Contacts of the helix formed by residues 53 - 59 (chain A) in PDB entry 5D0A
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 ASP 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* 2.8 23.7 + - - +
52A PRO* 1.3 71.2 - - - +
54A ILE* 1.3 63.9 + - - +
55A GLU* 3.2 16.6 + - - +
56A LYS* 3.2 43.9 + - + +
57A ARG* 3.2 16.5 + - - +
362C GLU* 3.3 23.0 - - - +
365C LYS* 3.4 31.6 + - - -
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Residues in contact with ILE 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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34A LYS* 4.1 25.4 - - + -
37A LEU* 4.1 33.2 - - + +
38A ILE* 3.8 25.6 - - + +
41A GLU* 5.7 0.7 - - + -
46A LEU* 6.4 0.7 - - + -
51A GLU 5.7 0.7 - - - +
52A PRO 3.3 9.9 + - - +
53A ASP* 1.3 69.1 + - - +
55A GLU* 1.3 66.5 + - - +
57A ARG* 3.3 17.3 + - + +
58A VAL* 3.1 16.8 + - + +
366C LEU* 3.9 24.5 - - + -
369C GLU* 3.8 21.3 + - + +
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Residues in contact with GLU 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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34A LYS* 3.0 29.0 + - - -
53A ASP* 3.2 12.2 + - - +
54A ILE* 1.3 79.6 - - - +
56A LYS* 1.3 61.9 + - - +
58A VAL* 3.4 3.2 + - - +
59A THR* 2.6 38.5 + - - -
62A LEU* 4.2 17.3 - - + +
356C LEU* 3.9 20.1 - - + +
357C GLU* 4.6 9.9 - - - +
365C LYS* 4.6 11.2 - - - +
369C GLU* 2.7 27.0 + - - +
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Residues in contact with LYS 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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51A GLU* 4.5 6.2 + - + +
53A ASP* 3.2 38.1 + - + +
55A GLU* 1.3 78.4 - - + +
57A ARG* 1.3 61.2 + - - +
58A VAL 3.3 0.9 + - - -
59A THR 3.6 7.2 + - - +
62A LEU* 4.6 16.2 - - + -
63A LEU* 3.6 41.4 - - + +
137A GLU* 4.1 27.4 + - + +
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Residues in contact with ARG 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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30A PHE* 4.7 1.7 - - - -
33A LEU* 4.1 5.9 - - + +
37A LEU* 3.5 40.8 - - + +
50A GLU* 3.7 17.9 - - - +
51A GLU* 3.3 32.5 - - + +
53A ASP 3.2 17.2 + - - +
54A ILE* 3.3 9.8 + - - +
56A LYS* 1.3 75.3 - - - +
58A VAL* 1.3 58.5 + - - +
59A THR 3.6 0.2 - - - -
136A GLY 5.3 0.6 + - - -
137A GLU 2.9 25.3 + - - +
138A LEU* 3.3 43.7 + - - +
139A SER* 3.4 21.4 + - - +
503A B12 2.8 41.8 + - - +
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Residues in contact with VAL 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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29A THR* 3.1 11.3 - - - -
30A PHE* 2.8 54.3 + - - +
33A LEU* 3.9 14.4 - - + -
34A LYS* 3.7 40.2 - - + +
37A LEU* 4.2 6.7 - - + -
54A ILE* 3.1 19.1 - - + +
55A GLU* 3.5 11.0 - - - +
57A ARG* 1.3 81.4 - - - +
59A THR* 1.3 64.1 + - - +
60A PRO* 3.3 6.6 - - - +
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Residues in contact with THR 59 (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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29A THR* 4.0 20.1 - - + +
55A GLU* 2.6 31.8 + - - -
56A LYS 3.6 5.3 + - - +
57A ARG 3.6 0.4 - - - -
58A VAL* 1.3 86.8 + - - +
60A PRO* 1.3 66.6 - - + +
61A LYS* 4.2 9.2 - - + +
62A LEU* 3.1 40.9 + - + +
63A LEU* 3.5 9.4 + - - +
138A LEU* 5.2 0.2 - - - -
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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