Contacts of the helix formed by residues 32 - 45 (chain A) in PDB entry 4U7C
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 ASP 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LYS* 1.3 61.9 + - - +
34A GLU* 3.2 8.1 - - + +
35A LYS* 3.0 17.4 + - + +
36A ILE* 2.9 38.8 + - - +
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Residues in contact with LYS 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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32A ASP* 1.3 75.5 - - - +
34A GLU* 1.3 57.1 + - - +
36A ILE* 4.3 10.9 - - - +
37A ASN* 2.9 43.2 + - - +
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Residues in contact with GLU 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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32A ASP* 3.2 6.3 - - + +
33A LYS* 1.3 77.9 - - - +
35A LYS* 1.3 61.2 + - - +
37A ASN* 4.2 2.4 - - - +
38A LYS* 2.9 31.1 + - - +
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Residues in contact with LYS 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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32A ASP* 3.0 21.4 + - + +
34A GLU* 1.3 78.0 - - - +
36A ILE* 1.3 60.9 + - + +
38A LYS* 3.3 8.6 + - + +
39A ILE* 2.9 36.5 + - + +
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Residues in contact with ILE 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 ASP* 2.9 27.6 + - - +
33A LYS* 3.6 9.4 - - - +
35A LYS* 1.3 77.5 - - + +
37A ASN* 1.3 72.2 + - - +
39A ILE* 3.3 7.0 - - - +
40A ILE* 2.9 47.9 + - + +
145A ARG 5.6 2.2 - - - +
146A PHE 4.4 10.1 - - - +
147A GLY* 3.9 25.8 - - - +
160A LEU* 4.3 11.2 - - + -
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Residues in contact with ASN 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 LYS* 2.9 30.2 + - - +
34A GLU* 4.3 2.7 - - - +
36A ILE* 1.3 87.9 - - - +
38A LYS* 1.3 57.1 + - - +
40A ILE* 3.9 8.3 - - - +
41A MET* 2.9 34.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 20.9 + - - +
35A LYS* 3.4 13.9 - - + +
36A ILE 3.1 0.2 - - - -
37A ASN* 1.3 78.4 - - - +
39A ILE* 1.3 57.8 + - - +
41A MET* 3.7 7.5 - - - +
42A GLU* 2.9 30.1 + - - +
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Residues in contact with ILE 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 LYS* 2.9 27.3 + - + +
36A ILE* 3.3 6.5 - - - +
38A LYS* 1.3 71.2 - - - +
40A ILE* 1.3 70.2 + - - +
42A GLU* 4.1 11.9 - - + -
43A ALA* 2.9 31.0 + - + +
159A ARG* 3.9 33.4 - - + +
160A LEU* 3.5 22.2 - - + -
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Residues in contact with ILE 40 (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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36A ILE* 2.9 38.5 + - + +
37A ASN* 3.9 9.0 - - - +
39A ILE* 1.3 79.0 - - - +
41A MET* 1.3 58.6 + - - +
43A ALA* 3.1 2.6 + - - +
44A THR* 2.9 42.1 + - + +
152A MET* 4.8 11.0 - - + -
156A ILE* 4.4 25.9 - - + +
160A LEU* 3.8 22.2 - - + -
4D G 5.8 3.4 - - - +
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Residues in contact with MET 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASN 2.9 20.0 + - - +
38A LYS* 3.7 5.8 - - - +
40A ILE* 1.3 77.6 - - - +
42A GLU* 1.3 63.2 + - - +
44A THR* 3.6 8.5 - - - -
45A LYS* 2.8 47.5 + - + +
50A TYR* 4.6 19.3 - - + +
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Residues in contact with GLU 42 (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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38A LYS 2.9 18.6 + - - +
39A ILE* 3.7 16.6 - - + +
41A MET* 1.3 84.8 - - - +
43A ALA* 1.3 59.2 + - - +
44A THR 3.7 0.2 + - - -
45A LYS* 4.4 6.8 + - - +
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Residues in contact with ALA 43 (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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39A ILE* 2.9 21.4 + - + +
40A ILE* 3.8 3.8 - - - +
42A GLU* 1.3 76.8 - - - +
44A THR* 1.3 58.3 + - - +
45A LYS 5.4 0.2 - - - -
155A PHE* 5.5 7.4 - - + -
156A ILE* 5.8 10.1 - - + -
159A ARG* 3.3 48.2 + - + +
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Residues in contact with THR 44 (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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40A ILE* 2.9 28.3 + - + +
41A MET* 3.5 13.5 - - - +
43A ALA* 1.3 80.0 - - - +
45A LYS* 1.3 68.9 + - - +
46A GLY 3.4 0.3 + - - -
47A SER* 3.2 23.3 + - - -
50A TYR* 3.5 25.9 - - + +
156A ILE* 5.3 5.4 - - - -
4D G 2.3 44.8 + - - -
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Residues in contact with LYS 45 (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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41A MET* 2.8 30.6 + - - +
42A GLU* 4.4 6.1 + - - +
43A ALA 3.8 0.9 - - - -
44A THR* 1.3 79.7 - - - +
46A GLY* 1.3 62.4 + - - +
47A SER 3.4 0.5 + - - -
50A TYR* 3.9 16.2 - - + -
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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