Contacts of the helix formed by residues 29 - 49 (chain A) in PDB entry 5A19
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 HIS 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.8 18.1 - - + +
26A GLY 3.2 15.9 + - - +
28A GLY* 1.3 76.2 - - - +
30A PRO* 1.4 74.3 - - + +
31A ASP* 3.4 18.7 + - + +
32A LYS* 2.9 8.6 + - - -
33A ILE 2.8 24.1 + - - -
179A ASP* 3.3 24.2 + - - +
180A SER 4.2 2.5 - - - +
181A LYS* 3.9 21.4 - - + -
258A ASP* 4.1 4.7 + - - -
265A LYS* 3.5 17.4 - - - -
403A PPK 2.7 44.3 + - - -
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Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 3.5 4.0 - - - +
29A HIS* 1.4 102.4 - - + +
31A ASP* 1.3 59.2 + - - +
33A ILE* 3.4 15.3 + - + +
34A CYS* 3.2 27.7 + - - -
60A ALA* 4.4 1.4 - - + +
179A ASP* 4.0 9.9 - - - +
254A GLY 3.6 13.0 - - - +
255A PRO* 4.2 11.4 - - + -
258A ASP* 3.1 42.6 - - + +
259A ALA 4.6 0.2 - - - +
260A GLY* 3.7 14.6 - - - +
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A HIS* 3.4 11.0 + - - +
30A PRO* 1.3 76.0 - - - +
32A LYS* 1.3 62.6 + - - +
34A CYS* 3.3 6.6 + - - +
35A ASP* 3.1 25.6 + - - +
259A ALA 4.0 1.0 - - - +
260A GLY* 3.2 7.0 - - - -
261A LEU* 3.0 32.7 + - - +
264A ARG* 3.6 15.9 - - + +
265A LYS* 2.8 26.1 + - + +
403A PPK 2.8 10.9 + - - -
409A MG 2.3 30.3 - - - -
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.6 24.0 - - + +
26A GLY 3.6 21.5 - - - +
27A GLU* 4.1 5.7 - - - +
29A HIS* 2.9 9.6 + - - +
31A ASP* 1.3 76.5 - - - +
33A ILE* 1.3 66.5 + - - +
35A ASP* 2.8 31.4 + - - +
36A GLN* 3.0 24.3 + - - +
265A LYS* 3.9 14.6 - - + -
268A VAL* 4.3 11.9 - - - -
269A ASP* 2.8 29.7 + - - -
375A ALA* 2.7 34.5 + - - +
376A ALA* 4.4 15.9 - - + +
377A TYR 5.1 1.3 - - - +
379A HIS* 5.0 0.4 + - - -
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 3.6 15.0 + - - +
28A GLY* 3.4 21.8 - - - +
29A HIS 2.8 13.5 + - - +
30A PRO* 3.5 11.9 - - + +
31A ASP 3.3 0.2 - - - -
32A LYS* 1.3 74.1 - - - +
34A CYS* 1.3 58.2 + - - +
36A GLN* 3.3 3.6 + - - +
37A ILE* 2.9 50.1 + - + +
60A ALA* 4.8 10.3 - - + -
65A ILE* 5.0 2.5 - - + -
87A VAL* 4.8 8.7 - - + -
90A ILE* 4.1 18.6 - - + +
92A TYR* 3.8 14.8 - - + -
99A PHE* 6.1 1.8 - - + -
255A PRO* 3.7 30.3 - - + -
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Residues in contact with CYS 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 PRO 3.2 13.6 + - - -
31A ASP 3.4 8.5 - - - +
32A LYS 3.2 0.2 - - - -
33A ILE* 1.3 77.7 - - - +
35A ASP* 1.3 59.1 + - - +
38A SER* 2.9 34.0 + - - -
58A THR* 3.5 25.1 + - - +
59A VAL 3.8 0.9 - - - -
60A ALA* 3.5 22.2 - - - -
260A GLY 3.3 28.3 - - - -
261A LEU 3.6 0.4 - - - -
262A THR* 3.2 23.1 + - - +
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP 3.1 15.6 + - - +
32A LYS* 2.8 40.6 + - - +
34A CYS* 1.3 75.0 - - - +
36A GLN* 1.3 58.0 + - - +
38A SER* 3.4 0.8 + - - -
39A ASP* 3.0 24.9 + - - +
262A THR* 3.5 6.4 - - - +
263A GLY* 3.0 31.1 + - - -
265A LYS* 4.3 8.1 + - - +
269A ASP* 4.2 7.7 - - - +
283A SER* 3.4 30.8 + - - +
375A ALA* 3.8 5.4 - - - +
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 3.6 24.7 + - - +
32A LYS 3.0 14.9 + - - +
33A ILE 3.8 3.4 - - - +
35A ASP* 1.3 78.4 - - - +
37A ILE* 1.3 52.4 + - + +
39A ASP 3.4 0.5 + - - -
40A ALA* 2.8 33.1 + - - +
86A ALA* 4.1 3.4 - - - +
89A HIS* 3.5 18.4 - - - -
90A ILE* 3.5 31.0 - - + +
372A GLN* 2.9 44.7 + - + +
375A ALA* 3.6 12.0 - - + +
376A ALA* 4.9 4.2 - - - +
407A PG4 3.7 13.2 - - - +
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Residues in contact with ILE 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 ILE* 2.9 43.4 + - + +
34A CYS* 4.0 3.1 - - - +
36A GLN* 1.3 72.3 - - + +
38A SER* 1.3 60.0 + - - +
40A ALA* 3.2 7.8 + - + +
41A VAL* 2.9 29.8 + - + +
58A THR* 3.8 19.3 - - + +
65A ILE* 3.6 29.4 - - + -
67A LEU* 3.8 18.2 - - + -
82A VAL* 6.1 0.2 - - + -
83A VAL* 3.9 22.4 - - + +
86A ALA* 4.1 18.2 - - + -
87A VAL* 4.1 4.5 - - + -
90A ILE* 5.4 1.6 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS 2.9 11.6 + - - -
35A ASP 3.6 4.9 - - - -
37A ILE* 1.3 75.9 - - - +
39A ASP* 1.3 57.9 + - - +
41A VAL* 3.5 4.0 + - - +
42A LEU 3.1 19.8 + - - -
56A CYS* 3.0 30.2 + - - +
58A THR* 2.8 15.1 + - - -
262A THR* 2.8 27.4 + - - -
283A SER 4.0 3.4 - - - -
284A GLY* 3.6 23.3 - - - -
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP 3.0 10.5 + - - +
36A GLN 3.9 1.6 - - - +
38A SER* 1.3 75.2 - - - +
40A ALA* 1.3 59.2 + - - +
41A VAL 3.2 0.2 - - - -
42A LEU* 3.7 6.8 - - - +
43A ASP* 2.8 34.3 + - - +
283A SER* 2.7 26.6 + - - -
284A GLY 3.0 10.6 + - - -
292A ARG* 2.7 42.7 + - - -
371A TYR* 3.3 21.4 - - + +
372A GLN* 3.7 11.4 - - - +
374A THR* 3.7 0.3 + - - -
375A ALA* 3.5 7.0 - - + +
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Residues in contact with ALA 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 GLN 2.8 22.0 + - - +
37A ILE* 3.2 11.4 + - + +
39A ASP* 1.3 71.3 - - - +
41A VAL* 1.3 57.9 + - - +
43A ASP* 3.6 4.0 + - - +
44A ALA* 3.1 29.5 + - - +
82A VAL* 3.7 19.6 - - + +
86A ALA* 4.2 9.4 - - + -
372A GLN* 3.8 27.9 - - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 2.9 22.7 + - + +
38A SER 3.6 7.9 - - - +
40A ALA* 1.3 74.2 - - - +
42A LEU* 1.3 64.4 + - - +
44A ALA* 3.3 4.7 + - - +
45A HIS* 3.1 33.3 + - + +
54A VAL* 4.7 1.1 - - + -
56A CYS* 3.9 25.6 - - + -
67A LEU* 4.0 25.4 - - + -
71A ILE* 4.5 4.7 - - + -
77A VAL* 5.6 0.2 - - - -
79A TYR* 3.8 28.5 - - + -
82A VAL* 4.3 12.8 - - + -
83A VAL* 4.9 1.3 - - + -
110A LEU* 4.7 0.2 - - + -
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Residues in contact with LEU 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 SER 3.1 14.9 + - - +
39A ASP* 3.3 10.5 + - - +
41A VAL* 1.3 75.0 - - - +
43A ASP* 1.3 64.2 + - - +
45A HIS* 3.3 2.9 + - - +
46A LEU* 3.0 48.6 + - + +
54A VAL* 3.7 36.8 - - + +
284A GLY* 4.6 4.9 - - - -
285A LYS 3.1 27.6 - - - +
286A ASP* 4.1 15.3 - - + +
292A ARG* 3.3 20.4 - - - +
371A TYR* 3.6 19.3 - - + -
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Residues in contact with ASP 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 ASP 2.8 20.3 + - - +
40A ALA* 3.8 5.8 - - - +
42A LEU* 1.3 73.2 - - - +
44A ALA* 1.3 57.0 + - - +
46A LEU* 3.3 1.4 + - - -
47A GLN* 3.0 41.9 + - - +
369A PRO* 3.0 34.5 - - + +
370A ILE 4.0 0.7 - - - -
371A TYR* 2.9 29.5 + - - +
372A GLN* 3.0 31.8 + - - +
373A ARG* 5.7 0.5 + - - -
407A PG4 5.6 0.9 - - - +
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Residues in contact with ALA 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 ALA 3.1 17.8 + - - +
41A VAL 3.3 6.5 + - - +
43A ASP* 1.3 76.4 - - - +
45A HIS* 1.3 62.6 + - - +
47A GLN* 3.6 23.8 + - - +
48A GLN* 3.8 11.4 + - - +
77A VAL* 3.9 30.8 - - + +
82A VAL* 4.0 15.3 - - + -
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Residues in contact with HIS 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 VAL* 3.1 37.3 + - + +
42A LEU 3.7 6.3 - - - +
44A ALA* 1.3 76.3 - - - +
46A LEU* 1.3 52.7 + - - +
48A GLN* 3.1 3.6 + - - -
49A ASP* 2.8 38.2 + - - +
52A ALA* 3.8 14.8 - - + -
54A VAL* 4.3 9.9 - - + -
71A ILE* 3.5 22.0 - - + +
73A SER* 3.0 22.9 + - - -
75A ALA* 3.6 10.6 - - + +
77A VAL* 3.7 18.9 - - + +
79A TYR* 2.8 29.4 + - - -
112A GLN* 3.7 17.7 - - - -
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Residues in contact with LEU 46 (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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42A LEU* 3.0 36.3 + - + +
43A ASP 3.3 4.0 + - - +
45A HIS* 1.3 73.6 - - - +
47A GLN* 1.3 64.6 + - - +
48A GLN 3.3 0.5 + - - -
49A ASP 3.5 8.3 - - - +
50A PRO* 3.5 47.2 - - - +
52A ALA* 4.1 18.2 - - + +
286A ASP* 5.4 3.6 - - + -
366A LEU 4.4 1.8 - - - +
367A LYS* 3.7 25.8 - - - +
368A LYS 4.1 2.7 - - - +
369A PRO* 4.2 11.5 - - + +
371A TYR* 3.7 34.5 - - + -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 3.0 26.7 + - - +
44A ALA* 3.7 15.0 - - - +
46A LEU* 1.3 76.8 - - - +
48A GLN* 1.3 61.9 + - + +
50A PRO* 5.5 0.9 - - - +
369A PRO* 3.9 24.2 + - + +
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.8 11.6 + - - +
45A HIS 3.1 1.8 + - - -
47A GLN* 1.3 83.4 - - + +
49A ASP* 1.3 58.4 + - - +
50A PRO* 3.9 7.5 - - - +
74A ARG* 4.7 1.7 - - - +
75A ALA* 3.3 21.5 - - + +
76A ALA* 3.0 45.1 + - - +
77A VAL* 4.3 4.4 - - - +
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS 2.8 16.7 + - - +
46A LEU* 3.5 6.7 - - - -
48A GLN* 1.3 74.3 - - - +
50A PRO* 1.4 61.2 - - - +
51A ASP* 2.8 23.7 + - - +
52A ALA* 2.9 32.4 + - - +
73A SER* 3.6 18.0 - - - +
74A ARG* 2.9 46.2 + - + +
75A ALA 4.3 4.3 - - - +
115A PRO* 4.9 3.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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