Contacts of the helix formed by residues 47 - 51 (chain A) in PDB entry 2A5E
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 ARG 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 5.7 0.7 - - - -
41A PRO* 5.7 7.3 - - - +
42A ASN* 4.7 2.1 + - - +
45A GLY* 3.9 24.4 + - - -
46A ARG* 1.3 83.1 + - - +
48A PRO* 1.3 69.5 - - + +
49A ILE* 3.1 9.0 + - + +
50A GLN* 3.7 22.8 - - + +
51A VAL* 3.1 22.7 + - - +
69A GLU* 3.1 60.5 + - + +
72A CYS* 3.8 24.0 - - - +
73A ALA* 4.2 17.6 + - - -
74A ASP* 5.5 0.6 + - - -
75A PRO* 5.8 3.2 - - - +
81A PRO* 5.3 1.6 - - + -
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Residues in contact with PRO 48 (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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16A LEU* 3.7 12.3 - - + -
17A ALA* 4.2 16.5 - - + -
20A ALA* 4.2 4.2 - - - +
38A PRO 3.2 25.4 - - - +
39A ASN* 5.0 0.4 - - - -
40A ALA* 4.9 10.1 - - + +
42A ASN* 4.5 6.2 - - - +
47A ARG* 1.3 89.8 - - + +
49A ILE* 1.3 60.5 + - - +
51A VAL* 3.9 12.8 - - + +
52A MET* 4.2 0.2 - - - +
63A LEU* 3.1 37.7 - - + +
68A ALA* 3.9 7.6 - - - -
69A GLU* 3.3 19.5 - - + +
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Residues in contact with ILE 49 (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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47A ARG* 3.1 1.5 - - + +
48A PRO* 1.3 78.5 - - - +
50A GLN* 1.3 66.3 + - - +
51A VAL 2.7 5.7 + - - -
52A MET* 2.7 43.0 - - + +
54A MET* 3.0 15.8 - - + +
60A ALA* 3.7 17.5 - - + +
63A LEU* 3.5 16.8 - - + -
64A LEU* 3.5 27.4 - - + +
68A ALA* 3.0 34.8 - - + -
69A GLU 4.8 4.3 - - - +
70A PRO* 5.0 4.5 - - + -
81A PRO* 4.7 11.9 - - + -
93A THR* 5.2 3.1 - - + -
97A LEU* 5.5 4.7 - - + -
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Residues in contact with GLN 50 (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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46A ARG* 4.1 28.2 + - + +
47A ARG* 3.7 41.5 + - + +
49A ILE* 1.3 79.5 - - - +
51A VAL* 1.3 57.2 + - - +
54A MET* 3.4 9.0 - - - +
74A ASP* 4.9 7.1 + - - +
79A THR* 2.5 51.6 + - - +
80A ARG 3.4 5.2 - - - +
81A PRO* 4.0 10.7 - - + +
84A ASP* 2.4 53.1 - - - +
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Residues in contact with VAL 51 (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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17A ALA* 3.4 16.7 - - + +
18A THR* 5.9 0.4 - - - -
21A ALA* 2.9 34.0 + - + +
42A ASN* 5.2 4.0 - - + +
44A TYR* 4.7 22.4 - - + -
46A ARG* 4.5 20.0 - - + +
47A ARG 3.1 20.6 - - - +
48A PRO* 3.9 12.1 - - + +
49A ILE 2.8 1.2 - - - -
50A GLN* 1.3 79.3 - - - +
52A MET* 1.3 55.2 + - - +
53A MET 3.3 6.3 - - - +
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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