Contacts of the helix formed by residues 40 - 55 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C TYR* 4.2 2.5 - - - -
38C GLY* 3.9 0.8 - - - -
39C ARG* 1.3 73.9 - - + +
41C ARG* 1.3 57.4 + - - +
42C ARG* 2.6 42.0 - - - +
43C ILE* 2.7 50.4 + - + +
44C ALA* 3.0 11.1 + - - +
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Residues in contact with ARG 41 (chain C).
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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10C ARG* 6.0 3.2 - - - +
11C ASP* 3.6 37.4 + - - +
12C LEU* 6.3 0.8 - - - +
24C TYR* 3.5 37.0 - - + +
39C ARG 3.3 6.9 + - - -
40C ASP* 1.3 69.0 - - - +
42C ARG* 1.3 61.1 + - + +
44C ALA* 3.2 1.4 + - - +
45C ILE* 2.8 58.7 + - + +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 4.3 11.4 + - - +
40C ASP* 2.6 33.9 - - - +
41C ARG* 1.3 80.0 - - - +
43C ILE* 1.3 57.9 + - + +
45C ILE* 3.0 30.8 - - - +
46C THR* 3.3 8.0 + - - -
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 4.8 13.9 - - + +
37C LEU* 6.3 2.7 - - + -
40C ASP* 2.7 33.8 + - + +
42C ARG* 1.3 75.3 - - + +
44C ALA* 1.3 63.1 + - - +
46C THR* 3.1 8.0 + - - +
47C GLU* 3.1 34.5 + - + +
60D LYS* 4.6 19.7 - - - +
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.4 4.5 - - + -
24C TYR* 4.0 27.8 - - + -
37C LEU* 3.7 29.9 - - + +
38C GLY 6.0 0.2 - - - +
40C ASP 3.0 9.7 + - - +
41C ARG* 3.3 9.6 - - - +
43C ILE* 1.3 73.3 - - - +
45C ILE* 1.3 71.1 - - - +
47C GLU* 3.1 3.0 + - - -
48C ALA* 2.7 27.3 + - - +
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP* 4.0 10.8 - - + +
13C PRO* 3.7 32.7 - - + +
16C LEU* 4.8 0.6 - - - +
41C ARG* 2.8 39.4 + - + +
42C ARG* 3.0 15.0 - - - +
44C ALA* 1.3 75.8 - - - +
46C THR* 1.3 73.3 + - - +
48C ALA* 2.7 20.8 - - - +
49C ILE* 2.6 39.5 - - + +
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 3.6 25.2 + - + +
43B ILE* 4.2 29.4 - - + -
42C ARG 3.3 10.6 + - - -
43C ILE* 3.1 14.1 + - - -
44C ALA 3.1 1.6 - - - -
45C ILE* 1.3 85.2 - - - +
47C GLU* 1.3 61.7 + - - +
49C ILE* 3.0 23.8 + - + +
50C GLN* 3.1 15.4 + - + +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 4.0 21.0 - - - +
46B THR* 5.1 2.4 - - - +
37C LEU* 4.6 4.5 - - + -
43C ILE* 3.1 19.6 + - + +
44C ALA 3.7 4.5 - - - +
46C THR* 1.3 74.1 - - - +
48C ALA* 1.3 68.9 + - - +
50C GLN* 3.4 12.6 + - - +
51C ALA* 3.1 21.0 + - - +
60D LYS* 3.6 24.4 + - - +
61D HIS 3.3 8.7 - - - +
62D LYS* 3.4 8.3 - - - +
63D PRO* 2.3 61.7 - - + +
64D LEU 5.1 0.6 + - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PRO* 4.3 8.5 - - + -
16C LEU* 3.2 31.0 - - + -
26C TYR* 3.3 17.0 - - - -
37C LEU* 4.8 0.2 - - - +
44C ALA 2.7 13.1 + - - +
45C ILE* 2.7 18.8 - - - +
47C GLU* 1.3 77.2 - - - +
49C ILE* 1.3 63.7 + - + +
51C ALA 2.9 12.5 + - - -
52C ASN* 3.1 16.3 + - - +
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PRO* 4.9 9.4 - - + -
45C ILE* 2.6 43.1 - - + +
46C THR* 3.3 9.4 - - + +
48C ALA* 1.3 73.5 - - - +
50C GLN* 1.3 64.8 + - - +
52C ASN* 2.7 30.7 + - + +
53C ILE* 3.0 26.4 + - + +
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 4.8 21.7 - - + +
46C THR* 3.1 15.0 + - + +
47C GLU* 3.6 17.1 - - - +
49C ILE* 1.3 78.1 - - - +
51C ALA* 1.3 60.3 + - - +
53C ILE* 3.2 9.0 + - - +
54C GLU* 3.2 18.4 + - - +
61C HIS* 3.3 39.4 + - - +
62D LYS* 4.9 4.7 - - - +
64D LEU* 3.5 27.2 - - + +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TYR* 2.9 40.6 + - + +
47C GLU 3.1 7.4 + - - +
48C ALA 2.9 2.2 + - - +
50C GLN* 1.3 75.9 - - - +
52C ASN* 1.3 61.0 + - - +
54C GLU* 2.7 37.1 + - + +
55C LEU* 3.3 5.8 + - + +
63D PRO 5.0 4.9 - - - +
64D LEU* 5.0 15.5 - - - +
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Residues in contact with ASN 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PRO* 4.9 4.2 - - - +
14C PRO* 3.5 41.7 + - - +
15C ASN* 4.0 6.1 + - - +
16C LEU* 4.4 0.3 - - - +
26C TYR* 2.8 29.0 + - - -
48C ALA 3.1 15.3 + - - +
49C ILE* 2.7 28.5 + - + +
51C ALA* 1.3 71.8 - - - +
53C ILE* 1.3 63.8 + - + +
55C LEU* 4.3 5.1 + - - +
56C PHE* 2.9 33.8 + - + -
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 3.0 26.3 + - + +
50C GLN* 3.2 6.7 + - - +
52C ASN* 1.3 83.8 - - + +
54C GLU* 1.4 55.5 + - - +
56C PHE* 2.8 43.5 + - + +
57C SER* 3.3 7.1 + - - +
59C HIS* 5.1 0.9 - - - -
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP* 5.8 0.7 - - - -
30C ARG* 5.8 0.5 - - - -
50C GLN 3.2 12.7 + - - +
51C ALA* 2.7 31.8 + - + +
53C ILE* 1.4 69.4 - - - +
55C LEU* 1.3 97.5 + - + +
56C PHE 2.9 1.1 - - - -
57C SER 2.7 20.6 + - - -
58C GLY* 3.1 16.5 + - - -
59C HIS 3.7 21.5 + - - +
60C LYS* 4.9 14.9 - - + +
64D LEU* 5.8 6.7 - - + -
67D ARG* 3.3 28.5 - - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASN* 4.0 23.6 - - - +
26C TYR* 4.3 7.6 - - + +
28C ASP* 3.3 31.0 - - - +
29C PRO* 4.3 12.3 - - + -
30C ARG* 5.1 11.2 - - + +
51C ALA 3.3 14.9 + - - +
52C ASN* 4.5 6.1 - - - +
54C GLU* 1.3 113.1 + - + +
56C PHE* 1.3 66.1 + - + +
57C SER* 3.1 5.7 + - - -
58C GLY 5.0 0.5 + - - -
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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