Contacts of the helix formed by residues 41 - 52 (chain B) in PDB entry 4ZM0
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 LYS 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.1 13.7 - - - -
27A GLU* 3.4 44.4 + - + +
35A PRO* 3.0 31.1 + - + +
36A ALA* 3.7 0.8 - - - +
37A VAL* 3.7 27.6 - - + -
39B VAL 3.3 4.2 + - - -
40B SER* 1.4 68.2 - - - +
42B ALA* 1.3 55.6 + - - +
44B PHE* 4.1 0.2 - - - +
45B GLU* 2.8 60.9 + - + +
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Residues in contact with ALA 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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34A GLU* 6.2 4.0 - - + +
35A PRO* 4.5 3.0 + - + +
40B SER* 3.0 7.4 - - - +
41B LYS* 1.3 78.5 - - - +
43B THR* 1.3 58.2 + - - +
45B GLU* 3.6 5.2 - - - +
46B ALA* 2.9 30.9 + - - +
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Residues in contact with THR 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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23B GLY* 6.0 1.7 - - - -
25B GLU* 4.9 1.8 - - - +
39B VAL* 4.2 10.8 - - + -
40B SER* 2.8 29.4 + - - -
42B ALA* 1.3 72.7 - - - +
44B PHE* 1.3 57.9 + - - +
46B ALA* 2.8 11.6 + - - +
47B TYR* 2.8 61.6 + - + +
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Residues in contact with PHE 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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1A MET* 5.5 0.4 - - + -
25A GLU* 3.2 37.9 - - + -
37A VAL* 3.6 28.5 - - + -
39A VAL* 4.1 17.5 - - + -
44A PHE* 4.0 25.8 - + - -
47A TYR* 3.5 39.3 - + + -
39B VAL* 3.6 19.5 - - + -
40B SER 3.1 5.4 + - - +
41B LYS 4.1 0.2 - - - +
43B THR* 1.3 77.2 - - - +
45B GLU* 1.3 62.0 + - - +
47B TYR* 3.1 12.7 + + + -
48B LYS* 3.0 42.0 + - + +
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Residues in contact with GLU 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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1A MET* 3.4 24.7 - - - +
41B LYS* 2.8 44.9 + - + +
42B ALA* 3.6 5.4 - - - +
44B PHE* 1.3 75.4 - - - +
46B ALA* 1.3 57.7 + - - +
48B LYS* 3.4 33.3 + - - +
49B LYS* 3.2 25.8 + - - +
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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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42B ALA 2.9 13.0 + - - +
43B THR* 2.8 12.4 + - - +
45B GLU* 1.3 76.3 - - - +
47B TYR* 1.4 64.9 + - + +
49B LYS* 3.9 9.4 - - + +
50B ALA* 3.3 19.6 + - - +
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Residues in contact with TYR 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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44A PHE* 3.6 25.4 - + - -
47A TYR* 3.9 14.4 - - + +
48A LYS* 3.4 42.5 - - + -
50A ALA* 3.4 19.3 - - + +
51A ALA* 5.6 5.8 - - + -
25B GLU* 3.1 17.9 + - - -
43B THR* 2.8 33.0 + - + +
44B PHE* 3.1 24.0 + + + +
46B ALA* 1.4 74.5 - - - +
48B LYS* 1.3 67.2 + - - +
50B ALA* 2.9 15.0 + - + -
51B ALA 3.0 10.9 + - - -
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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
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1A MET* 3.7 10.7 - - - +
25A GLU* 2.7 33.2 + - - -
47A TYR* 3.7 40.5 - - + +
44B PHE* 3.0 38.9 + - + +
45B GLU* 3.4 30.5 + - - +
47B TYR* 1.3 75.1 - - - +
49B LYS* 1.3 60.8 + - - +
51B ALA* 3.6 3.3 + - - +
52B LEU* 3.3 22.2 + - - +
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Residues in contact with LYS 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 GLU 3.2 17.9 + - - +
46B ALA* 4.0 9.0 - - + +
47B TYR 3.0 1.0 + - - -
48B LYS* 1.3 77.0 - - - +
50B ALA* 1.3 61.8 + - - +
52B LEU* 3.2 25.2 + - + +
53B ASP* 3.9 11.0 + - - +
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Residues in contact with ALA 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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50A ALA* 3.9 23.9 - - + +
53A ASP* 4.4 23.7 - - + +
46B ALA 3.3 14.3 + - - +
47B TYR* 2.9 8.4 + - + +
49B LYS* 1.3 75.1 - - - +
51B ALA* 1.3 60.9 + - - +
53B ASP* 3.5 18.6 + - - +
54B ALA* 5.4 0.7 - - - +
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Residues in contact with ALA 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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46A ALA 5.8 0.7 - - - +
47A TYR* 4.2 23.8 - - + +
49A LYS 5.3 1.1 - - - -
50A ALA* 3.5 20.5 - - + +
47B TYR 3.0 14.8 + - - +
48B LYS 3.8 5.2 - - - +
50B ALA* 1.3 74.4 - - - +
52B LEU* 1.3 56.7 + - - +
53B ASP 3.1 7.7 + - - -
54B ALA* 3.3 22.4 + - - +
56B PHE* 5.1 4.2 - - - -
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Residues in contact with LEU 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 3.3 10.9 + - - +
49B LYS* 3.2 18.2 + - + +
51B ALA* 1.3 77.1 - - - +
53B ASP* 1.3 61.4 + - - +
54B ALA 3.5 3.2 + - - -
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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