Contacts of the helix formed by residues 40 - 52 (chain B) in PDB entry 1Z7K
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 ASN 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN* 3.6 5.2 - - - +
24B ASN* 3.3 28.4 + - - +
26B ALA 2.9 22.5 - - - +
28B ASN* 3.3 22.0 - - + +
30B VAL* 4.2 5.4 - - - -
38B TYR* 3.2 7.6 + - - +
39B ASP* 1.3 79.0 - - - +
41B GLU* 1.3 64.3 + - - +
42B CYS* 2.9 14.8 - - - +
43B VAL* 2.8 50.8 + - - +
44B LEU 3.2 8.8 + - - -
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Residues in contact with GLU 41 (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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4B MET* 3.5 34.8 - - - +
5B ASP 4.7 4.8 + - - +
8B ARG* 4.8 5.4 - - - -
9B TYR* 2.7 29.2 + - - +
28B ASN* 4.2 0.8 + - - +
30B VAL* 4.0 21.7 - - + +
40B ASN* 1.3 76.2 - - - +
42B CYS* 1.3 62.0 + - - +
44B LEU* 3.2 4.4 + - - +
45B CYS* 2.9 25.8 + - - -
57B LYS* 2.7 37.1 + - + +
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Residues in contact with CYS 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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9B TYR* 3.6 44.8 + - + -
21B ILE* 3.7 6.5 - - - +
22B LEU 3.6 8.1 - - - -
23B CYS* 1.9 61.9 - - + -
24B ASN* 4.4 5.2 - - - +
40B ASN* 2.9 9.8 - - - +
41B GLU* 1.3 78.5 - - - +
43B VAL* 1.3 56.5 + - - +
45B CYS* 3.1 5.5 + - - +
46B ALA 2.9 23.9 + - - -
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Residues in contact with VAL 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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192A GLN* 3.9 32.3 - - + +
23B CYS* 4.3 9.4 - - + -
38B TYR* 4.7 9.2 - - + -
39B ASP* 4.2 21.8 - - + +
40B ASN* 2.8 32.3 - - - +
42B CYS* 1.3 74.7 - - - +
44B LEU* 1.3 61.1 + - - +
46B ALA* 3.7 5.7 - - + +
47B HIS* 2.9 29.2 + - + +
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Residues in contact with LEU 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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4B MET* 3.7 26.0 - - + -
30B VAL* 4.3 16.4 - - + -
32B GLY* 4.9 1.3 - - - -
38B TYR* 3.9 36.5 - - + +
40B ASN 3.2 9.4 + - - +
41B GLU* 3.2 10.2 + - - +
43B VAL* 1.3 76.7 - - - +
45B CYS* 1.3 62.5 + - - +
47B HIS* 3.1 3.7 + - - +
48B ASN* 3.0 40.4 + - - +
55B VAL* 3.8 20.2 - - + +
56B GLY 4.0 19.7 - - - +
57B LYS* 4.3 3.6 - - + +
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Residues in contact with CYS 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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4B MET* 3.9 11.9 - - - -
5B ASP 4.8 0.4 - - - -
6B CYS* 2.0 60.3 - - + +
9B TYR* 4.1 14.8 - - + -
21B ILE* 4.8 9.8 - - + +
41B GLU* 2.9 18.8 + - - -
42B CYS* 3.2 10.5 - - - +
44B LEU* 1.3 77.3 - - - +
46B ALA* 1.3 61.2 + - - +
48B ASN* 3.3 5.3 + - - +
49B LEU* 3.1 23.3 + - - +
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Residues in contact with ALA 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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217A TYR* 5.9 1.1 - - + -
21B ILE* 4.3 26.6 - - + +
23B CYS* 4.5 6.3 - - - -
42B CYS 2.9 18.1 + - - +
43B VAL* 3.7 8.5 - - + +
45B CYS* 1.3 69.7 - - - +
47B HIS* 1.3 60.8 + - - +
49B LEU* 3.3 4.4 + - - +
50B GLU* 2.8 44.7 + - - +
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Residues in contact with HIS 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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34B ASP* 4.8 1.1 - - - -
38B TYR* 3.2 40.4 + + + -
43B VAL* 2.9 19.0 + - + +
44B LEU* 3.1 5.8 + - - +
46B ALA* 1.3 76.3 - - - +
48B ASN* 1.3 60.3 + - - +
50B GLU* 3.2 4.4 + - - -
51B GLN* 2.8 62.5 + - + +
53B THR* 3.6 23.7 + - + -
55B VAL* 4.5 6.2 - - + +
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Residues in contact with ASN 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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4B MET* 4.2 10.1 - - - +
6B CYS* 5.6 1.6 - - - -
44B LEU* 3.0 21.1 + - - +
45B CYS* 3.7 8.2 - - - +
46B ALA 3.3 0.2 - - - -
47B HIS* 1.3 77.9 + - - +
49B LEU* 1.3 57.9 + - - +
52B GLY* 2.8 31.5 + - - -
53B THR* 2.7 37.8 + - - +
54B SER* 4.1 2.4 - - - +
55B VAL* 2.8 49.2 + - - +
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Residues in contact with LEU 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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19B VAL* 3.6 37.0 - - + +
21B ILE* 3.4 25.6 - - + -
45B CYS 3.1 13.8 + - - +
46B ALA 3.7 2.9 - - - +
48B ASN* 1.3 82.0 - - - +
50B GLU* 1.3 63.9 + - - +
52B GLY* 3.8 5.4 + - - -
1D NAG 4.0 23.6 - - + -
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Residues in contact with GLU 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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217A TYR* 2.6 36.1 + - - +
19B VAL 3.9 16.6 - - - +
20B MET* 5.2 1.1 - - - +
21B ILE* 5.6 1.9 + - - +
46B ALA* 2.8 27.3 + - - +
47B HIS* 3.8 4.3 - - - +
49B LEU* 1.3 81.7 - - - +
51B GLN* 1.3 76.5 + - - +
52B GLY 3.5 0.2 - - - -
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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
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47B HIS* 2.8 42.5 + - + +
50B GLU* 1.3 91.6 + - - +
52B GLY* 1.3 61.0 + - - +
53B THR* 3.5 22.0 + - + +
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Residues in contact with GLY 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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48B ASN 2.8 12.7 + - - -
49B LEU 3.8 4.7 + - - -
50B GLU 3.5 2.2 - - - -
51B GLN* 1.3 78.7 - - - +
53B THR* 1.4 61.0 + - - +
54B SER* 5.3 0.3 - - - -
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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