3 - - - +
60B CYS* 1.3 60.1 + - + +
61B GLY 3.8 0.2 - - - -
62B LYS* 2.7 26.8 + - - +
148B ARG* 2.4 35.1 + - - +
161B CYS* 3.8 12.7 - - - +
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Residues in contact with CYS 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 VAL 3.0 9.9 + - - -
59B GLU* 1.3 79.3 - - + +
61B GLY* 1.3 56.6 + - - +
62B LYS* 3.3 9.1 + - - +
63B TYR* 4.8 2.2 + - - -
120B GLN* 4.0 3.8 - - - +
148B ARG* 3.6 39.7 - - + +
149B LEU* 3.6 13.8 - - - +
150B VAL* 3.7 17.0 + - - +
161B CYS* 2.0 52.9 - - + -
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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