Contacts of the helix formed by residues 40 - 55 (chain A) in PDB entry 1Z1G
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLY* 3.8 1.0 - - - -
39A ARG* 1.3 74.6 - - + +
41A ARG* 1.3 53.7 + - - +
42A ARG* 3.0 27.2 - - - +
43A ILE* 2.7 72.5 + - + +
44A ALA* 2.8 19.5 + - - +
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Residues in contact with ARG 41 (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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11A ASP* 2.8 36.9 + - - +
24A TYR* 3.6 32.3 - - + +
39A ARG 3.3 7.4 + - - +
40A ASP* 1.3 69.5 - - - +
42A ARG* 1.3 64.0 + - + +
44A ALA* 3.4 0.9 - - - +
45A ILE* 2.9 50.7 + - + +
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Residues in contact with ARG 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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40A ASP* 3.0 25.1 - - - +
41A ARG* 1.3 79.6 - - + +
43A ILE* 1.3 62.6 + - + +
45A ILE* 3.0 29.9 - - - +
46A THR* 3.3 7.4 + - - -
42D ARG* 6.0 0.4 - - - -
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Residues in contact with ILE 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 ASP* 2.7 44.8 + - + +
42A ARG* 1.3 78.0 - - + +
44A ALA* 1.3 58.0 + - - +
46A THR* 3.1 13.7 - - + -
47A GLU* 3.0 31.4 + - + +
60B LYS* 4.3 20.4 - - - +
42D ARG* 4.5 24.2 - - + -
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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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16A LEU* 4.5 7.2 - - + -
24A TYR* 4.1 26.9 - - + -
37A LEU* 3.4 30.9 - - + +
38A GLY 5.9 0.9 - - - +
40A ASP 2.8 11.1 + - - +
41A ARG* 3.4 9.6 - - - +
43A ILE* 1.3 72.4 - - - +
45A ILE* 1.3 57.0 + - - +
47A GLU* 3.1 2.9 + - - -
48A ALA* 2.7 38.0 + - - +
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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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11A ASP* 4.3 15.7 - - - +
13A PRO* 3.9 32.3 - - + -
16A LEU* 4.9 1.0 - - - +
41A ARG* 2.9 33.3 + - + +
42A ARG* 3.0 14.6 - - - +
44A ALA* 1.3 76.3 - - - +
46A THR* 1.3 89.1 + - - +
48A ALA* 2.8 10.3 - - - +
49A ILE* 2.8 41.0 + - + +
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Residues in contact with THR 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 ARG 3.3 11.6 + - - -
43A ILE* 3.1 20.8 + - + +
44A ALA 3.0 0.8 - - - -
45A ILE* 1.3 91.0 - - - +
47A GLU* 1.3 78.6 + - + +
49A ILE* 3.0 14.1 + - - +
50A GLN* 3.2 13.8 + - + +
60B LYS* 5.6 1.6 - - - +
42D ARG* 3.7 24.8 + - - +
43D ILE* 4.5 20.4 - - + -
46D THR* 6.5 0.4 - - + -
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Residues in contact with GLU 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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37A LEU* 4.3 8.5 - - + -
43A ILE* 3.0 17.9 + - + +
44A ALA* 3.8 4.7 - - - +
46A THR* 1.3 80.8 - - + +
48A ALA* 1.3 69.7 + - - +
50A GLN* 3.2 17.4 - - - +
51A ALA* 3.1 19.4 + - - +
60B LYS* 3.6 30.8 + - - +
61B HIS 3.4 11.6 - - - +
62B LYS* 4.5 1.0 - - - -
63B PRO* 3.0 47.5 - - + +
43D ILE* 5.2 5.7 - - - +
46D THR* 5.4 0.7 - - - +
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Residues in contact with ALA 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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13A PRO* 4.5 13.0 - - + -
16A LEU* 4.3 17.3 - - + -
26A TYR* 4.3 18.4 - - + -
37A LEU* 4.4 4.4 - - + +
44A ALA 2.7 15.2 + - - +
45A ILE* 2.8 17.7 + - - +
47A GLU* 1.3 77.1 - - - +
49A ILE* 1.3 62.9 + - - +
51A ALA* 2.8 17.3 + - - +
52A ASN* 3.1 15.3 + - - +
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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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13A PRO* 5.4 8.5 - - + -
45A ILE* 2.8 43.9 + - + +
46A THR* 3.0 5.8 + - - +
48A ALA* 1.3 72.2 - - + +
50A GLN* 1.3 66.0 + - - +
52A ASN* 2.7 33.1 + - + +
53A ILE* 3.0 12.1 + - + +
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Residues in contact with GLN 50 (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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46A THR* 3.2 12.9 + - + +
47A GLU* 3.2 24.2 - - - +
49A ILE* 1.3 74.1 - - - +
51A ALA* 1.3 58.1 + - - +
53A ILE* 2.4 42.7 - - - +
54A GLU* 3.3 4.0 + - - +
61A HIS* 3.1 48.5 + - - +
62B LYS* 5.2 6.8 - - - +
63B PRO* 6.1 3.1 - - + +
64B LEU* 5.2 9.4 + - - +
43D ILE* 5.4 13.7 - - + +
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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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26A TYR* 2.9 43.8 + - + +
47A GLU 3.7 6.3 - - - +
48A ALA* 2.8 6.9 + - - +
50A GLN* 1.3 75.8 - - - +
52A ASN* 1.3 56.1 + - - +
53A ILE 3.1 5.2 - - - -
54A GLU* 3.0 33.2 + - - +
55A LEU* 3.3 8.7 + - - +
63B PRO* 4.8 14.1 - - + +
64B LEU* 6.0 3.1 - - - +
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Residues in contact with ASN 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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13A PRO* 4.8 7.1 - - - +
14A PRO* 3.8 19.0 + - - +
15A ASN* 2.5 22.9 + - - +
26A TYR* 2.4 34.2 + - - -
48A ALA 3.2 7.2 - - - +
49A ILE* 2.7 27.3 + - + +
51A ALA* 1.3 69.3 - - - +
53A ILE* 1.3 59.4 + - - +
55A LEU* 4.1 6.5 - - - -
56A PHE* 3.2 30.8 - - + +
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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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49A ILE* 3.0 8.9 + - + +
50A GLN* 2.4 42.8 - - + +
52A ASN* 1.3 79.6 - - - +
54A GLU* 1.4 62.9 + - + +
56A PHE* 2.7 33.7 + - + +
57A SER* 3.3 11.0 + - - +
59A HIS* 5.0 5.8 - - + +
60A LYS* 6.0 0.2 - - - -
61A HIS* 5.7 5.8 - - + +
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Residues in contact with GLU 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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26A TYR* 6.4 0.4 - - - -
28A ASP* 6.0 0.5 - - - -
30A ARG* 4.1 22.2 + - - -
50A GLN 3.7 8.7 - - - +
51A ALA* 3.0 21.5 - - + +
53A ILE* 1.4 74.8 - - + +
55A LEU* 1.3 99.6 + - - +
56A PHE 2.9 5.3 + - - -
57A SER 3.0 10.9 + - - -
58A GLY* 3.4 13.0 + - - -
59A HIS 3.8 15.9 - - - +
60A LYS* 3.1 44.9 + - + +
64B LEU* 5.1 5.3 - - + -
67B ARG* 3.4 12.3 - - - +
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Residues in contact with LEU 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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15A ASN* 4.5 14.1 - - - +
26A TYR* 3.7 24.5 - - + +
28A ASP* 6.1 0.7 - - - +
29A PRO* 5.2 18.8 - - + -
30A ARG* 4.6 20.9 + - - +
51A ALA 3.3 8.2 + - - +
52A ASN* 3.9 7.2 - - - +
54A GLU* 1.3 90.5 + - - +
56A PHE* 1.3 89.7 + - + +
57A SER 3.7 0.2 + - - -
58A GLY 5.3 0.3 + - - -
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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