Contacts of the helix formed by residues 48 - 61 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A LYS* 6.4 0.9 - - + -
289A GLU* 3.6 16.7 + - - -
292A LEU* 3.9 12.3 - - + +
311A HIS* 3.0 43.3 - - + +
47B PRO* 1.3 79.8 - - - +
49B GLN* 1.3 59.0 + - - +
50B GLN* 4.2 0.2 - - - +
51B GLN* 2.7 32.2 + - - +
52B ARG* 3.0 35.4 + - - +
409B GLU* 3.2 11.0 - - - +
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Residues in contact with GLN 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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288A LYS* 5.6 4.2 + - - +
18B LYS 3.9 12.5 + - - -
19B ASP* 3.1 23.8 + - - +
20B ILE 3.3 21.6 - - - +
21B LYS* 3.2 42.8 - - + +
22B THR* 5.0 0.2 - - - +
48B THR* 1.3 73.8 - - - +
50B GLN* 1.3 61.6 + - - +
52B ARG* 3.6 11.9 + - - +
53B ALA* 3.3 18.4 + - - +
408B THR* 5.6 2.1 - - - +
409B GLU* 2.9 20.4 + - + +
412B GLU* 5.1 0.3 - - - +
431B LYS* 5.6 2.0 - - - +
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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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289A GLU* 3.1 55.3 + - + +
303A LYS* 3.8 10.9 + - - +
17B GLU* 3.2 34.9 - - - +
18B LYS* 3.6 34.9 - - - +
48B THR* 3.3 2.6 + - - +
49B GLN* 1.3 80.0 - - + +
51B GLN* 1.3 66.3 + - + +
53B ALA* 3.9 0.2 - - - +
54B ALA* 3.2 22.7 + - - +
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 5.6 1.0 - - - +
303A LYS 4.7 3.9 - - - +
304A ALA* 3.5 44.6 + - + +
306A LEU 5.9 0.2 + - - -
311A HIS* 4.2 4.9 + - - -
46B GLU* 3.7 28.7 + - + +
47B PRO* 3.6 22.8 - - - +
48B THR* 2.7 37.4 + - - +
50B GLN* 1.3 77.5 - - + +
52B ARG* 1.3 58.8 + - - +
54B ALA* 3.3 7.6 + - - +
55B MET* 3.0 30.8 + - - +
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Residues in contact with ARG 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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22B THR* 3.6 26.4 + - + +
23B SER* 6.2 1.6 - - - -
43B VAL* 3.1 42.0 - - + +
44B ARG* 3.1 31.4 + - - +
46B GLU* 3.0 18.9 + - - +
47B PRO 5.3 0.6 + - - -
48B THR 3.0 23.1 + - - +
49B GLN* 3.8 11.0 - - - +
50B GLN 3.4 0.2 - - - -
51B GLN* 1.3 72.9 - - - +
53B ALA* 1.3 66.6 + - - +
55B MET* 3.5 0.5 + - - +
56B LEU* 3.2 10.7 + - - +
409B GLU* 4.4 24.3 + - - +
412B GLU* 6.1 1.4 - - - +
413B ASP* 2.8 40.6 + - - -
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Residues in contact with ALA 53 (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 3.4 26.0 - - - +
17B GLU* 3.5 13.9 - - + +
20B ILE* 3.6 17.7 - - + -
22B THR* 3.6 10.5 - - - +
49B GLN 3.3 13.9 + - - +
50B GLN 3.9 0.9 - - - +
52B ARG* 1.3 74.8 - - - +
54B ALA* 1.3 66.2 + - - +
56B LEU* 3.0 4.9 + - - +
57B ILE* 2.9 29.9 + - + +
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Residues in contact with ALA 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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13B ARG* 3.8 6.3 + - - +
17B GLU* 3.2 31.4 - - - +
50B GLN 3.2 16.6 + - - +
51B GLN* 3.5 9.0 - - + +
53B ALA* 1.3 76.7 - - - +
55B MET* 1.3 63.9 + - + +
57B ILE* 4.0 2.1 - - - +
58B LYS* 3.1 24.7 + - - +
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Residues in contact with MET 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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42B LYS* 4.1 31.2 - - - +
43B VAL* 3.7 26.7 - - + -
46B GLU* 3.6 34.1 - - + +
51B GLN 3.0 14.9 + - - +
52B ARG 3.7 4.9 - - - +
53B ALA 3.1 0.2 + - - -
54B ALA* 1.3 76.4 - - - +
56B LEU* 1.3 54.4 + - - +
58B LYS* 3.2 22.3 - - + +
59B MET* 2.9 34.5 - - + +
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Residues in contact with LEU 56 (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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20B ILE* 4.9 4.7 - - + -
22B THR* 4.4 13.9 - - + -
25B ILE* 4.3 18.8 - - + -
26B MET* 4.1 20.9 - - + -
29B MET* 5.1 1.8 - - - -
35B LEU* 4.0 32.1 - - + -
43B VAL* 3.8 11.9 - - + +
52B ARG 3.2 12.9 + - - +
53B ALA 3.0 4.5 + - - +
55B MET* 1.3 76.8 - - - +
57B ILE* 1.3 65.8 + - - +
59B MET* 3.1 22.8 + - + +
60B ILE* 3.2 28.9 + - + +
71B PHE* 4.4 11.2 - - + -
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Residues in contact with ILE 57 (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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9B LEU* 3.9 21.3 - - + +
13B ARG* 3.9 36.3 - - + +
16B LEU* 3.3 41.5 - - + +
17B GLU* 4.3 3.1 - - + -
20B ILE* 5.0 3.6 - - + -
53B ALA* 2.9 26.8 + - + +
54B ALA 4.0 3.6 - - - +
56B LEU* 1.3 70.9 - - + +
58B LYS* 1.3 68.4 + - - +
59B MET 3.0 2.8 + - - -
60B ILE* 3.1 16.5 + - - +
61B LEU* 3.3 18.2 + - + +
71B PHE* 4.4 18.6 - - + -
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Residues in contact with LYS 58 (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 ARG* 3.2 28.0 - - - +
54B ALA 3.1 7.8 + - - +
55B MET* 3.2 25.6 - - + +
57B ILE* 1.3 79.2 - - - +
59B MET* 1.3 62.5 + - + +
61B LEU* 3.8 11.2 - - - +
62B LYS* 3.4 42.3 - - - +
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Residues in contact with MET 59 (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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39B GLU* 3.2 45.5 - - + +
42B LYS* 3.8 32.1 - - + +
43B VAL* 3.5 27.4 - - + -
55B MET* 2.9 28.5 - - + +
56B LEU* 3.4 14.1 - - + +
57B ILE 3.0 0.6 - - - -
58B LYS* 1.3 79.1 - - + +
60B ILE* 1.3 62.7 + - - +
62B LYS* 3.4 23.0 + - - +
63B LYS* 3.7 14.0 + - - +
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Residues in contact with ILE 60 (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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1B MET* 3.3 14.6 - - + +
9B LEU* 3.9 18.4 - - + -
29B MET* 3.6 33.0 - - + -
56B LEU* 3.2 27.0 + - + +
57B ILE* 3.1 8.3 + - - +
59B MET* 1.3 71.2 - - - +
61B LEU* 1.3 54.4 + - - +
62B LYS 3.0 5.6 - - - -
63B LYS* 2.7 45.9 + - + +
67B SER 4.6 13.0 - - - +
68B TYR* 4.9 1.8 - - - -
71B PHE* 3.6 37.0 - - + -
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Residues in contact with LEU 61 (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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1B MET* 4.3 14.0 + - - +
6B ARG* 3.8 36.7 - - + +
9B LEU* 3.6 30.3 - - + -
10B LEU* 3.9 20.6 - - + -
13B ARG* 3.3 33.2 - - - +
57B ILE* 3.3 21.3 + - + +
58B LYS* 3.8 9.6 - - - +
60B ILE* 1.3 77.8 - - - +
62B LYS* 1.3 63.6 + - + +
63B LYS 3.6 4.9 + - - +
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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