Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 5JQE
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 GLY 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.9 0.8 - - - +
27A LYS* 1.3 74.7 - - - +
29A TYR* 1.3 57.3 + - - -
31A GLY* 3.5 1.2 + - - -
32A LEU* 3.1 21.5 + - - +
305A VAL* 3.2 24.5 - - - +
308A ASP* 3.3 33.0 - - - -
309A LYS* 3.8 12.3 + - - +
311A LEU* 5.7 1.4 - - - +
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Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.7 28.3 - - + -
24A ASN 4.1 2.0 - - - +
25A GLY* 3.4 40.8 - - - -
27A LYS 3.1 7.6 + - - +
28A GLY* 1.3 76.0 - - - +
30A ASN* 1.3 98.5 + - + +
32A LEU* 3.2 10.0 + - - +
33A ALA* 2.7 23.9 + - - +
49A VAL* 3.7 13.0 - - + +
50A GLU 5.6 0.4 - - - -
51A HIS* 3.8 38.0 + + + +
308A ASP* 3.7 0.6 + - - -
309A LYS* 5.3 3.1 - - - -
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 1.3 98.7 + - + +
31A GLY* 1.3 63.0 + - - +
32A LEU 3.3 0.2 - - - -
33A ALA* 3.5 14.4 - - + +
34A GLU* 3.3 19.1 + - - +
308A ASP* 2.6 31.9 - - - +
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.9 2.7 - - - -
29A TYR 3.3 0.2 - - - -
30A ASN* 1.3 74.4 - - - +
32A LEU* 1.3 59.1 + - - +
34A GLU* 3.3 14.7 + - - +
35A VAL* 3.4 13.0 + - - +
304A ALA* 3.8 26.6 - - - +
305A VAL* 4.3 6.1 - - - -
308A ASP* 2.7 24.6 + - - -
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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
----------------------------------------------------------
21A ILE* 3.8 20.2 - - + -
23A ILE* 4.0 20.6 - - + -
28A GLY 3.1 14.7 + - - +
29A TYR* 3.2 7.6 + - - +
31A GLY* 1.3 73.3 - - - +
33A ALA* 1.3 60.6 + - - +
34A GLU 3.0 4.9 - - - -
35A VAL* 3.1 25.5 - - + +
36A GLY* 3.1 7.4 + - - -
49A VAL* 3.8 27.8 - - + +
73A PHE* 4.0 13.7 - - + -
291A PHE* 4.2 14.6 - - + -
296A LEU* 3.6 30.7 - - + -
305A VAL* 4.0 10.2 - - + +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR 2.7 18.9 + - - +
30A ASN* 3.6 17.5 - - + +
31A GLY 3.3 0.6 - - - -
32A LEU* 1.3 73.7 - - - +
34A GLU* 1.3 56.5 + - - +
36A GLY* 3.6 3.6 + - - +
37A LYS* 3.2 48.7 + - - +
47A VAL* 5.2 2.3 - - - +
49A VAL* 3.6 22.6 - - + +
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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 ASN 3.3 11.9 + - - +
31A GLY* 3.3 11.6 + - - +
32A LEU 3.0 1.0 - - - -
33A ALA* 1.3 76.7 - - - +
35A VAL* 1.3 64.9 + - - +
36A GLY 3.1 1.1 - - - -
37A LYS* 3.3 10.5 + - + +
38A LYS* 3.0 28.0 + - - +
304A ALA* 4.2 14.0 - - + +
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Residues in contact with VAL 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 GLY 3.4 5.7 + - - +
32A LEU* 3.1 43.3 - - + +
34A GLU* 1.3 81.2 + - - +
36A GLY* 1.3 56.0 + - - +
38A LYS* 3.6 12.1 + - + +
39A PHE* 3.0 26.3 + - - +
291A PHE* 4.2 6.7 - - + -
295A TYR* 3.8 38.4 - - + +
296A LEU* 4.2 10.5 - - + +
301A GLY* 4.1 17.5 - - - +
304A ALA* 4.8 3.4 - - + -
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Residues in contact with GLY 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 3.1 11.9 + - - -
33A ALA 3.8 5.4 - - - -
34A GLU 3.1 1.2 - - - -
35A VAL* 1.3 78.4 - - - +
37A LYS* 1.3 57.3 + - - +
39A PHE* 3.8 4.3 - - - +
40A GLU* 3.5 20.3 + - - +
47A VAL* 3.4 39.0 + - - +
291A PHE* 4.0 10.1 - - - -
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 6.2 0.2 - - - +
33A ALA* 3.2 38.4 + - - +
34A GLU* 3.3 10.8 + - + +
35A VAL 3.3 0.6 - - - -
36A GLY* 1.3 77.9 - - - +
38A LYS* 1.3 64.3 + - - +
39A PHE 3.1 0.4 - - - -
40A GLU* 3.6 33.2 - - - +
41A LYS* 3.6 11.8 + - - +
46A LYS* 6.4 0.2 - - + -
47A VAL 5.0 11.0 - - - +
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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* 3.0 18.5 + - - +
35A VAL* 3.6 14.8 - - + +
37A LYS* 1.3 75.0 - - - +
39A PHE* 1.3 61.4 + - - +
41A LYS* 3.5 14.8 - - + +
42A ASP* 3.5 30.6 + - - +
295A TYR* 3.9 31.9 - - + -
300A GLU* 6.4 1.8 - - - -
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Residues in contact with PHE 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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19A LEU* 4.2 9.2 - - + -
35A VAL 3.0 18.4 + - - +
36A GLY 3.8 4.7 - - - +
37A LYS 3.1 0.4 - - - -
38A LYS* 1.3 80.2 - - - +
40A GLU* 1.3 61.5 + - - +
42A ASP* 3.3 7.8 + - - +
43A THR* 2.8 52.1 + - + -
45A ILE 3.9 13.2 - - - -
47A VAL* 4.1 8.5 - - + -
287A LEU* 3.9 34.5 - - + -
290A GLU* 4.7 6.3 - - + -
291A PHE* 3.8 37.9 - + + -
295A TYR* 3.5 41.3 - + + -
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 3.5 4.7 + - - +
37A LYS* 3.6 33.0 - - - +
39A PHE* 1.3 75.0 - - - +
41A LYS* 1.3 63.2 + - + +
42A ASP 3.1 5.8 - - - -
43A THR* 2.9 1.4 + - - -
44A GLY* 2.4 42.4 + - - +
45A ILE 3.4 25.4 - - - +
46A LYS* 3.1 35.6 - - - +
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Residues in contact with LYS 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 LYS 3.6 10.7 + - - +
38A LYS* 3.5 16.6 - - + +
40A GLU* 1.3 82.4 - - + +
42A ASP* 1.3 71.3 + - - +
43A THR 3.4 0.2 - - - -
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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