Contacts of the helix formed by residues 27 - 39 (chain A) in PDB entry 1JQE
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 THR 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 73.4 - - - +
28A GLU* 1.3 54.5 + - - +
29A HIS 3.5 2.0 - - - -
30A GLN* 3.2 31.0 + - - +
31A CYS* 2.7 35.3 + - - +
221A LEU 4.9 0.2 + - - -
222A SER* 3.0 18.7 + - - -
223A THR* 2.9 32.7 + - - +
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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
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19A PHE* 3.9 13.3 - - - -
22A PHE* 3.3 21.2 - - + -
23A LEU* 4.2 4.3 - - + -
26A SER* 3.2 18.6 + - - +
27A THR* 1.3 76.0 - - - +
29A HIS* 1.3 65.3 + - + +
31A CYS* 3.1 6.1 + - - +
32A MET* 2.9 44.8 + - + +
143A GLN* 2.9 41.1 + - - +
222A SER* 3.4 10.8 + - - -
283A ASN* 3.0 22.6 + - - +
285A LEU* 3.7 6.5 - - + +
400A SAH 5.1 0.3 + - - -
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Residues in contact with HIS 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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20A ARG* 4.8 2.4 + - - -
23A LEU* 3.6 42.0 + - + +
26A SER 5.2 0.6 + - - -
27A THR 3.5 0.2 - - - -
28A GLU* 1.3 82.0 - - + +
30A GLN* 1.3 57.9 + - - +
32A MET* 3.4 14.7 + - - +
33A GLN* 2.8 28.9 + - - +
65A GLU* 3.5 36.2 - - + +
66A ILE* 3.8 22.4 - - + +
400A SAH 2.7 31.1 + - - -
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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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27A THR* 3.2 30.6 + - - +
28A GLU 3.2 0.6 - - - -
29A HIS* 1.3 74.3 - - - +
31A CYS* 1.3 60.1 + - - +
33A GLN* 3.2 8.5 + - + +
34A GLU* 2.9 32.7 + - - +
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Residues in contact with CYS 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 THR* 2.7 19.0 + - - +
28A GLU 3.3 4.9 - - - +
30A GLN* 1.3 76.5 - - - +
32A MET* 1.3 63.1 + - - +
34A GLU* 3.0 13.5 + - - +
35A PHE* 3.0 18.2 + - - +
220A LEU* 3.5 48.1 - - - +
221A LEU 3.6 14.8 - - - +
222A SER* 3.9 15.7 - - - -
285A LEU* 4.1 5.8 - - + -
287A PHE* 4.1 10.3 - - - -
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Residues in contact with MET 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 31.7 + - + +
29A HIS* 3.7 15.3 - - + +
31A CYS* 1.3 76.4 - - - +
33A GLN* 1.3 51.6 + - - +
35A PHE* 3.0 4.0 + - - +
36A MET* 2.7 45.2 + - + +
66A ILE* 3.7 34.8 - - + -
142A ILE* 3.6 19.5 - - + -
143A GLN* 3.6 31.9 - - + -
171A ILE* 4.1 6.3 - - + -
285A LEU* 3.9 12.8 - - + -
287A PHE* 4.1 22.4 - - + -
400A SAH 4.1 2.9 - - - +
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Residues in contact with GLN 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 HIS 2.8 18.5 + - - +
30A GLN* 3.4 10.3 - - + +
31A CYS 3.2 0.2 - - - -
32A MET* 1.3 75.3 - - - +
34A GLU* 1.3 58.1 + - - +
36A MET* 3.2 7.6 + - - +
37A ASP* 2.8 67.2 + - - +
66A ILE* 4.9 3.8 - - + +
69A GLN* 2.8 51.3 + - - +
73A LYS* 4.7 0.6 - - - +
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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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30A GLN* 2.9 16.7 + - + +
31A CYS* 3.0 14.2 + - - +
33A GLN* 1.3 76.6 - - - +
35A PHE* 1.3 57.7 + - - +
37A ASP* 3.8 5.3 - - - +
38A LYS* 2.9 65.7 + - + +
220A LEU* 3.7 23.3 - - + +
221A LEU 5.7 0.5 - - - +
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Residues in contact with PHE 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 CYS 3.0 5.9 + - - +
32A MET 3.0 8.6 + - - +
34A GLU* 1.3 78.0 - - - +
36A MET* 1.3 74.1 + - + +
38A LYS* 5.0 0.2 - - - -
39A LYS* 2.7 57.8 + - + +
40A LEU* 3.1 10.4 + - + -
43A ILE* 3.5 32.1 - - + -
169A LEU* 4.3 15.3 - - + -
218A TYR* 4.2 17.7 - + + -
220A LEU* 4.3 13.9 - - + +
287A PHE* 3.3 65.5 - + + -
289A VAL* 4.7 0.4 - - + -
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Residues in contact with MET 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 MET* 2.7 27.5 + - + +
33A GLN* 3.7 15.7 - - - +
35A PHE* 1.3 96.4 - - + +
37A ASP* 1.3 56.9 + - - +
40A LEU* 3.3 36.5 - - + +
41A PRO* 3.1 24.4 - - - +
66A ILE* 4.1 22.4 - - + -
69A GLN* 4.5 16.2 - - + -
70A ILE* 3.9 10.8 - - + -
73A LYS* 3.5 15.3 - - + -
169A LEU* 4.0 17.5 - - + -
171A ILE* 4.2 14.1 - - + -
287A PHE* 4.6 1.6 - - + -
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Residues in contact with ASP 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 GLN* 2.8 47.3 + - - +
34A GLU* 3.8 6.5 - - - +
36A MET* 1.3 78.1 - - - +
38A LYS* 1.3 63.8 + - + +
41A PRO* 3.9 12.3 - - - +
73A LYS* 2.8 28.0 + - - +
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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 46.3 + - + +
35A PHE* 5.0 0.2 - - - -
37A ASP* 1.3 83.9 - - + +
39A LYS* 1.3 81.4 + - + +
40A LEU 3.9 0.2 - - - -
41A PRO* 4.3 4.5 - - - +
42A GLY 5.4 1.0 + - - -
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Residues in contact with LYS 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 PHE* 2.7 51.2 + - + +
38A LYS* 1.3 92.6 + - + +
40A LEU* 1.3 64.1 + - - +
41A PRO* 3.4 3.4 - - - -
42A GLY* 3.4 4.9 + - - -
43A ILE* 3.3 25.3 + - + +
218A TYR* 5.1 20.4 - - + -
220A LEU* 5.6 6.1 - - + -
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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