Contacts of the helix formed by residues 53 - 58 (chain B) in PDB entry 6BAA
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.3 4.6 - - - +
52B GLN* 1.3 80.8 - - - +
54B ARG* 1.3 60.0 + - - +
55B PHE* 2.9 9.7 + - - +
56B LEU* 3.1 15.7 + - - +
57B GLN* 3.1 18.9 + - - +
130F SER* 4.0 13.0 + - - -
131F ASN 3.2 11.5 + - - -
132F PHE* 3.9 15.0 - - - -
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Residues in contact with ARG 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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50B ARG 4.9 0.6 + - - -
51B GLU* 6.1 0.2 - - - +
52B GLN* 3.0 46.2 - - + +
53B GLY* 1.3 77.9 - - - +
55B PHE* 1.3 61.9 + - - +
56B LEU 3.2 0.4 + - - -
57B GLN* 3.3 25.6 - - + +
58B ASP* 3.4 22.9 + - - +
176C ARG 5.3 1.7 - - - +
179C GLU* 2.9 49.2 + - + +
180C THR* 4.5 9.8 - - + +
182C ILE* 4.2 11.7 - - - +
205C LEU* 3.8 26.5 - - - +
206C ARG* 4.3 10.1 + - - +
401C ATP 4.3 8.9 + - - -
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Residues in contact with PHE 55 (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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51B GLU* 5.0 20.6 - - + +
53B GLY* 2.9 4.0 - - - -
54B ARG* 1.3 82.0 - - - +
56B LEU* 1.3 77.5 + - + +
58B ASP* 4.0 4.9 + - - +
62B THR* 3.6 25.7 + - + -
206C ARG* 3.2 57.2 - - - +
53F SER* 3.8 33.2 - - - -
56F SER* 6.0 0.2 - - - -
57F LYS* 5.0 15.7 - - + -
60F ILE* 6.0 6.3 - - + -
130F SER* 5.2 4.5 - - - +
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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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53B GLY* 3.1 8.7 + - - +
55B PHE* 1.3 101.7 - - + +
57B GLN* 1.3 66.2 + - - +
58B ASP 3.1 2.8 + - - -
59B VAL* 2.9 26.8 + - - +
62B THR* 5.2 2.7 - - + -
46F ILE* 5.2 11.4 - - + +
49F ILE* 4.6 20.9 - - + -
50F GLY* 5.1 13.5 - - - +
53F SER* 5.2 0.2 - - - +
126F ASN 5.9 2.9 - - - +
130F SER* 5.8 10.3 - - - +
132F PHE* 5.7 12.1 - - + -
135F LEU* 5.0 16.4 - - + -
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Residues in contact with GLN 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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52B GLN 5.4 0.9 - - - -
53B GLY 3.1 16.0 + - - +
54B ARG* 3.3 31.9 + - - +
56B LEU* 1.3 76.7 - - - +
58B ASP* 1.3 53.2 + - - +
59B VAL* 2.8 19.8 + - - +
60B PHE* 5.8 0.9 - - - -
176C ARG* 4.2 31.3 + - - +
179C GLU* 4.0 10.7 - - - +
132F PHE* 3.0 38.6 - - + -
134F LYS* 4.4 16.4 - - - +
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Residues in contact with ASP 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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54B ARG 3.4 13.7 + - - +
55B PHE 4.4 3.4 - - - +
56B LEU 3.1 3.5 - - - -
57B GLN* 1.3 75.0 - - - +
59B VAL* 1.3 55.1 + - - +
60B PHE* 4.1 1.7 + - - +
61B THR* 2.6 43.5 + - - +
62B THR* 2.7 29.3 + - - +
173C GLN 5.7 0.3 - - - +
176C ARG* 4.1 30.1 - - + +
177C ARG* 3.1 26.2 + - - +
180C THR* 5.6 1.8 - - + -
206C ARG* 5.6 4.1 - - - +
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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