Contacts of the helix formed by residues 41 - 63 (chain T) in PDB entry 5GAG
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 LYS 41 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009A A 3.2 26.2 + - - +
2010A G 3.3 24.9 + - - +
16T LYS 5.2 3.8 + - - +
19T LEU* 4.3 17.0 - - - +
20T VAL* 3.6 19.1 - - + -
39T THR* 3.5 12.1 + - + +
40T ASN* 1.3 85.0 - - - +
42T LYS* 1.3 60.4 + - - +
43T ALA* 4.0 2.2 - - + +
44T ALA* 3.3 32.4 - - + +
45T VAL* 4.0 7.3 + - - +
22b LEU* 3.7 34.4 - - + +
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Residues in contact with LYS 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327A A 3.8 24.0 + - - -
2010A G 3.0 37.7 + - - +
2011A U 3.0 33.0 + - - +
11T ARG* 3.4 28.9 + - - +
12T SER* 4.3 7.4 - - - +
41T LYS* 1.3 69.4 - - - +
43T ALA* 1.3 65.4 + - - +
44T ALA 3.0 1.8 - - - -
45T VAL* 2.8 26.5 + - - +
46T LEU* 3.1 20.7 + - + +
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Residues in contact with ALA 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2010A G 4.7 1.2 + - - +
12T SER* 4.6 3.8 - - - +
16T LYS* 4.1 6.3 - - + +
17T VAL* 3.7 38.4 - - + -
20T VAL* 4.0 16.2 - - + -
41T LYS* 4.0 2.2 - - + +
42T LYS* 1.3 82.9 - - - +
44T ALA* 1.3 62.9 + - - +
46T LEU* 4.3 10.5 - - - -
47T VAL* 2.9 32.1 + - - +
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Residues in contact with ALA 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T VAL* 4.0 13.1 - - - +
36T LEU* 3.7 15.6 - - - +
39T THR* 3.6 37.9 - - + +
41T LYS* 3.3 21.0 - - + +
42T LYS 3.0 0.2 - - - -
43T ALA* 1.3 77.7 - - - +
45T VAL* 1.3 58.5 + - + +
48T LYS* 3.0 31.2 + - - +
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Residues in contact with VAL 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T LYS 4.6 7.9 - - - +
42T LYS* 2.8 12.2 + - - +
44T ALA* 1.3 78.6 - - + +
46T LEU* 1.3 78.2 + - + +
48T LYS* 3.2 6.5 + - - +
49T LYS* 3.0 37.4 + - + +
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Residues in contact with LEU 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7T HIS* 3.8 24.6 + - + +
10T ALA* 4.0 20.4 - - + -
11T ARG 4.1 16.8 - - - +
12T SER* 4.1 13.7 - - - +
17T VAL* 4.6 2.0 - - + -
42T LYS* 3.1 17.0 + - + +
43T ALA* 3.7 14.1 - - - +
45T VAL* 1.3 88.7 - - + +
47T VAL* 1.3 65.6 + - + +
49T LYS* 3.0 15.6 + - + +
50T VAL* 3.0 17.9 + - - +
103T ILE* 3.9 16.8 - - + -
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Residues in contact with VAL 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17T VAL* 3.9 26.5 - - + -
20T VAL* 4.1 16.8 - - + -
21T ALA* 4.6 6.1 - - + -
24T ILE* 4.2 17.7 - - + -
36T LEU* 4.0 17.9 - - + -
43T ALA 2.9 20.2 + - - +
44T ALA 3.9 2.5 - - - +
46T LEU* 1.3 77.5 - - + +
48T LYS* 1.3 64.8 + - - +
50T VAL* 3.2 10.4 + - - +
51T LEU* 2.9 20.4 + - + +
74T ILE* 4.3 12.3 - - + -
103T ILE* 4.4 12.8 - - + -
105T VAL* 5.0 2.4 - - + +
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Residues in contact with LYS 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T LEU* 3.6 23.3 - - + -
36T LEU* 3.6 31.8 - - + +
37T THR* 2.6 41.4 + - - +
44T ALA 3.0 19.6 + - - +
45T VAL* 3.6 6.3 - - + +
46T LEU 3.1 0.2 - - - -
47T VAL* 1.3 76.3 - - - +
49T LYS* 1.3 65.4 + - + +
51T LEU* 2.9 12.7 + - - +
52T GLU* 3.0 37.5 + - - +
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Residues in contact with LYS 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A C 4.8 1.2 + - - -
488A G 2.9 29.2 + - - -
489A G 3.6 13.5 + - - -
491A G 2.5 35.8 + - - +
492A A 5.0 4.5 - - - -
1284A A 5.6 0.8 - - - -
45T VAL* 3.0 29.0 + - + +
46T LEU* 3.5 9.4 - - + +
48T LYS* 1.3 75.3 - - + +
50T VAL* 1.3 64.5 + - + +
52T GLU* 3.5 15.8 + - - +
53T SER* 3.0 24.8 + - - -
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Residues in contact with VAL 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ALA* 3.8 27.0 - - + +
6T LYS 4.7 0.4 - - - -
7T HIS* 3.5 33.9 - - + +
46T LEU 3.0 18.2 + - - +
47T VAL* 3.4 8.7 - - - +
49T LYS* 1.3 77.5 - - + +
51T LEU* 1.3 55.9 + - - +
53T SER* 3.2 8.5 - - - -
54T ALA* 2.9 26.6 + - - +
103T ILE* 4.2 12.8 - - + +
105T VAL* 3.5 25.6 - - + -
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Residues in contact with LEU 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T ILE* 4.3 8.5 - - + -
29T VAL* 4.5 6.5 - - + +
32T ALA* 3.8 28.7 - - + -
33T LEU* 3.9 17.9 - - + -
36T LEU* 4.1 13.5 - - + -
47T VAL* 2.9 13.6 + - + +
48T LYS* 2.9 10.9 + - - +
50T VAL* 1.3 73.8 - - - +
52T GLU* 1.3 66.8 + - - +
54T ALA* 2.9 16.0 + - - +
55T ILE* 3.0 23.3 + - + +
71T VAL* 3.8 18.2 - - + -
105T VAL* 3.6 28.7 - - + +
107T VAL* 4.5 6.7 - - + -
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Residues in contact with GLU 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A C 4.3 7.4 - - - +
488A G 5.2 9.7 - - - +
33T LEU* 3.7 24.1 - - + +
48T LYS* 3.0 47.6 + - - +
49T LYS* 3.8 18.8 - - - +
51T LEU* 1.3 71.6 - - - +
53T SER* 1.3 64.1 + - - +
55T ILE* 3.0 14.7 + - - +
56T ALA* 3.0 21.3 + - - +
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Residues in contact with SER 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A C 2.8 40.9 + - - -
493A G 3.6 11.8 + - - -
494A G 5.1 1.7 + - - -
5T ALA* 4.3 8.8 - - - +
49T LYS 3.0 15.2 + - - -
50T VAL* 3.2 14.4 - - - -
52T GLU* 1.3 77.6 - - - +
54T ALA* 1.3 63.2 + - - +
56T ALA* 3.1 4.7 + - - +
57T ASN* 2.9 30.1 + - - +
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Residues in contact with ALA 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T THR* 4.2 4.0 - - - +
4T ILE 4.6 2.9 - - - -
5T ALA* 3.7 25.3 - - + +
50T VAL 2.9 13.5 + - - +
51T LEU* 2.9 11.2 + - - +
53T SER* 1.3 75.0 - - - +
55T ILE* 1.3 57.9 + - - +
57T ASN* 3.2 8.3 + - - +
58T ALA* 2.9 27.7 + - - +
105T VAL* 4.7 6.3 - - + +
107T VAL* 4.3 26.4 - - + +
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Residues in contact with ILE 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T VAL* 4.2 27.6 - - + -
33T LEU* 4.8 16.8 - - + -
51T LEU* 3.0 25.5 + - + +
52T GLU* 3.0 14.8 + - - +
54T ALA* 1.3 75.0 - - + +
56T ALA* 1.3 66.6 + - - +
58T ALA* 3.2 7.0 + - - +
59T GLU* 3.0 22.5 + - - +
66T ILE* 3.5 45.3 - - + -
69T LEU* 4.1 15.3 - - + -
107T VAL* 5.3 3.1 - - + -
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Residues in contact with ALA 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A C 3.9 9.4 - - - +
487A C 3.3 37.0 - - - +
52T GLU 3.0 12.0 + - - +
53T SER 3.1 8.3 + - - +
55T ILE* 1.3 75.2 - - - +
57T ASN* 1.3 59.9 + - - +
59T GLU* 3.3 6.7 + - - +
60T HIS* 2.9 34.3 + - - +
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Residues in contact with ASN 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A C 4.4 3.1 + - - +
487A C 4.9 1.4 - - - +
494A G 3.5 21.1 + - - +
495A G 3.0 41.1 + - - +
3T THR* 3.5 14.1 - - + +
4T ILE 3.2 17.4 + - - -
5T ALA* 4.6 5.1 - - - +
53T SER* 2.9 20.2 + - - +
54T ALA* 3.3 9.6 - - - +
55T ILE 3.2 0.2 - - - -
56T ALA* 1.3 76.5 - - - +
58T ALA* 1.3 66.5 + - - +
60T HIS* 5.3 0.4 - - - -
61T ASN* 2.9 35.0 + - - +
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Residues in contact with ALA 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T THR* 3.4 25.5 - - - +
54T ALA 2.9 12.7 + - - +
55T ILE* 3.2 7.6 + - - +
57T ASN* 1.3 74.6 - - - +
59T GLU* 1.3 59.5 + - - +
62T ASP* 2.9 27.9 + - - +
63T GLY 3.0 7.8 + - - -
64T ALA* 3.3 14.8 + - + +
66T ILE* 6.4 0.2 - - + -
69T LEU* 4.2 26.9 - - + -
107T VAL* 4.6 1.3 - - + -
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Residues in contact with GLU 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55T ILE 3.0 15.8 + - - +
56T ALA* 4.0 5.3 - - - +
57T ASN 3.2 0.2 - - - -
58T ALA* 1.3 78.5 - - - +
60T HIS* 1.3 60.1 + - - +
63T GLY* 3.1 23.3 + - - -
64T ALA 3.6 19.1 - - - +
65T ASP* 5.7 0.7 - - - -
66T ILE* 3.2 30.9 - - + +
400i ARG* 5.3 9.5 + - - +
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Residues in contact with HIS 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A C 3.2 35.6 + - - -
486A C 3.0 46.0 + - - +
495A G 4.2 0.4 + - - -
56T ALA 2.9 18.6 + - - +
57T ASN* 5.3 0.4 - - - -
59T GLU* 1.3 73.9 - - - +
61T ASN* 1.3 83.3 + - - +
63T GLY* 4.3 1.2 + - - -
400i ARG* 4.1 27.5 + - - +
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Residues in contact with ASN 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A G 2.8 50.9 + - - +
496A G 3.0 44.0 + - - +
3T THR* 5.7 0.4 - - + -
57T ASN* 2.9 18.8 + - - +
60T HIS* 1.3 93.5 + - - +
62T ASP* 1.3 72.5 + - - +
63T GLY 4.0 0.2 + - - -
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Residues in contact with ASP 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A G 6.1 0.3 - - - +
1T MET* 3.5 38.5 - - - +
2T GLU 3.9 5.9 - - - +
3T THR* 3.0 29.9 + - - +
57T ASN 4.6 1.6 - - - -
58T ALA 2.9 12.8 + - - +
61T ASN* 1.3 91.7 - - - +
63T GLY* 1.3 63.2 + - - +
64T ALA* 3.1 6.7 + - + +
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Residues in contact with GLY 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T ALA 3.0 3.6 + - - -
59T GLU* 3.1 20.5 + - - -
60T HIS 4.3 1.2 + - - -
61T ASN 3.6 1.2 - - - -
62T ASP* 1.3 76.9 - - - +
64T ALA* 1.3 62.7 + - - +
65T ASP* 3.9 1.2 + - - -
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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
------------------------------------------------------------
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