Contacts of the helix formed by residues 43 - 47 (chain A) in PDB entry 4AG1
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 ALA 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 1.3 81.4 + - - +
44A ALA* 1.3 64.5 + - - +
45A HIS* 3.2 12.1 - - + +
46A CYS* 3.2 24.4 + - - +
89A ASP* 3.6 28.3 - - - +
91A MET* 3.5 11.9 - - - +
183A GLY* 3.5 21.2 - - - +
195A ILE* 4.6 1.1 - - + -
196A VAL 4.0 7.9 - - - +
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Residues in contact with ALA 44 (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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43A ALA* 1.3 71.8 - - - +
45A HIS* 1.3 58.1 + - - +
46A CYS 3.0 5.1 + - - -
47A ALA* 3.1 22.0 + - - +
77A ARG* 3.5 28.1 + - + -
81A TYR* 3.6 24.4 - - + -
88A HIS 4.0 0.4 - - - +
89A ASP* 2.8 11.8 + - - +
90A ILE 3.4 22.8 - - - +
91A MET* 3.9 11.0 - - - -
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 2.9 19.8 + - - -
30A CYS* 4.9 1.8 - - - -
43A ALA* 3.2 5.6 - - + +
44A ALA* 1.3 76.6 - - - +
46A CYS* 1.3 61.8 + - - +
47A ALA* 3.3 2.0 - - - -
81A TYR* 3.1 23.6 - - - +
86A LEU* 5.1 1.9 - - + +
89A ASP* 2.8 28.4 + - - -
182A SER* 3.1 30.6 + - - -
197A SER 3.0 28.9 - - - -
16C TRP* 5.0 0.6 + - - -
17C THR* 3.8 23.5 - - + +
39C GLU* 4.5 1.9 - - - +
50C TYR* 3.6 22.0 + + + +
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Residues in contact with CYS 46 (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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18A LEU* 4.8 2.0 - - + -
20A ILE* 3.2 26.0 - - + +
28A LYS* 3.7 4.5 - - - +
30A CYS* 2.0 54.3 - - + -
42A THR* 4.0 13.2 - - + +
43A ALA* 3.4 26.7 - - - +
44A ALA 3.0 1.2 - - - -
45A HIS* 1.3 79.6 - - - +
47A ALA* 1.3 65.8 + - - +
51A ILE* 4.1 2.6 - - - +
91A MET* 4.0 5.2 - - + -
182A SER* 4.1 9.2 - - - -
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Residues in contact with ALA 47 (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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20A ILE* 3.9 0.4 - - - -
28A LYS* 2.9 22.5 + - - -
44A ALA 3.1 15.8 + - - +
45A HIS 3.3 1.6 - - - +
46A CYS* 1.3 78.0 - - - +
48A GLY* 1.3 58.9 + - - +
51A ILE* 4.5 0.4 - - - -
75A GLN* 3.4 16.8 - - + +
77A ARG* 4.1 22.2 - - + +
91A MET* 3.6 16.4 - - - +
31C GLU* 5.4 1.3 - - - +
39C GLU* 4.1 6.9 - - - +
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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