Contacts of the helix formed by residues 36 - 50 (chain J) in PDB entry 5A31
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 36 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J ARG* 4.2 9.8 + - - -
33J SER* 3.9 9.1 + - - +
34J ARG 3.1 6.1 + - - +
35J GLU* 1.3 75.4 - - - +
37J PRO* 1.3 84.6 - - + -
38J GLN* 5.0 3.9 + - - +
39J ASP* 2.9 37.8 + - + +
40J ILE* 2.9 29.2 + - - +
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Residues in contact with PRO 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J GLU 4.9 0.2 - - - +
36J GLU* 1.3 93.6 - - + +
38J GLN* 1.3 66.8 + - + +
40J ILE 3.6 0.2 + - - -
41J TYR* 3.2 19.9 + - - +
65J LEU* 3.6 20.3 - - + +
69J TYR* 2.9 45.8 - - + +
72J CYS* 4.8 1.4 - - - -
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Residues in contact with GLN 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J GLU* 3.3 5.1 - - - +
37J PRO* 1.3 84.3 - - + +
39J ASP* 1.3 65.7 + - - +
41J TYR* 3.3 24.0 - - + +
42J TRP* 3.5 18.0 + - - +
69J TYR* 6.4 0.7 - - + -
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Residues in contact with ASP 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ARG* 3.1 31.5 + - - +
26J ALA 4.9 2.9 - - - +
29J VAL* 3.8 19.0 - - + +
30J ALA* 4.5 15.2 - - - +
33J SER* 2.6 33.2 + - - -
34J ARG 4.8 0.2 - - - +
36J GLU* 2.9 30.0 + - + +
38J GLN* 1.3 77.6 - - - +
40J ILE* 1.3 63.8 + - - +
42J TRP* 3.3 16.5 + - - +
43J LEU* 3.4 10.2 + - - +
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Residues in contact with ILE 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ALA* 4.9 9.0 - - + -
35J GLU* 3.8 16.8 - - + -
36J GLU 2.9 37.7 + - - +
39J ASP* 1.3 73.5 - - - +
41J TYR* 1.3 66.7 + - - +
43J LEU* 3.2 12.3 + - + -
44J ALA* 2.9 20.3 + - - +
59J ALA* 4.3 15.9 - - + +
60J LEU* 4.8 3.4 - - + -
63J ARG* 3.5 44.2 - - + +
65J LEU* 3.7 27.8 - - + -
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Residues in contact with TYR 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J PRO 3.2 14.6 + - - +
38J GLN* 3.3 19.7 - - + +
40J ILE* 1.3 76.7 - - - +
42J TRP* 1.3 94.8 + + - +
44J ALA* 3.2 5.3 + - - +
45J GLN* 2.8 38.5 + - - +
60J LEU* 4.9 1.3 - - + -
65J LEU* 4.5 0.8 - - - +
71J ALA* 4.1 30.6 + - + +
72J CYS* 3.5 25.4 - - - -
74J TYR* 5.5 4.5 - - - -
75J LEU* 3.8 23.8 - - + +
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Residues in contact with TRP 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ARG* 5.4 11.1 - - + +
10J VAL* 5.0 16.8 - - + -
11J ARG* 3.3 63.5 - - + +
14J LEU* 4.5 14.7 - - + +
26J ALA* 4.6 9.2 - - + -
29J VAL* 6.3 3.1 - - + -
38J GLN* 3.5 16.6 + - - +
39J ASP* 3.3 10.5 + - - +
40J ILE 3.2 0.4 - - - -
41J TYR* 1.3 105.2 - + - +
43J LEU* 1.3 60.2 + - - +
45J GLN* 3.4 27.6 - - + +
46J CYS* 2.8 33.1 + - - +
15K ASP* 4.9 9.0 - - - -
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 3.7 27.1 - - + -
26J ALA* 4.1 15.5 - - + +
27J ASP* 4.1 37.0 - - + +
30J ALA* 4.5 11.7 - - + -
39J ASP 3.4 8.9 + - - +
40J ILE* 3.2 13.5 + - + +
42J TRP* 1.3 76.7 - - - +
44J ALA* 1.3 64.7 + - - +
46J CYS* 3.3 1.4 + - - +
47J LEU* 3.0 35.6 + - + +
55J ARG* 5.6 0.9 - - - +
59J ALA* 5.1 6.5 - - + -
63J ARG* 5.0 15.5 - - - +
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Residues in contact with ALA 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ILE* 2.9 13.1 + - - +
41J TYR 3.5 7.9 - - - +
43J LEU* 1.3 79.1 - - - +
45J GLN* 1.3 61.9 + - - +
47J LEU* 3.3 2.9 + - - -
48J TYR* 3.0 20.1 + - - +
56J ALA* 3.5 21.5 - - + +
59J ALA* 4.7 5.2 - - + -
60J LEU* 3.5 40.6 - - + -
75J LEU* 3.8 5.3 - - + +
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Residues in contact with GLN 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J LEU* 4.4 12.3 - - + -
41J TYR* 2.8 34.0 + - - +
42J TRP* 3.2 33.8 + - + +
44J ALA* 1.3 72.0 - - - +
46J CYS* 1.3 63.6 + - - +
48J TYR* 3.2 4.5 + - - +
49J LEU* 3.0 28.9 + - + +
75J LEU* 3.4 24.7 - - - +
15K ASP 4.6 9.1 + - - -
16K GLN 5.7 0.6 + - - -
17K GLN* 2.9 40.8 + - - +
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Residues in contact with CYS 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J VAL* 4.7 1.8 - - - -
14J LEU* 3.6 29.4 - - - +
19J TYR 4.5 1.8 - - - -
22J ALA* 3.7 8.1 - - - -
23J LEU* 3.5 42.0 - - + -
26J ALA* 4.0 5.8 - - + -
42J TRP* 2.8 21.7 + - - +
43J LEU* 3.4 7.4 - - - +
45J GLN* 1.3 70.3 - - - +
47J LEU* 1.3 55.9 + - - +
49J LEU* 3.3 9.8 - - - +
50J THR* 2.2 38.5 + - - -
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Residues in contact with LEU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 3.7 17.0 - - + -
43J LEU* 3.0 33.2 + - + +
44J ALA* 3.7 2.5 - - - +
46J CYS* 1.3 79.0 - - - +
48J TYR* 1.3 63.3 + - - +
50J THR* 2.9 12.0 + - - -
52J GLN* 3.0 40.5 + - + +
55J ARG* 3.6 65.3 - - + +
56J ALA* 3.6 17.9 - - + +
59J ALA* 4.9 3.8 - - + -
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Residues in contact with TYR 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J ALA 3.0 13.6 + - - +
45J GLN* 3.2 7.6 + - - +
47J LEU* 1.3 75.3 - - - +
49J LEU* 1.3 69.6 + - - +
51J ALA* 3.1 11.1 + - - -
53J TYR* 3.2 45.7 + + - -
56J ALA* 4.2 9.0 - - + -
75J LEU* 3.8 19.5 - - + -
78J ARG* 3.4 36.4 + - - +
79J CYS* 4.2 13.5 - - + -
82J ALA* 3.7 18.0 - - + +
17K GLN* 3.4 32.1 - - - -
19K TYR* 6.4 1.3 - + - -
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J LEU* 3.9 21.8 - - + -
19J TYR* 3.1 67.9 - - + +
45J GLN* 3.0 24.5 + - + +
46J CYS* 3.3 13.2 - - - +
48J TYR* 1.3 81.8 - - + +
50J THR* 1.3 58.2 + - - +
51J ALA* 3.2 2.1 + - - +
17K GLN* 3.6 28.3 - - - +
19K TYR* 5.2 4.3 - - - +
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Residues in contact with THR 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J TYR* 4.7 14.5 - - + +
20J GLN* 4.5 11.0 - - + +
23J LEU* 4.0 14.8 - - + +
46J CYS* 2.2 31.3 + - - +
47J LEU* 2.9 9.0 + - - -
49J LEU* 1.3 79.7 - - - +
51J ALA* 1.3 67.9 + - - +
52J GLN* 3.4 11.2 + - + +
265K LYS* 3.8 26.0 - - - +
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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