Contacts of the helix formed by residues 50 - 60 (chain A) in PDB entry 1A03
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.1 25.3 - - - +
45A GLY* 3.1 18.8 - - - +
46A SER 3.3 0.7 + - - -
47A LYS* 2.8 45.2 + - - +
49A GLN* 1.3 68.7 - - - +
51A ALA* 1.3 58.6 + - - +
53A ILE* 2.8 10.5 + - - +
54A VAL* 2.8 34.7 + - + +
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Residues in contact with ALA 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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47A LYS 2.9 10.3 + - - +
48A LEU* 3.4 16.2 - - + +
50A ASP* 1.3 75.1 - - - +
52A GLU* 1.3 57.1 + - - +
54A VAL* 3.2 10.2 + - - +
55A LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 52 (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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41A GLU* 3.1 23.2 - - - +
48A LEU* 2.8 14.4 + - + +
49A GLN* 2.8 40.3 + - - +
51A ALA* 1.3 75.9 - - - +
53A ILE* 1.3 53.8 + - - +
55A LYS* 3.6 11.1 - - + +
56A LEU* 2.8 31.9 + - + +
76A PHE* 6.4 1.8 - - + -
80A LEU* 4.4 19.1 - - + +
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Residues in contact with ILE 53 (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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38A ILE* 3.7 40.2 - - + +
41A GLU* 3.3 21.8 - - + +
42A LEU* 3.3 47.8 - - + +
49A GLN 2.7 23.6 + - - +
50A ASP* 2.8 9.6 + - - +
52A GLU* 1.3 68.2 - - - +
54A VAL* 1.3 63.0 + - + +
56A LEU* 3.5 5.3 - - + +
57A MET* 2.8 39.0 + - + +
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Residues in contact with VAL 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 ASP* 2.8 23.2 + - + +
51A ALA* 3.5 10.8 - - - +
53A ILE* 1.3 73.2 - - + +
55A LYS* 1.3 63.8 + - - +
57A MET* 3.9 12.2 - - + +
58A ASP* 2.9 32.6 + - + +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ALA 2.9 16.5 + - - +
52A GLU* 3.6 11.9 - - + +
54A VAL* 1.3 77.2 - - - +
56A LEU* 1.3 63.5 + - - +
58A ASP* 3.8 4.0 - - - +
59A ASP* 2.8 32.6 + - + +
76A PHE* 3.6 18.0 - - + -
79A ALA* 3.4 30.8 - - - +
80A LEU* 3.3 29.8 - - + +
83A ILE* 4.0 25.8 - - + -
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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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34A LEU* 4.5 6.3 - - + -
37A LEU* 4.0 23.1 - - + -
38A ILE* 4.4 19.1 - - + -
41A GLU* 3.4 26.7 - - - +
52A GLU* 2.8 22.1 + - + +
53A ILE* 3.5 5.2 - - - +
55A LYS* 1.3 72.5 - - - +
57A MET* 1.3 55.9 + - - +
59A ASP* 4.0 0.3 - - - +
60A LEU* 2.8 66.0 + - + +
76A PHE* 3.4 42.1 - - + -
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Residues in contact with MET 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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31A LYS* 5.9 3.6 - - - -
34A LEU* 5.9 0.9 - - + -
38A ILE* 5.3 14.8 - - + -
53A ILE* 2.8 29.4 + - + +
54A VAL* 3.9 11.4 - - + +
56A LEU* 1.3 73.8 - - + +
58A ASP* 1.3 60.9 + - - +
61A ASP* 2.8 56.2 + - + +
65A ASP* 5.2 5.8 - - - +
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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 VAL* 2.9 24.2 + - + +
55A LYS* 3.8 4.1 - - - +
57A MET* 1.3 80.4 - - - +
59A ASP* 1.3 63.5 + - - +
61A ASP 4.2 2.1 + - - +
62A ARG* 2.7 48.3 + - - +
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Residues in contact with ASP 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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55A LYS* 2.8 25.6 + - + +
56A LEU 4.0 1.3 - - - +
58A ASP* 1.3 78.8 + - - +
60A LEU* 1.3 57.5 + - - +
62A ARG* 3.2 23.1 - - - +
72A GLU* 4.4 3.6 - - - +
75A THR* 4.0 7.1 + - - +
76A PHE* 3.2 36.5 + - + +
79A ALA* 3.3 27.2 - - + +
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Residues in contact with LEU 60 (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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19A TYR* 5.6 1.3 - - + +
29A LEU* 3.9 23.8 - - + -
34A LEU* 4.2 13.0 - - + -
37A LEU* 6.1 0.4 - - + -
56A LEU* 2.8 48.1 + - + +
59A ASP* 1.3 76.7 - - - +
61A ASP* 1.3 62.3 + - - +
62A ARG 2.9 8.5 + - - -
68A VAL* 3.5 18.5 - - + +
72A GLU* 3.0 28.2 - - - +
73A TYR* 3.6 40.2 - - + +
76A PHE* 4.2 12.1 - - + -
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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