Contacts of the helix formed by residues 27 - 44 (chain A) in PDB entry 5MQF
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 GLU 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 SER* 1.3 72.8 - - - +
28A GLU* 1.3 60.7 + - - +
30A LEU* 3.0 9.0 + - - +
31A GLN* 2.9 29.8 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 3.4 0.2 - - - -
27A GLU* 1.3 78.6 - - - +
29A LYS* 1.3 58.2 + - - +
31A GLN* 3.4 5.0 + - - +
32A GLU* 2.9 32.2 + - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 3.4 24.2 + - - +
27A GLU 3.2 0.8 - - - -
28A GLU* 1.3 78.5 - - - +
30A LEU* 1.3 51.5 + - - +
32A GLU* 4.6 3.1 - - - -
33A LYS* 2.6 42.6 + - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 2.8 17.7 + - - +
27A GLU* 3.0 10.0 + - - +
29A LYS* 1.3 77.4 - - - +
31A GLN* 1.3 59.3 + - - +
33A LYS* 4.4 2.2 - - - +
34A ALA* 2.8 29.3 + - - +
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Residues in contact with GLN 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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27A GLU 2.9 14.7 + - - +
28A GLU* 4.0 5.6 - - - +
30A LEU* 1.3 75.7 - - - +
32A GLU* 1.3 60.4 + - - +
34A ALA* 3.2 5.8 + - - +
35A ARG* 2.9 29.1 + - - +
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Residues in contact with GLU 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 GLU 2.9 18.0 + - - +
29A LYS* 4.6 2.7 - - - +
31A GLN* 1.3 76.4 - - - +
33A LYS* 1.3 59.2 + - - +
35A ARG* 3.2 6.8 + - - +
36A LYS* 2.9 29.9 + - - +
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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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29A LYS* 2.6 25.4 + - + +
30A LEU* 4.4 2.7 - - - +
32A GLU* 1.3 76.7 - - - +
34A ALA* 1.3 57.3 + - - +
35A ARG 3.4 0.2 - - - -
36A LYS* 4.2 5.8 - - - +
37A TRP* 2.9 30.3 + - - +
213F ILE* 5.3 7.2 - - - +
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Residues in contact with ALA 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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30A LEU 2.8 23.7 + - - +
31A GLN* 3.5 7.6 - - - +
32A GLU 3.2 0.4 - - - -
33A LYS* 1.3 76.1 - - - +
35A ARG* 1.3 59.8 + - - +
37A TRP* 3.8 4.6 - - - +
38A GLN* 2.9 28.6 + - - +
194F TYR* 5.3 12.6 - - + -
213F ILE* 5.9 2.5 - - - -
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Residues in contact with ARG 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 GLN 2.9 16.0 + - - +
32A GLU* 3.8 5.8 - - - +
34A ALA* 1.3 75.6 - - - +
36A LYS* 1.3 60.8 + - - +
38A GLN* 3.2 6.6 + - - +
39A GLN* 2.9 28.9 + - - +
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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 GLU 2.9 17.2 + - - +
33A LYS* 4.2 6.3 - - - +
35A ARG* 1.3 75.7 - - - +
37A TRP* 1.3 57.5 + - - +
39A GLN* 3.6 6.4 + - - +
40A LEU* 2.9 27.2 + - - +
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Residues in contact with TRP 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 20.3 + - - +
34A ALA* 3.9 6.1 - - - +
35A ARG 3.2 0.2 - - - -
36A LYS* 1.3 75.6 - - - +
38A GLN* 1.3 58.9 + - - +
40A LEU* 3.4 7.1 - - - +
41A GLN* 2.9 31.9 + - - +
195F GLN* 6.4 1.1 - - + -
213F ILE* 4.1 24.5 - - + -
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Residues in contact with GLN 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 ALA 2.9 18.5 + - - +
35A ARG* 3.2 7.8 + - - +
37A TRP* 1.3 77.0 - - - +
39A GLN* 1.3 50.6 + - - +
41A GLN* 4.7 2.0 - - - +
42A ALA* 2.6 41.0 + - - +
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Residues in contact with GLN 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 ARG 2.9 16.5 + - - +
36A LYS* 3.7 6.7 - - - +
38A GLN* 1.3 75.5 - - - +
40A LEU* 1.3 58.5 + - - +
42A ALA* 4.1 4.9 - - - -
43A LYS* 2.9 28.9 + - - +
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Residues in contact with LEU 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 LYS 2.9 19.4 + - - +
37A TRP* 3.1 10.3 + - - +
39A GLN* 1.3 75.1 - - - +
41A GLN* 1.3 60.6 + - - +
43A LYS* 3.0 7.1 + - - +
44A ARG* 2.9 27.3 + - - +
286F LYS* 5.7 9.4 - - + -
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Residues in contact with GLN 41 (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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37A TRP 2.9 16.5 + - - +
38A GLN* 4.7 1.6 - - - +
40A LEU* 1.3 74.5 - - - +
42A ALA* 1.3 57.4 + - - +
44A ARG* 3.3 9.4 + - - +
45A TYR* 2.9 27.7 + - - +
172F ASP* 4.8 18.4 - - + -
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Residues in contact with ALA 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 GLN 2.6 25.8 + - - +
39A GLN* 4.1 4.5 - - - -
41A GLN* 1.3 75.6 - - - +
43A LYS* 1.3 53.0 + - - +
45A TYR* 3.2 7.6 + - - +
46A ALA* 2.7 34.4 + - - +
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Residues in contact with LYS 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 GLN 2.9 22.1 + - - +
40A LEU* 3.0 7.4 + - - +
42A ALA* 1.3 76.4 - - - +
44A ARG* 1.3 60.5 + - - +
46A ALA* 3.2 19.8 + - - +
47A GLU* 4.3 2.3 + - - +
121E ASN* 5.4 6.5 - - - +
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Residues in contact with ARG 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 LEU 2.9 11.2 + - - +
41A GLN* 3.6 11.7 - - - +
43A LYS* 1.3 77.6 - - - +
45A TYR* 1.3 60.0 + - - +
46A ALA 3.6 0.3 + - - -
47A GLU* 4.0 13.5 + - - +
121E ASN* 5.9 5.4 - - - -
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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