Contacts of the helix formed by residues 40 - 49 (chain A) in PDB entry 1ZGA
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ALA 3.3 1.5 + - - -
37A MET* 3.2 12.1 + - - -
38A GLU 3.2 5.1 - - - -
39A LEU* 1.3 79.3 - - - +
41A ILE* 1.3 59.4 + - - +
42A ALA* 3.3 2.9 - - - -
43A ASP* 3.4 15.4 + - - +
44A ALA* 2.9 28.8 + - - +
61A LEU* 4.4 0.3 - - - +
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Residues in contact with ILE 41 (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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36A ALA* 3.2 35.2 + - + +
39A LEU* 4.0 19.7 - - + -
40A GLY* 1.3 76.8 - - - +
42A ALA* 1.3 59.3 + - - +
44A ALA* 3.2 7.9 + - - +
45A ILE* 2.9 30.7 + - + +
57A LEU* 3.9 20.0 - - + -
61A LEU* 4.2 11.2 - - + -
71A LEU* 4.2 11.0 - - + -
74A PHE* 6.1 1.8 - - + -
75A LEU* 3.8 24.0 - - + -
78A LEU* 5.1 1.8 - - + -
84A PHE* 3.4 30.7 - - + -
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Residues in contact with ALA 42 (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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36A ALA 4.6 1.6 + - - -
37A MET* 6.5 0.2 - - - -
40A GLY* 3.3 0.6 - - - -
41A ILE* 1.3 79.1 - - - +
43A ASP* 1.3 53.1 + - - +
45A ILE 3.2 0.9 + - - -
46A HIS* 2.7 37.9 + - - +
84A PHE* 5.1 1.9 - - + -
104A LEU* 3.5 21.3 - - + +
108A SER* 3.5 25.8 - - - +
111A LEU* 3.6 30.5 - - + +
112A ILE* 4.1 4.5 - - + +
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Residues in contact with ASP 43 (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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40A GLY* 3.4 14.7 + - - +
41A ILE 3.4 0.4 - - - -
42A ALA* 1.3 79.2 - - - +
44A ALA* 1.3 55.2 + - - +
46A HIS* 4.1 4.9 - - - -
47A ASN* 2.7 51.9 + - - +
111A LEU 4.4 3.8 - - - +
112A ILE* 3.1 14.3 - - - +
113A SER* 2.5 51.0 + - - -
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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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40A GLY 2.9 15.0 + - - +
41A ILE* 3.3 9.9 - - - +
42A ALA 3.2 0.2 - - - -
43A ASP* 1.3 78.0 - - - +
45A ILE* 1.3 62.3 + - - +
47A ASN* 3.9 5.2 - - - +
48A HIS* 3.1 22.9 + - - +
52A MET* 3.5 6.1 - - - +
57A LEU* 3.7 21.8 - - + -
60A SER* 3.9 20.2 + - - +
61A LEU* 4.3 8.1 - - + -
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Residues in contact with ILE 45 (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 ILE* 2.9 22.7 + - + +
42A ALA 3.8 2.5 - - - +
44A ALA* 1.3 72.2 - - - +
46A HIS* 1.3 67.8 + - - +
48A HIS* 3.0 12.2 + - - +
49A GLY* 3.1 10.7 + - - -
50A LYS 4.2 12.4 + - - +
52A MET* 3.8 19.5 - - + -
57A LEU* 4.5 5.6 - - + -
84A PHE* 3.8 34.3 - - + -
102A TYR* 3.6 36.1 - - + +
103A SER* 4.4 2.0 - - - -
104A LEU* 3.7 27.6 - - + +
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Residues in contact with HIS 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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42A ALA 2.7 22.3 + - - +
43A ASP* 3.7 4.5 - - - +
45A ILE* 1.3 74.0 - - - +
47A ASN* 1.3 74.5 + - - +
49A GLY* 3.1 15.6 + - - -
104A LEU* 4.0 6.8 - - + +
112A ILE* 3.6 41.8 - - + +
115A LYS* 3.9 26.5 + - - -
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Residues in contact with ASN 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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43A ASP* 2.7 37.0 + - - +
44A ALA* 4.0 4.8 - - - +
46A HIS* 1.3 84.2 - - - +
48A HIS* 1.3 66.1 + - - +
49A GLY* 3.4 0.7 + - - -
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Residues in contact with HIS 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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44A ALA 3.1 15.0 + - - +
45A ILE 3.0 10.6 + - - +
47A ASN* 1.3 78.0 - - - +
49A GLY* 1.3 59.7 + - - +
50A LYS* 3.0 50.6 + - + +
51A PRO 3.9 2.6 + - - -
52A MET* 3.2 37.2 - - + +
56A GLU* 4.1 24.2 + - + -
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Residues in contact with GLY 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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45A ILE 3.1 3.1 + - - -
46A HIS 3.1 15.2 + - - -
47A ASN 4.3 0.7 - - - -
48A HIS* 1.3 80.3 - - - +
50A LYS* 1.3 63.5 + - - +
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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