Contacts of the helix formed by residues 43 - 54 (chain B) in PDB entry 1Z5S
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 HIS 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR 4.3 9.3 + - - -
42B THR* 1.3 74.3 + - - +
44B LEU* 1.3 66.2 + - - +
45B LYS* 2.8 13.4 + - + +
46B LYS* 2.9 31.4 + - + +
47B LEU 4.1 0.2 + - - -
73B ASP 4.4 6.7 - - - +
74B ASN* 4.3 23.3 + - + +
75B HIS 3.3 2.7 - - - +
76B THR* 3.0 12.8 - - - -
2630D LEU* 4.0 18.9 - - + +
2632D VAL* 5.5 0.2 - - - +
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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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24B LEU* 4.6 4.5 - - + -
38B VAL* 5.6 6.1 - - + -
42B THR* 3.4 3.0 + - - +
43B HIS* 1.3 70.6 - - - +
45B LYS* 1.3 63.4 + - - +
46B LYS 3.1 0.2 - - - -
47B LEU* 2.8 44.6 + - + +
48B LYS* 2.9 12.3 + - - +
71B ILE* 3.7 34.8 - - + -
72B ALA 4.5 1.8 - - - +
75B HIS* 2.6 29.9 + - + +
76B THR* 3.9 7.2 - - - +
77B PRO* 4.3 7.9 - - + -
80B LEU* 3.7 11.7 - - + -
82B MET* 3.5 33.2 - - + -
88B ILE* 5.1 1.8 - - + -
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Residues in contact with LYS 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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43B HIS* 2.8 8.2 + - + +
44B LEU* 1.3 78.3 - - - +
46B LYS* 1.3 58.9 + - + +
48B LYS* 3.0 9.9 + - + +
49B GLU* 2.7 67.4 + - + +
59B MET* 4.9 10.5 - - - -
73B ASP* 3.0 55.5 + - - +
74B ASN* 5.5 1.8 - - - +
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Residues in contact with LYS 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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42B THR* 4.8 0.4 - - - -
43B HIS* 2.9 26.8 + - - +
45B LYS* 1.3 83.0 - - - +
47B LEU* 1.3 60.7 + - - +
49B GLU* 3.6 21.6 + - - +
50B SER* 3.1 24.4 + - - -
2629D SER* 5.9 1.7 + - - -
2630D LEU* 3.4 44.9 - - + +
2632D VAL* 3.9 22.7 - - + +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.4 33.9 - - + -
26B VAL* 3.8 11.0 - - + -
36B PHE* 3.7 37.7 - - + -
38B VAL* 4.3 8.1 - - + -
43B HIS 4.1 0.4 + - - -
44B LEU* 2.8 33.0 + - + +
46B LYS* 1.3 71.2 - - - +
48B LYS* 1.3 74.6 + - - +
50B SER* 3.2 5.9 + - - -
51B TYR* 3.1 15.5 + - + +
64B PHE* 5.0 9.6 - - + -
88B ILE* 4.1 14.4 - - + -
2632D VAL* 4.1 14.6 - - + +
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU 2.9 11.7 + - - +
45B LYS* 3.1 9.9 - - + +
47B LEU* 1.3 83.3 - - - +
49B GLU* 1.3 66.7 + - - +
51B TYR* 3.0 17.7 + - - +
52B CYS* 3.3 7.3 + - - -
59B MET* 3.3 46.3 + - - +
60B ASN* 5.5 0.8 - - - +
62B LEU 6.0 1.1 - - - -
63B ARG* 6.2 0.2 - - - +
64B PHE* 3.4 38.8 - - + -
73B ASP* 3.4 29.8 + - - +
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Residues in contact with GLU 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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45B LYS* 2.7 51.1 + - + +
46B LYS* 3.6 30.6 + - - +
48B LYS* 1.3 71.4 - - - +
50B SER* 1.3 66.9 + - - +
52B CYS* 3.2 13.4 + - - +
53B GLN* 3.2 15.6 + - + +
59B MET* 3.2 37.4 - - + +
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Residues in contact with SER 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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36B PHE* 3.7 11.6 - - - -
46B LYS 3.1 11.0 + - - -
47B LEU* 3.2 11.4 + - - -
49B GLU* 1.3 78.4 - - - +
51B TYR* 1.3 67.1 + - - +
53B GLN* 3.0 18.1 + - - +
54B ARG* 2.8 23.3 + - - +
2632D VAL* 5.0 9.1 + - - +
2634D ILE* 3.7 25.3 - - - +
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Residues in contact with TYR 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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26B VAL* 3.5 31.6 - - + -
28B GLY* 3.9 13.3 - - - -
32B SER* 3.6 27.1 + - - -
34B ILE* 3.4 31.2 - - + +
36B PHE* 4.0 16.9 - + + -
47B LEU* 3.1 6.3 + - + +
48B LYS 3.0 12.2 + - - +
50B SER* 1.3 82.0 + - - +
52B CYS* 1.3 62.9 + - - +
54B ARG* 3.0 4.7 + - - +
55B GLN* 3.0 36.5 + - + +
62B LEU* 3.6 32.8 - - + -
64B PHE* 3.8 12.8 - + + -
90B VAL* 4.1 11.4 - - + +
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Residues in contact with CYS 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 LYS 3.5 17.3 - - - -
49B GLU* 3.2 7.8 + - - +
51B TYR* 1.3 81.7 - - - +
53B GLN* 1.3 51.3 + - - +
55B GLN* 3.2 4.8 + - - -
56B GLY 2.6 30.8 + - - -
57B VAL* 2.8 35.0 + - - +
58B PRO 4.3 2.2 - - - -
59B MET* 3.9 33.0 - - + +
62B LEU* 4.3 9.2 - - - -
64B PHE* 4.2 16.2 - - - -
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Residues in contact with GLN 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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49B GLU 3.2 10.9 + - - +
50B SER* 3.0 33.3 + - - +
52B CYS* 1.3 75.3 - - - +
54B ARG* 1.3 78.6 + - - +
55B GLN 2.9 9.1 + - - -
56B GLY* 3.4 9.7 + - - +
57B VAL 5.1 0.2 - - - +
2634D ILE* 4.8 2.8 - - - +
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Residues in contact with ARG 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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34B ILE* 5.1 10.5 - - + +
50B SER 2.8 18.8 + - - +
51B TYR* 3.3 3.6 - - - +
53B GLN* 1.3 88.4 - - - +
55B GLN* 1.3 67.8 + - - +
2634D ILE* 3.3 50.3 + - + +
2637D GLU* 3.1 32.3 + - - +
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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