Contacts of the helix formed by residues 27 - 39 (chain A) in PDB entry 5ZJS
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 SER 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TYR* 1.3 73.7 - - - +
28A LYS* 1.3 70.7 + - - +
29A PHE* 3.2 15.6 + - - +
30A GLN* 2.8 30.3 + - - -
31A THR* 3.0 28.6 + - - -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR 4.0 0.2 + - - -
27A SER* 1.3 75.7 + - - +
29A PHE* 1.3 59.9 + - - +
31A THR* 3.5 5.5 + - - -
32A LEU* 2.9 39.5 + - + +
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.2 10.4 + - - +
28A LYS* 1.3 76.6 - - - +
30A GLN* 1.3 74.1 + - + +
32A LEU* 3.1 11.9 + - + +
33A GLU* 2.9 55.7 + - + +
55A ASN 4.7 7.9 - - - -
56A LEU* 4.0 14.1 - - + -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.2 18.8 - - + +
27A SER* 2.8 39.4 + - - +
28A LYS 3.5 0.2 - - - -
29A PHE* 1.3 84.9 - - + +
31A THR* 1.3 57.6 + - - +
33A GLU 3.2 1.0 + - - -
34A LEU* 2.9 37.5 + - + +
56A LEU* 2.6 49.4 + - + +
57A GLN* 3.9 13.3 + - - +
58A LEU* 4.0 14.8 - - + +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 4.2 12.2 + - - +
27A SER 3.0 18.4 + - - -
28A LYS* 3.6 7.1 - - - +
29A PHE 3.2 0.2 - - - -
30A GLN* 1.3 78.5 - - - +
32A LEU* 1.3 60.2 + - + +
34A LEU* 3.3 9.7 + - - +
35A GLU* 2.9 43.0 + - + +
66A TRP* 4.4 11.8 + - + +
9D A 4.7 6.1 + - - -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 2.9 26.8 + - + +
29A PHE* 3.1 10.3 + - + +
31A THR* 1.3 79.1 - - + +
33A GLU* 1.3 61.4 + - + +
35A GLU* 3.5 7.7 + - + +
36A LYS* 2.9 29.9 + - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 2.9 42.5 + - + +
30A GLN 3.6 7.0 - - - +
32A LEU* 1.3 77.6 - - + +
34A LEU* 1.3 59.8 + - - +
36A LYS* 3.2 11.4 + - - +
37A GLU* 2.9 28.4 + - - +
52A LEU* 6.0 1.3 - - - +
56A LEU* 3.6 31.6 - - + +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 4.6 5.6 - - + -
30A GLN 2.9 25.8 + - - +
31A THR* 3.7 2.0 - - - +
33A GLU* 1.3 77.3 - - - +
35A GLU* 1.3 57.4 + - - +
37A GLU* 3.2 6.9 + - - +
38A PHE* 2.9 26.9 + - - +
52A LEU* 3.9 24.2 - - + -
56A LEU* 3.6 18.8 - - + -
58A LEU* 4.5 13.2 - - + -
63A VAL* 4.7 12.1 - - + -
66A TRP* 3.5 57.2 - - + +
67A PHE* 4.0 12.8 - - + -
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 2.9 30.4 + - + +
32A LEU* 3.8 9.2 - - + +
34A LEU* 1.3 75.4 - - - +
36A LYS* 1.3 58.8 + - - +
38A PHE* 2.9 23.7 + - - +
39A LEU* 3.2 11.1 + - - +
66A TRP* 4.1 10.5 - - + -
70A ARG* 2.7 49.7 + - - -
73A LYS* 4.8 7.4 + - - -
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 2.9 19.0 + - - +
33A GLU* 3.2 15.0 + - - +
35A GLU* 1.3 76.6 - - - +
37A GLU* 1.3 61.2 + - - +
39A LEU* 3.7 18.9 - - - +
40A PHE* 4.1 10.4 - - - -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU 2.9 12.2 + - - +
34A LEU* 3.6 10.1 - - - +
36A LYS* 1.3 74.3 - - - +
38A PHE* 1.3 60.6 + - - +
39A LEU 3.1 2.2 - - - -
40A PHE* 3.2 12.1 + - - +
41A ASN* 3.0 48.3 + - - +
44A VAL* 5.0 4.9 - - + -
48A LYS* 3.7 30.6 + - - +
52A LEU* 4.2 28.6 - - + +
67A PHE* 4.3 11.9 - - + -
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 2.9 13.6 + - - +
35A GLU* 2.9 18.8 + - - +
37A GLU* 1.3 75.1 - - - +
39A LEU* 1.3 62.7 + - - +
40A PHE 3.3 0.2 - - - -
41A ASN 3.7 13.1 + - - -
42A ALA* 3.6 38.5 + - + +
66A TRP* 4.3 2.7 - + + -
67A PHE* 3.8 20.6 - + - -
70A ARG* 3.6 59.0 - - + -
71A ARG* 4.2 11.9 - - + -
74A ASN* 4.0 24.0 - - - -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU 3.2 8.8 + - - +
36A LYS* 3.7 15.0 - - - +
37A GLU 3.1 0.4 - - - -
38A PHE* 1.3 80.7 - - - +
40A PHE* 1.3 83.8 + - + +
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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