Contacts of the helix formed by residues 40 - 55 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B TYR* 4.0 1.8 - - - -
38B GLY 3.9 0.8 - - - -
39B ARG* 1.3 77.7 + - - +
41B ARG* 1.3 55.2 - - - +
42B ARG* 4.2 17.4 - - + +
43B ILE* 2.8 42.0 + - + +
44B ALA* 2.9 17.5 + - - +
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Residues in contact with ARG 41 (chain B).
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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10B ARG* 5.2 10.1 - - - +
11B ASP* 3.4 31.3 + - - -
12B LEU* 4.5 18.8 - - + +
24B TYR* 3.2 43.6 + - + +
39B ARG 3.4 0.6 + - - +
40B ASP* 1.3 70.8 - - - +
42B ARG* 1.3 60.3 + - + +
44B ALA* 3.4 4.4 - - - +
45B ILE* 2.6 51.6 + - + +
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASP* 4.5 16.2 - - + -
41B ARG* 1.3 87.2 - - + +
43B ILE* 1.3 59.0 + - + +
45B ILE* 3.4 14.9 - - - +
46B THR* 2.7 28.6 + - - -
42C ARG* 4.3 18.4 + - - +
43C ILE* 4.8 12.9 - - + +
46C THR* 3.6 28.1 + - + +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 6.5 1.6 - - + -
38B GLY* 6.5 1.1 - - - -
40B ASP* 2.8 25.4 + - + +
42B ARG* 1.3 80.0 - - + +
44B ALA* 1.3 65.7 + - - +
46B THR* 2.9 36.4 - - + +
47B GLU* 3.1 10.0 + - - +
46C THR* 4.2 22.4 - - + -
47C GLU* 4.0 20.0 - - - +
50C GLN* 4.8 19.3 - - + +
61C HIS* 4.3 22.7 - - + +
60D LYS* 5.7 0.4 - - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.5 6.3 - - + -
24B TYR* 4.1 21.1 - - + -
37B LEU* 3.7 32.6 - - + +
38B GLY 5.9 0.7 - - - +
40B ASP 2.9 11.8 + - - +
41B ARG* 3.4 13.9 - - - +
43B ILE* 1.3 73.0 - - - +
45B ILE* 1.3 57.8 + - + +
47B GLU* 3.0 4.2 + - - -
48B ALA* 2.7 34.4 + - - +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 4.0 20.6 - - - +
13B PRO* 4.6 18.8 - - + -
16B LEU* 4.7 0.6 - - - +
41B ARG* 2.6 38.2 + - + +
42B ARG* 3.4 13.9 - - - +
44B ALA* 1.3 76.5 - - - +
46B THR* 1.3 67.6 + - - +
48B ALA* 2.5 30.6 - - - +
49B ILE* 2.9 20.6 + - + +
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Residues in contact with THR 46 (chain B).
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 2.7 21.4 + - - -
43B ILE* 2.9 30.0 - - + +
44B ALA 3.0 0.4 - - - -
45B ILE* 1.3 86.3 - - - +
47B GLU* 1.3 66.7 + - - +
49B ILE* 3.3 4.8 + - - +
50B GLN* 3.0 28.5 + - + +
47C GLU* 5.1 2.2 - - - +
61C HIS* 5.8 2.2 - - + -
60D LYS* 3.6 38.0 - - + +
62D LYS* 6.5 2.0 - - + -
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 5.0 7.6 - - + +
43B ILE 3.1 2.4 + - - +
44B ALA 3.0 6.6 + - - +
46B THR* 1.3 82.0 - - - +
48B ALA* 1.3 61.5 + - - +
50B GLN* 3.1 16.0 - - + +
51B ALA* 3.0 22.3 + - - +
61C HIS* 2.1 53.2 + - + +
62C LYS 3.0 9.7 - - - +
63C PRO* 3.7 3.8 - - + -
64C LEU* 2.7 60.8 + - + +
67C ARG* 3.5 6.9 + - - -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 4.2 15.3 - - + -
14B PRO 5.8 0.2 - - - +
16B LEU* 3.9 20.4 - - + -
26B TYR* 4.7 8.3 - - + -
37B LEU* 5.1 0.6 - - - +
44B ALA 2.7 13.0 + - - +
45B ILE* 2.5 23.3 + - - +
47B GLU* 1.3 72.3 - - - +
49B ILE* 1.3 63.4 + - + +
51B ALA* 2.8 14.2 + - - +
52B ASN* 2.6 27.2 - - - +
64C LEU* 4.9 2.0 - - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 5.3 9.9 - - + -
14B PRO* 6.5 0.9 - - + -
45B ILE* 2.9 26.7 + - + +
46B THR* 3.3 3.1 + - - +
48B ALA* 1.3 81.4 - - + +
50B GLN* 1.3 67.0 + - - +
52B ASN* 2.7 26.5 + - + -
53B ILE* 2.7 26.3 + - + +
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR* 3.0 27.8 + - + +
47B GLU* 3.1 25.4 - - + +
49B ILE* 1.3 76.4 - - - +
51B ALA* 1.3 55.9 + - - +
53B ILE* 3.0 55.0 - - - +
54B GLU* 3.4 9.4 + - - +
63C PRO* 5.6 10.0 - - + +
64C LEU* 5.4 2.7 - - + +
65C THR* 4.7 10.3 + - - +
58D GLY* 5.2 5.1 - - - -
60D LYS* 4.9 21.5 + - - +
61D HIS* 4.7 5.6 - - - -
62D LYS* 4.7 13.7 + - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 4.3 14.0 + - + -
47B GLU 3.0 10.7 + - - +
48B ALA 2.8 14.1 + - - +
50B GLN* 1.3 73.1 - - - +
52B ASN* 1.3 58.8 + - - +
53B ILE 3.1 5.4 - - - -
54B GLU* 3.0 27.7 + - - +
55B LEU* 3.3 10.4 + - - +
64C LEU* 3.7 31.1 - - + +
65C THR 5.2 0.4 - - - +
68C ILE* 4.7 8.5 - - + +
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 6.2 0.7 - - - -
14B PRO* 3.1 28.5 + - + +
15B ASN* 2.7 31.4 - - - +
26B TYR* 3.4 17.7 - - - -
48B ALA* 2.6 27.2 - - - +
49B ILE* 2.7 21.4 + - + +
51B ALA* 1.3 70.4 - - - +
53B ILE* 1.3 54.2 - - - +
55B LEU* 5.1 2.0 - - - -
56B PHE* 1.9 39.8 - - + +
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Residues in contact with ILE 53 (chain B).
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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49B ILE* 2.7 27.1 - - + +
50B GLN* 3.0 50.9 - - - +
52B ASN* 1.3 79.0 - - - +
54B GLU* 1.3 61.4 + - - +
56B PHE 2.8 5.7 - - - -
57B SER* 2.5 46.1 + - - +
58B GLY 5.2 0.7 - - - +
57D SER* 3.1 30.7 - - - +
58D GLY* 5.0 12.6 - - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN 3.4 4.1 + - - +
51B ALA* 3.0 14.3 + - - +
53B ILE* 1.3 85.6 - - - +
55B LEU* 1.3 61.3 + - + +
57B SER* 4.7 3.3 + - - -
65C THR* 3.1 49.9 + - + +
68C ILE* 5.8 3.6 - - + -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 5.7 4.3 - - - +
28B ASP* 4.7 7.9 - - - +
29B PRO* 5.1 13.7 - - + -
30B ARG* 4.3 30.3 - - + -
51B ALA 3.3 9.3 + - - +
52B ASN* 5.1 2.5 - - - -
54B GLU* 1.3 78.3 - - - +
56B PHE* 1.3 75.5 + - + +
57B SER 3.8 1.3 + - - -
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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