Contacts of the helix formed by residues 48 - 61 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C GLU 3.4 0.2 - - - -
47C PRO* 1.3 87.0 - - + +
49C GLN* 1.3 60.9 + - - +
50C GLN* 3.9 8.5 + - - +
51C GLN* 2.8 37.7 + - - +
52C ARG* 3.0 34.6 + - - +
407C GLU* 5.7 3.8 - - - +
409C GLU* 3.2 10.8 - - - +
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Residues in contact with GLN 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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17C GLU 3.7 1.4 - - - +
18C LYS 3.6 10.5 + - - +
19C ASP* 3.5 21.2 + - - +
20C ILE 3.2 23.8 - - - +
21C LYS* 3.2 41.2 - - + +
22C THR* 4.7 0.3 + - - -
48C THR* 1.3 73.0 - - - +
50C GLN* 1.3 64.3 + - + +
52C ARG* 3.6 12.1 + - - +
53C ALA 3.4 15.6 + - - -
408C THR* 5.4 2.8 - - - +
409C GLU* 3.1 20.3 + - + +
412C GLU* 4.7 2.9 - - - +
431C LYS* 5.4 2.4 - - - +
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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
----------------------------------------------------------
17C GLU* 3.0 26.4 - - + +
18C LYS* 3.7 31.7 - - - +
48C THR* 3.4 7.7 + - - +
49C GLN* 1.3 76.8 - - + +
51C GLN* 1.3 60.8 + - + +
52C ARG 3.2 0.4 - - - -
53C ALA 3.7 0.2 + - - -
54C ALA* 3.1 29.8 + - - +
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Residues in contact with GLN 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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46C GLU* 3.5 31.7 + - + +
47C PRO* 3.6 24.0 - - - +
48C THR* 2.8 38.0 + - - +
49C GLN 3.4 0.6 - - - -
50C GLN* 1.3 78.5 - - + +
52C ARG* 1.3 58.2 + - - +
54C ALA* 3.9 6.0 - - - +
55C MET* 3.1 29.1 + - - +
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Residues in contact with ARG 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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22C THR* 3.4 22.8 - - - +
23C SER* 6.4 0.2 - - - -
43C VAL* 3.0 44.6 + - + +
44C ARG* 3.3 25.5 + - - +
46C GLU* 3.2 19.9 + - + +
47C PRO 5.4 0.2 + - - -
48C THR 3.0 23.2 + - - +
49C GLN* 3.8 10.3 - - - +
50C GLN 3.2 0.4 - - - -
51C GLN* 1.3 76.0 - - - +
53C ALA* 1.3 64.7 + - - +
55C MET* 3.4 0.9 + - - +
56C LEU* 3.1 13.2 + - - +
409C GLU* 4.2 29.9 + - - +
412C GLU* 5.9 2.6 + - - +
413C ASP* 3.0 37.7 + - - -
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Residues in contact with ALA 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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16C LEU 3.4 26.5 - - - +
17C GLU* 3.6 16.4 - - - +
20C ILE* 3.6 23.6 - - + +
22C THR* 3.9 4.4 + - - +
49C GLN 3.4 6.2 + - - +
52C ARG* 1.3 76.4 - - - +
54C ALA* 1.3 66.0 + - - +
56C LEU* 2.9 7.4 + - - +
57C ILE* 2.8 31.6 + - + +
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Residues in contact with ALA 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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13C ARG* 3.2 14.9 + - - +
17C GLU* 3.1 34.7 - - - +
50C GLN 3.1 21.6 + - - +
51C GLN* 3.9 6.7 - - - +
53C ALA* 1.3 73.7 - - - +
55C MET* 1.3 63.4 + - - +
57C ILE* 4.0 0.6 - - - +
58C LYS* 3.2 19.5 + - - +
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Residues in contact with MET 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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42C LYS* 3.7 34.1 - - + +
43C VAL* 3.6 27.1 - - + -
46C GLU* 3.3 34.3 - - + +
51C GLN 3.1 15.8 + - - +
52C ARG 3.5 5.4 - - - +
53C ALA 3.1 0.8 - - - -
54C ALA* 1.3 77.0 - - - +
56C LEU* 1.3 53.6 + - - +
58C LYS* 3.2 22.5 - - + +
59C MET* 2.8 31.9 - - + +
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Residues in contact with LEU 56 (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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20C ILE* 5.0 9.9 - - + -
22C THR* 3.8 22.7 - - + -
25C ILE* 4.4 21.3 - - + -
26C MET* 4.1 22.7 - - + +
29C MET* 5.2 2.2 - - - -
35C LEU* 4.3 17.0 - - + -
43C VAL* 4.0 9.6 - - + -
52C ARG 3.1 12.7 + - - +
53C ALA* 2.9 4.9 + - - +
55C MET* 1.3 77.4 - - - +
57C ILE* 1.3 64.9 + - + +
59C MET* 3.0 22.7 + - + +
60C ILE* 3.1 29.2 + - + +
71C PHE* 4.4 11.7 - - + -
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Residues in contact with ILE 57 (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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9C LEU* 3.9 19.2 - - + +
13C ARG* 3.6 36.8 - - + +
16C LEU* 3.4 41.1 - - + -
17C GLU* 4.3 5.8 - - + +
20C ILE* 5.3 2.2 - - + -
53C ALA* 2.8 31.8 + - + +
54C ALA 4.0 2.5 - - - +
56C LEU* 1.3 67.8 - - + +
58C LYS* 1.3 68.6 + - - +
59C MET 2.8 2.5 + - - -
60C ILE* 3.0 16.7 + - - +
61C LEU* 3.1 23.6 + - + +
71C PHE* 4.4 14.6 - - + -
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Residues in contact with LYS 58 (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 ARG* 3.3 26.2 - - - +
54C ALA 3.2 6.5 + - - +
55C MET* 3.2 22.7 - - + +
57C ILE* 1.3 78.4 - - - +
59C MET* 1.3 58.4 + - + +
61C LEU* 3.9 12.9 - - + +
62C LYS* 3.6 32.5 - - - +
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Residues in contact with MET 59 (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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39C GLU* 3.3 39.3 - - + +
42C LYS* 3.6 43.7 - - + +
43C VAL* 3.8 22.7 - - - -
55C MET* 2.8 24.0 - - + +
56C LEU* 3.3 14.4 - - + +
57C ILE 2.9 0.4 - - - -
58C LYS* 1.3 78.7 - - + +
60C ILE* 1.3 64.8 + - - +
62C LYS* 3.3 19.2 + - - +
63C LYS* 3.5 16.2 - - - +
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Residues in contact with ILE 60 (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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1C MET* 3.4 14.2 - - + +
9C LEU* 4.1 17.7 - - + -
29C MET* 3.8 22.9 - - + -
35C LEU* 5.8 0.4 - - + -
56C LEU* 3.1 29.3 + - + +
57C ILE* 3.0 7.8 + - - +
59C MET* 1.3 71.6 - - - +
61C LEU* 1.3 54.8 + - - +
62C LYS 3.0 5.6 - - - -
63C LYS* 2.8 44.4 + - + +
67C SER* 4.6 12.6 - - - +
68C TYR* 4.7 3.4 - - - +
71C PHE* 3.5 48.5 - - + -
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Residues in contact with LEU 61 (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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1C MET* 4.3 13.5 + - - +
6C ARG* 3.8 22.8 + - + +
9C LEU* 3.7 29.8 - - + -
10C LEU* 3.4 41.5 - - + -
13C ARG* 4.5 8.7 - - - +
57C ILE* 3.1 34.4 + - + +
58C LYS* 3.9 16.2 - - + +
60C ILE* 1.3 77.1 - - - +
62C LYS* 1.3 61.3 + - + +
63C LYS 3.2 6.2 + - - +
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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