Contacts of the helix formed by residues 4 - 27 (chain A) in PDB entry 1GC5
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 SER 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 3.6 26.1 - - - +
3A GLU* 1.3 78.2 + - - +
5A LEU* 1.3 58.9 + - - +
6A LYS* 3.5 8.6 + - - +
7A ASP* 3.0 30.1 + - - +
8A ARG* 3.0 23.7 + - - +
10A ARG* 5.1 0.3 + - - -
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Residues in contact with LEU 5 (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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3A GLU 3.6 1.0 + - - -
4A SER* 1.3 72.4 - - - +
6A LYS* 1.3 59.4 + - + +
8A ARG* 3.6 9.6 - - - +
9A ILE* 2.8 53.8 + - + +
404A GLU* 3.9 26.5 - - + +
407A ILE* 3.5 27.4 - - + -
408A VAL* 3.3 30.7 - - + -
411A GLU* 5.3 4.3 + - - +
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.2 8.4 + - - +
5A LEU* 1.3 77.5 - - + +
7A ASP* 1.3 63.7 + - - +
9A ILE* 3.6 13.4 + - + +
10A ARG* 3.1 45.4 + - - +
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Residues in contact with ASP 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 6.0 0.3 - - - -
3A GLU* 3.6 24.5 - - - +
4A SER* 3.0 26.3 + - - +
6A LYS* 1.3 74.3 - - - +
8A ARG* 1.3 62.0 + - - +
10A ARG* 2.6 40.8 + - - +
11A LEU* 2.9 28.5 + - - +
14A ARG* 5.3 0.7 + - - -
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 5.4 1.8 + - - -
3A GLU* 2.7 49.4 + - + +
4A SER 3.0 13.1 + - - +
5A LEU* 3.6 13.5 - - - +
7A ASP* 1.3 77.3 - - - +
9A ILE* 1.3 61.0 + - - +
11A LEU* 3.3 14.7 + - + +
12A TRP* 3.0 34.9 + - + +
407A ILE* 3.7 24.0 + - + +
410A GLU* 4.2 11.7 + - - -
411A GLU* 3.4 39.2 + - - +
414A GLU* 2.9 38.0 + - - -
422A ASN* 5.5 2.0 + - - -
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Residues in contact with ILE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 2.8 44.6 + - + +
6A LYS* 3.7 14.1 - - + +
7A ASP 3.2 0.2 - - - -
8A ARG* 1.3 75.8 - - - +
10A ARG* 1.3 62.5 + - + +
12A TRP* 3.7 2.9 + - - +
13A LYS* 3.1 36.7 + - + +
402A THR* 5.9 6.1 - - - +
404A GLU* 4.0 19.7 - - + +
407A ILE* 3.4 26.9 - - + -
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 5.1 0.6 + - - -
6A LYS* 3.1 35.8 + - - +
7A ASP* 2.6 41.2 + - - +
9A ILE* 1.3 77.4 - - + +
11A LEU* 1.3 64.3 - - - +
13A LYS* 3.1 32.2 + - + +
14A ARG* 3.3 28.0 + - - +
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Residues in contact with LEU 11 (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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3A GLU* 5.0 11.9 - - - +
7A ASP 2.9 12.2 + - - +
8A ARG* 3.3 23.1 + - + +
10A ARG* 1.3 78.2 - - - +
12A TRP* 1.3 71.9 + - + +
14A ARG* 3.2 27.3 + - - +
15A LEU* 3.2 29.1 + - + +
410A GLU* 5.3 0.2 - - - +
422A ASN* 2.9 49.4 - - + +
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Residues in contact with TRP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.0 28.1 + - - +
9A ILE* 4.1 5.8 - - - +
11A LEU* 1.3 84.0 - - + +
13A LYS* 1.3 59.5 + - - +
15A LEU* 3.6 31.4 - - + +
16A TYR* 2.9 42.3 + + + -
369A ARG* 4.3 2.0 - - - -
373A LEU* 4.0 26.9 - - + -
402A THR* 4.9 7.0 - - + +
407A ILE* 4.1 19.3 - - + +
410A GLU* 3.1 38.2 + - - -
422A ASN* 4.3 4.3 - - + -
423A GLY* 4.1 11.4 - - - -
434A PHE* 3.6 17.0 - + - -
435A VAL* 4.1 4.7 - - + -
436A PRO* 3.4 45.6 - - + +
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Residues in contact with LYS 13 (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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9A ILE* 3.1 32.8 + - + +
10A ARG* 3.1 23.9 + - + +
12A TRP* 1.3 78.4 - - - +
14A ARG* 1.3 64.2 + - + +
16A TYR* 3.4 6.9 + - - +
17A VAL* 3.2 29.1 + - + +
398A LEU* 5.1 0.3 - - - +
402A THR* 6.0 1.8 - - - +
438A LYS* 6.2 2.9 - - - +
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Residues in contact with ARG 14 (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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7A ASP 5.3 0.4 + - - -
10A ARG* 3.3 28.8 + - - +
11A LEU* 3.2 34.0 + - - +
12A TRP 3.2 0.2 - - - -
13A LYS* 1.3 75.4 - - + +
15A LEU* 1.3 66.9 + - + +
17A VAL* 3.2 12.6 - - + +
18A ASN* 3.0 30.1 + - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.2 20.2 + - + +
12A TRP* 3.3 38.8 + - + +
14A ARG* 1.3 81.2 - - + +
16A TYR* 1.3 53.4 + - - +
18A ASN* 3.1 10.5 + - + +
19A ALA* 2.7 35.9 + - - +
369A ARG* 3.8 39.9 - - - +
370A ASP* 5.4 0.7 - - - +
373A LEU* 3.8 12.8 - - + +
422A ASN* 3.9 18.2 - - + -
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 2.9 33.3 + + + +
13A LYS* 3.6 7.9 - - - +
14A ARG 3.3 0.2 - - - -
15A LEU* 1.3 76.1 - - - +
17A VAL* 1.3 63.6 + - - +
19A ALA* 3.3 2.0 + - - +
20A PHE* 3.0 24.1 + - - +
373A LEU* 3.3 46.8 - - + +
376A SER* 2.9 24.7 + - - -
377A LEU* 3.7 22.5 - - + +
398A LEU* 3.9 12.6 - - + -
402A THR* 3.7 20.4 - - + -
435A VAL* 4.3 0.2 - - - +
436A PRO 2.6 28.4 + - - -
437A THR* 3.4 5.2 - - - -
438A LYS* 3.5 28.5 - - + +
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Residues in contact with VAL 17 (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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13A LYS* 3.2 13.4 + - + +
14A ARG* 3.2 17.5 - - - +
16A TYR* 1.3 75.1 - - - +
18A ASN* 1.3 76.2 + - - +
20A PHE* 3.7 4.9 + - - +
21A GLU* 3.2 34.5 + - - +
398A LEU* 3.9 31.2 - - + -
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Residues in contact with ASN 18 (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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14A ARG* 3.0 24.5 + - - +
15A LEU* 3.5 10.2 - - + +
17A VAL* 1.3 90.1 + - - +
19A ALA* 1.3 66.7 + - - +
21A GLU* 3.3 9.5 + - - +
22A ASN* 2.9 34.7 + - - +
370A ASP* 5.2 1.1 - - - +
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Residues in contact with ALA 19 (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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15A LEU 2.7 19.9 + - - +
16A TYR 3.6 3.1 - - - +
18A ASN* 1.3 73.7 - - - +
20A PHE* 1.3 51.7 + - - +
22A ASN* 3.1 2.8 + - - +
23A ALA* 2.8 37.3 + - - +
370A ASP* 3.5 36.2 - - + +
373A LEU* 3.5 32.5 - - + -
374A PHE* 4.5 2.2 - - - +
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Residues in contact with PHE 20 (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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16A TYR 3.0 17.0 + - - +
17A VAL* 3.7 8.1 - - - +
19A ALA* 1.3 76.2 - - - +
21A GLU* 1.3 71.4 + - - +
23A ALA* 3.2 2.9 + - - +
24A LEU* 2.9 51.8 + - + +
374A PHE* 4.0 24.4 - + - +
377A LEU* 3.8 24.8 - - + +
391A ILE 3.9 13.5 - - - -
392A GLU* 5.3 0.9 - - - -
394A ILE* 3.6 26.7 - - + -
395A ARG* 3.5 50.7 - - + -
398A LEU* 5.1 7.0 - - + -
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Residues in contact with GLU 21 (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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17A VAL* 3.2 25.6 + - - +
18A ASN* 3.3 10.6 + - - +
20A PHE* 1.3 90.6 - - - +
22A ASN* 1.3 64.0 + - - +
24A LEU* 3.5 6.8 + - + +
25A ASN* 3.1 34.0 + - - +
395A ARG* 2.5 33.3 + - - +
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Residues in contact with ASN 22 (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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18A ASN* 2.9 24.0 + - - +
19A ALA* 3.3 5.8 - - - +
21A GLU* 1.3 80.8 - - - +
23A ALA* 1.3 61.6 + - - +
25A ASN* 3.4 6.5 + - - +
26A ALA* 3.1 23.9 + - - +
370A ASP* 3.0 22.8 + - - -
464A MET* 4.1 16.4 - - + +
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Residues in contact with ALA 23 (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 ALA 2.8 14.3 + - - +
20A PHE 3.5 0.7 - - - +
22A ASN* 1.3 74.8 - - - +
24A LEU* 1.3 64.5 + - - +
26A ALA* 3.2 2.9 + - - +
27A ILE* 2.8 33.8 + - - +
374A PHE* 3.3 46.9 - - + -
460A SER* 4.4 9.0 - - - -
464A MET* 4.3 10.9 - - + -
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Residues in contact with LEU 24 (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 PHE* 2.9 47.7 + - + +
21A GLU* 3.8 7.9 - - + +
23A ALA* 1.3 76.0 - - - +
25A ASN* 1.3 62.0 + - - +
27A ILE* 4.3 2.5 - - - +
28A PRO* 3.2 21.3 - - - +
374A PHE* 4.7 6.1 - - + -
391A ILE* 3.1 53.8 - - + -
392A GLU* 6.4 0.2 - - - -
395A ARG* 4.6 10.1 - - - +
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Residues in contact with ASN 25 (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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21A GLU* 3.1 24.1 + - - +
22A ASN* 3.9 6.3 - - - +
23A ALA 3.1 0.4 - - - -
24A LEU* 1.3 83.2 + - - +
26A ALA* 1.3 57.7 + - - +
28A PRO* 3.3 15.8 - - - +
29A ASN* 4.5 7.3 + - - +
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Residues in contact with ALA 26 (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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22A ASN 3.1 9.6 + - - +
23A ALA* 3.2 2.2 + - - +
25A ASN* 1.3 74.1 - - - +
27A ILE* 1.3 68.1 + - + +
28A PRO* 3.2 3.8 - - - -
29A ASN* 2.8 30.5 + - - +
460A SER 4.4 2.0 - - - +
463A GLY* 3.5 9.2 - - - +
464A MET* 3.3 48.7 - - + +
467A ARG 5.1 3.4 - - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 2.8 26.4 + - + +
24A LEU* 4.3 5.6 - - - +
26A ALA* 1.3 75.0 - - - +
28A PRO* 1.3 64.8 - - + +
29A ASN 2.9 5.9 + - - -
30A VAL* 3.2 23.7 + - - +
133A TYR* 3.7 33.2 - - + +
135A ILE* 3.7 32.4 - - + +
374A PHE* 4.4 17.3 - - + -
391A ILE* 5.0 7.0 - - + -
456A SER 5.4 0.2 - - - +
459A VAL* 4.8 1.6 - - + -
460A SER* 3.9 31.8 - - - +
463A GLY* 5.5 0.4 - - - -
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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