Contacts of the helix formed by residues 40 - 55 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D TYR* 3.3 4.8 - - - -
38D GLY* 3.7 2.2 - - - -
39D ARG* 1.3 80.8 + - - +
41D ARG* 1.4 52.6 + - - +
42D ARG* 3.4 23.1 + - - +
43D ILE* 2.9 35.3 + - + +
44D ALA* 3.0 12.6 + - - +
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Residues in contact with ARG 41 (chain D).
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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10D ARG* 5.9 0.2 - - - +
11D ASP* 2.6 51.2 + - - -
12D LEU* 4.4 16.0 - - + +
24D TYR* 2.7 41.4 + - + +
39D ARG 3.5 0.8 + - - -
40D ASP* 1.4 65.6 - - - +
42D ARG* 1.3 59.8 + - - +
44D ALA* 3.2 1.3 - - - +
45D ILE* 2.8 53.6 + - + +
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Residues in contact with ARG 42 (chain D).
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 6.0 0.2 - - - -
43A ILE* 4.5 22.7 - - + -
46A THR* 3.7 22.0 + - - +
40D ASP* 4.2 19.3 - - + +
41D ARG* 1.3 81.6 - - - +
43D ILE* 1.3 78.3 + - - +
45D ILE* 3.7 8.6 - - - +
46D THR* 2.7 27.9 + - - +
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Residues in contact with ILE 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 4.5 18.8 - - + -
47A GLU* 5.2 5.6 - - - +
50A GLN* 5.4 12.6 - - + +
61A HIS* 4.9 21.1 - - + +
37D LEU* 6.3 3.4 - - + -
40D ASP* 2.9 21.8 + - + +
42D ARG* 1.3 90.9 - - - +
44D ALA* 1.3 65.1 + - - +
46D THR* 2.8 27.8 + - + +
47D GLU* 3.2 15.9 + - + +
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.5 10.3 - - + -
24D TYR* 3.4 39.0 - - + -
37D LEU* 4.1 22.0 - - + +
40D ASP 3.0 5.1 + - - +
41D ARG* 3.2 10.3 - - - +
43D ILE* 1.3 74.8 - - - +
45D ILE* 1.3 69.6 + - + +
46D THR 3.1 0.3 + - - -
47D GLU* 3.2 4.2 + - - +
48D ALA* 2.8 23.2 + - - +
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Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASP* 4.7 9.9 - - + +
12D LEU* 3.8 11.9 - - + -
13D PRO* 3.5 34.5 - - + -
16D LEU* 4.8 2.0 - - + +
41D ARG* 2.8 40.8 + - + +
42D ARG* 3.7 8.5 - - - +
44D ALA* 1.3 82.9 - - + +
46D THR* 1.3 74.8 + - + +
48D ALA* 2.7 24.3 + - - +
49D ILE* 2.9 13.8 + - + +
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 5.4 1.1 - - - +
60B LYS* 3.2 44.9 - - + +
42D ARG 2.7 21.8 + - - +
43D ILE* 2.8 28.6 + - + +
44D ALA 3.1 0.2 - - - -
45D ILE* 1.3 89.9 - - + +
47D GLU* 1.3 64.1 + - - +
49D ILE* 3.2 9.4 + - - +
50D GLN* 3.3 16.1 + - + +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A HIS* 1.8 50.8 + - + +
62A LYS 4.0 4.7 - - - +
63A PRO* 4.3 3.5 - - - -
64A LEU* 2.9 45.0 + - + +
37D LEU* 5.2 9.4 - - + -
43D ILE* 3.2 9.1 + - + +
44D ALA 3.2 4.9 + - - +
46D THR* 1.3 82.1 - - - +
48D ALA* 1.3 62.5 + - - +
50D GLN* 3.0 29.0 - - + +
51D ALA* 3.0 9.2 + - - +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.2 3.6 - - - -
13D PRO* 4.2 17.0 - - + -
14D PRO 5.7 1.8 - - - +
16D LEU* 4.3 19.5 - - + -
26D TYR* 5.8 1.8 - - + -
37D LEU* 5.3 1.1 - - - +
44D ALA 2.8 14.3 + - - +
45D ILE* 2.7 21.5 + - - +
47D GLU* 1.3 74.7 - - - +
49D ILE* 1.3 65.8 + - - +
51D ALA* 2.7 26.5 + - - +
52D ASN* 3.0 8.1 + - - +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PRO* 4.4 20.6 - - + -
14D PRO* 5.3 5.6 - - + -
45D ILE* 2.9 15.9 + - + +
46D THR 3.2 2.7 + - - +
48D ALA* 1.3 80.0 - - - +
50D GLN* 1.3 57.1 + - - +
52D ASN* 2.5 35.4 + - + -
53D ILE* 2.9 15.7 + - + +
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.8 1.1 - - + +
65A THR* 5.5 6.1 - - - +
59B HIS 5.0 2.0 - - - +
60B LYS* 4.3 38.3 - - + +
61B HIS* 4.8 7.0 + - - +
62B LYS* 5.3 0.9 + - - +
46D THR* 3.3 17.3 + - - +
47D GLU* 3.0 29.4 - - + +
49D ILE* 1.3 74.2 - - - +
51D ALA* 1.3 57.7 + - - +
53D ILE* 2.7 61.1 + - - +
54D GLU* 3.4 12.4 + - - +
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Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.6 38.1 - - + +
65A THR 5.6 0.4 - - - +
68A ILE* 5.9 2.5 - - + -
26D TYR* 3.9 12.5 + - + -
47D GLU 3.0 4.6 + - - +
48D ALA* 2.7 19.1 + - - +
50D GLN* 1.3 73.3 - - - +
52D ASN* 1.3 65.7 - - - +
53D ILE 3.3 0.2 - - - -
54D GLU* 3.2 28.4 + - - +
55D LEU* 3.5 13.6 + - + +
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Residues in contact with ASN 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PRO* 5.6 0.4 - - - +
14D PRO* 2.8 35.7 + - + +
15D ASN* 2.7 33.9 + - - +
26D TYR* 3.5 5.5 + - - -
48D ALA* 3.3 9.5 - - - +
49D ILE* 2.5 27.4 + - + +
51D ALA* 1.3 86.4 - - - +
53D ILE* 1.3 51.1 - - - -
55D LEU* 4.9 2.2 - - - +
56D PHE* 1.7 37.2 + - - +
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER* 4.8 1.6 - - - +
58B GLY* 3.8 34.3 - - - +
49D ILE* 3.0 16.4 - - + +
50D GLN* 2.7 51.6 - - + +
52D ASN* 1.3 79.7 - - - +
54D GLU* 1.3 69.0 + - + +
55D LEU 3.4 0.2 - - - -
56D PHE 3.1 3.6 - - - -
57D SER* 2.9 45.6 + - - +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 2.8 50.3 + - + +
68A ILE* 5.8 2.2 - - + -
50D GLN 3.6 12.8 - - - +
51D ALA* 3.2 13.6 + - - +
53D ILE* 1.3 84.3 - - - +
55D LEU* 1.3 69.5 + - + +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.5 19.5 - - + -
26D TYR* 5.4 7.2 - - + +
28D ASP* 4.9 1.6 - - - +
29D PRO* 4.3 21.3 - - + -
30D ARG* 3.6 44.4 - - + +
51D ALA* 3.5 16.0 + - + +
52D ASN* 5.3 1.8 - - - +
53D ILE 4.1 0.2 - - - -
54D GLU* 1.3 84.1 - - + +
56D PHE* 1.3 74.1 + - + +
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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