Contacts of the helix formed by residues 48 - 61 (chain D) in PDB entry 1Z6T
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 THR 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C LYS* 4.2 13.5 - - + -
289C GLU* 2.4 34.2 + - - +
292C LEU* 3.8 21.5 - - + -
311C HIS* 3.9 12.3 - - + +
46D GLU 3.3 0.4 + - - -
47D PRO* 1.3 84.4 - - - +
49D GLN* 1.3 54.7 + - - +
50D GLN 4.1 1.3 - - - -
51D GLN* 3.1 19.8 + - - +
52D ARG* 2.8 38.8 + - - +
409D GLU* 3.5 12.6 - - - +
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Residues in contact with GLN 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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17D GLU 5.7 0.9 + - - +
18D LYS 4.6 8.1 + - - -
19D ASP* 4.0 17.0 + - - +
20D ILE 3.9 15.2 + - - +
21D LYS* 3.6 43.1 - - + +
22D THR* 5.1 0.5 + - - +
48D THR* 1.3 73.9 - - - +
50D GLN* 1.3 62.6 + - + +
52D ARG* 3.6 9.5 + - - +
53D ALA* 3.1 25.8 + - - +
408D THR* 4.3 12.6 - - - +
409D GLU* 3.0 25.4 + - + +
412D GLU* 4.9 0.9 - - - +
431D LYS* 5.6 2.0 - - - +
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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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289C GLU* 3.5 46.5 - - + +
290C LYS* 6.2 1.2 - - - +
303C LYS* 4.6 4.7 + - - -
17D GLU* 3.4 28.3 - - + +
18D LYS* 4.2 30.0 + - - +
48D THR* 3.3 1.8 + - - -
49D GLN* 1.3 81.1 - - + +
51D GLN* 1.3 60.8 + - + +
53D ALA* 3.4 1.6 + - - +
54D ALA* 2.8 30.1 + - - +
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Residues in contact with GLN 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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289C GLU* 3.2 23.8 + - - +
292C LEU* 4.4 4.8 - - - +
303C LYS* 4.6 18.4 + - - +
304C ALA* 4.7 17.1 - - + +
311C HIS* 4.3 9.1 + - - -
46D GLU* 3.7 25.5 - - + +
47D PRO* 3.4 21.8 - - - +
48D THR* 3.1 24.0 + - - +
50D GLN* 1.3 74.7 - - + +
52D ARG* 1.3 64.5 + - - +
54D ALA* 3.7 7.8 - - + +
55D MET* 3.0 24.9 + - - +
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Residues in contact with ARG 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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22D THR* 3.6 22.6 + - - +
23D SER* 6.0 3.6 - - - -
26D MET* 6.3 0.2 - - - -
43D VAL* 3.0 37.5 - - + +
44D ARG* 3.4 30.2 + - - +
46D GLU* 3.3 22.4 + - + +
47D PRO 5.4 1.8 + - - -
48D THR 2.8 22.9 + - - +
49D GLN* 3.6 8.7 - - - +
51D GLN* 1.3 77.7 - - - +
53D ALA* 1.3 56.5 + - - +
55D MET* 3.5 0.9 + - - +
56D LEU* 3.0 24.6 + - - +
409D GLU* 4.4 23.0 + - - +
410D GLU* 5.2 1.2 + - - -
413D ASP* 3.0 39.4 + - - -
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Residues in contact with ALA 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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17D GLU* 3.7 22.9 - - - +
20D ILE* 3.7 31.9 - - + +
22D THR* 3.7 10.7 - - - +
49D GLN 3.1 15.6 + - - +
50D GLN 3.6 7.2 - - - +
51D GLN 3.3 0.2 - - - -
52D ARG* 1.3 72.0 - - - +
54D ALA* 1.3 66.3 + - - +
56D LEU* 3.1 2.4 + - - +
57D ILE* 2.9 28.2 + - + +
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Residues in contact with ALA 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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13D ARG* 3.7 6.0 + - - +
17D GLU* 3.5 29.2 - - - +
50D GLN 2.8 22.7 + - - +
51D GLN* 3.7 10.3 - - + +
53D ALA* 1.3 70.8 - - - +
55D MET* 1.3 57.2 + - - +
57D ILE* 3.6 1.3 + - - +
58D LYS* 3.0 31.6 + - - +
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Residues in contact with MET 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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42D LYS* 3.7 38.8 - - - +
43D VAL* 3.7 29.8 - - + +
46D GLU* 4.0 28.0 - - + +
51D GLN 3.0 17.3 + - - +
52D ARG* 3.5 4.9 - - - +
54D ALA* 1.3 73.5 - - - +
56D LEU* 1.3 67.5 + - - +
58D LYS* 3.2 27.1 + - + +
59D MET* 3.0 27.6 + - - +
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Residues in contact with LEU 56 (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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20D ILE* 4.7 3.1 - - + -
22D THR* 4.0 21.1 - - + -
25D ILE* 4.2 18.6 - - + -
26D MET* 3.9 28.5 - - + -
29D MET* 4.8 2.7 - - - -
35D LEU* 3.9 29.4 - - + -
43D VAL* 4.0 11.8 - - + +
52D ARG 3.0 15.0 + - - +
53D ALA 3.1 6.0 + - - +
55D MET* 1.3 75.2 - - - +
57D ILE* 1.3 56.6 + - + +
59D MET* 2.7 26.8 + - + +
60D ILE* 2.9 33.1 + - + +
71D PHE* 4.3 6.7 - - + -
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Residues in contact with ILE 57 (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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9D LEU* 4.5 21.5 - - + -
13D ARG* 3.4 32.5 - - + +
16D LEU* 3.4 35.2 - - + -
17D GLU* 3.9 19.3 - - + +
20D ILE* 4.5 8.1 - - + -
53D ALA 2.9 20.4 + - - +
54D ALA* 4.1 2.9 - - - +
56D LEU* 1.3 76.5 - - - +
58D LYS* 1.3 55.8 + - - +
60D ILE* 3.7 8.1 - - - +
61D LEU* 2.9 30.8 + - + +
71D PHE* 4.2 20.9 - - + -
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Residues in contact with LYS 58 (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 ARG* 3.2 26.1 - - - +
42D LYS* 5.5 6.5 - - - +
54D ALA 3.0 16.1 + - - +
55D MET* 3.2 30.8 - - + +
57D ILE* 1.3 75.7 - - - +
59D MET* 1.3 60.6 + - + +
61D LEU* 3.7 13.4 - - + +
62D LYS* 4.0 34.7 + - - +
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Residues in contact with MET 59 (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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35D LEU* 4.6 5.8 - - + -
39D GLU* 3.3 66.0 - - + +
42D LYS* 3.7 34.8 - - + +
43D VAL* 3.8 18.2 - - + -
55D MET* 3.0 17.2 + - - +
56D LEU* 2.7 16.7 + - + +
58D LYS* 1.3 69.5 - - + +
60D ILE* 1.3 64.2 + - - +
61D LEU 3.1 1.3 - - - -
62D LYS* 2.8 21.7 + - - +
63D LYS* 3.4 17.1 - - - +
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Residues in contact with ILE 60 (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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1D MET* 3.8 12.7 - - + +
9D LEU* 3.8 20.2 - - + -
29D MET* 3.8 21.8 - - + -
35D LEU* 5.6 1.1 - - + -
56D LEU* 2.9 35.7 + - + +
57D ILE* 3.7 7.9 - - - +
59D MET* 1.3 76.1 - - + +
61D LEU* 1.3 63.9 + - - +
63D LYS* 3.1 30.4 + - + +
67D SER 5.0 1.1 - - - +
68D TYR* 4.9 8.7 - - - +
71D PHE* 3.4 53.4 - - + -
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Residues in contact with LEU 61 (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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1D MET* 4.8 4.5 - - - +
6D ARG* 4.6 26.6 + - + +
9D LEU* 3.4 32.1 - - + -
10D LEU* 3.5 32.8 - - + +
13D ARG* 3.6 39.5 - - - +
57D ILE* 2.9 21.3 + - + +
58D LYS* 3.7 8.7 - - + +
59D MET 3.0 0.6 + - - -
60D ILE* 1.3 75.6 - - - +
62D LYS* 1.3 60.0 + - + +
63D LYS 3.2 6.1 + - - +
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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