Contacts of the helix formed by residues 53 - 58 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.3 4.4 - - - +
52A GLN* 1.3 79.9 - - - +
54A ARG* 1.3 60.4 + - - +
55A PHE* 2.9 8.9 + - - -
56A LEU* 3.1 16.3 + - - +
57A GLN* 3.1 19.0 + - - +
130E SER* 4.0 13.1 + - - -
131E ASN 3.2 12.2 + - - -
132E PHE* 3.9 14.5 - - - -
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ARG 4.9 0.6 + - - -
52A GLN* 3.0 45.7 - - + +
53A GLY* 1.3 77.3 - - - +
55A PHE* 1.3 62.4 + - - +
56A LEU 3.2 0.4 + - - -
57A GLN* 3.3 25.9 - - + +
58A ASP* 3.4 22.3 + - - +
176B ARG 5.3 1.6 - - - +
179B GLU* 2.9 47.9 + - + +
180B THR* 4.5 9.5 - - + +
182B ILE* 4.2 12.1 - - - +
205B LEU* 3.7 26.7 - - - +
206B ARG* 4.3 9.7 + - - +
401B ATP 4.3 8.5 + - - -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 5.0 21.3 - - + +
53A GLY* 2.9 4.2 - - - +
54A ARG* 1.3 80.7 - - - +
56A LEU* 1.3 79.3 + - + +
58A ASP* 4.0 5.2 - - - +
62A THR* 3.6 26.4 + - + -
206B ARG* 3.2 56.1 - - - +
53E SER* 3.8 32.3 - - - -
56E SER* 6.0 0.4 - - - -
57E LYS* 5.0 16.4 - - + -
60E ILE* 6.0 6.5 - - + -
130E SER* 5.2 4.5 - - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLY* 3.1 9.3 + - - +
55A PHE* 1.3 102.5 - - + +
57A GLN* 1.3 67.2 + - - +
58A ASP 3.1 3.1 + - - -
59A VAL* 2.9 26.3 + - - +
62A THR* 5.2 2.7 - - + -
46E ILE* 5.2 11.7 - - + +
49E ILE* 4.6 20.6 - - + -
50E GLY* 5.1 13.2 - - - +
53E SER* 5.2 0.2 - - - +
126E ASN 5.9 2.7 - - - +
130E SER* 5.8 9.6 - - - +
132E PHE* 5.7 11.7 - - + -
135E LEU* 5.0 15.9 - - + -
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN 5.4 1.1 - - - -
53A GLY 3.1 16.0 + - - +
54A ARG* 3.3 31.9 + - - +
56A LEU* 1.3 77.1 - - - +
58A ASP* 1.3 54.0 + - - +
59A VAL* 2.8 20.1 + - - +
60A PHE* 5.8 0.7 - - - -
176B ARG* 4.2 31.5 + - - +
179B GLU* 4.0 10.2 - - - +
132E PHE* 3.0 38.3 - - + -
134E LYS* 4.4 16.4 - - - +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG 3.4 13.2 + - - +
55A PHE* 4.0 3.8 - - - +
56A LEU 3.1 3.9 - - - -
57A GLN* 1.3 73.8 - - - +
59A VAL* 1.3 55.2 + - - +
60A PHE* 4.1 1.7 + - - +
61A THR* 2.6 41.5 + - - +
62A THR* 2.7 30.0 + - - +
173B GLN 5.7 0.2 - - - +
176B ARG* 4.1 30.0 - - + +
177B ARG* 3.1 29.0 + - - +
180B THR* 5.6 2.5 - - + -
206B ARG* 5.6 3.7 - - - +
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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