Contacts of the helix formed by residues 9 - 26 (chain A) in PDB entry 1SNG
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 ARG 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE 3.9 1.4 + - - -
8A LEU* 1.3 71.5 - - - +
10A ASP* 1.3 66.9 + - - +
11A ASP* 3.0 33.8 + - - +
12A HIS* 3.6 9.9 - - + +
13A LEU* 3.0 21.3 + - - +
64A THR* 4.1 10.5 + - - +
68A PRO* 4.2 10.1 + - - +
69A LEU* 3.8 28.3 - - - +
72A ALA* 3.9 31.6 - - - +
73A LEU* 6.1 3.4 - - - -
350A GLY* 3.0 23.2 + - - +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 3.4 7.0 + - - +
9A ARG* 1.3 72.7 - - - +
11A ASP* 1.3 58.8 + - - +
13A LEU* 3.3 12.5 + - - +
14A GLU* 3.0 35.2 + - + +
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.0 38.8 + - - -
10A ASP* 1.3 78.5 - - - +
12A HIS* 1.3 74.6 + - - +
14A GLU* 3.9 6.4 - - - +
15A PHE* 3.0 29.1 + - - +
62A LEU 3.6 16.9 - - - +
63A GLY* 3.9 14.0 - - - +
64A THR* 3.6 18.3 - - - +
69A LEU* 3.8 7.4 - - - +
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Residues in contact with HIS 12 (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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8A LEU* 4.9 1.8 - - + -
9A ARG* 3.3 23.1 + - + +
10A ASP 3.3 0.6 - - - -
11A ASP* 1.3 83.7 + - - +
13A LEU* 1.3 61.4 + - - +
15A PHE* 3.4 8.0 + + - +
16A ALA* 2.8 32.2 + - - +
36A PRO* 3.6 41.6 - - + +
37A TYR 3.9 2.0 - - - -
40A ALA* 4.1 12.5 - - + +
62A LEU 5.4 0.2 - - - -
69A LEU* 5.1 6.8 - - + +
73A LEU* 4.1 20.5 - - + +
350A GLY 3.9 3.8 - - - +
351A ALA* 3.6 10.9 - - - -
352A ILE* 3.0 40.4 + - + -
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Residues in contact with LEU 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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7A PHE* 4.3 15.0 - - + -
8A LEU* 3.8 27.6 - - + +
9A ARG 3.0 13.0 + - - +
10A ASP* 3.5 16.8 - - - +
12A HIS* 1.3 77.2 - - - +
14A GLU* 1.3 64.4 + - - +
16A ALA* 4.6 2.9 - - - -
17A LEU* 3.0 47.3 + - + +
237A ALA* 3.9 16.4 - - + +
240A LEU* 3.8 17.7 - - + -
241A THR* 3.4 26.5 - - - +
352A ILE* 4.6 4.0 - - + -
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Residues in contact with GLU 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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10A ASP* 3.0 23.7 + - + +
11A ASP* 3.9 7.0 - - - +
13A LEU* 1.3 78.4 - - + +
15A PHE* 1.3 63.4 + - - +
17A LEU* 4.2 0.5 - - - +
18A HIS* 3.0 55.0 + - + +
237A ALA* 3.6 26.2 - - - +
238A PRO* 5.0 4.7 - - - +
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Residues in contact with PHE 15 (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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11A ASP 3.0 20.0 + - - +
12A HIS* 3.6 11.4 - - - +
14A GLU* 1.3 77.4 - - - +
16A ALA* 1.3 75.9 + - + +
18A HIS* 3.9 4.7 - - - +
19A LEU* 3.1 37.7 + - + +
34A TRP* 4.2 12.8 - + - -
36A PRO* 3.9 9.9 - - + -
39A VAL* 4.0 22.9 - - + -
40A ALA* 3.8 31.2 - - + -
43A LEU* 4.2 4.0 - - + -
61A LEU* 3.7 53.5 - - + +
62A LEU* 4.1 18.2 - - + +
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Residues in contact with ALA 16 (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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12A HIS* 2.8 21.5 + - - +
13A LEU 3.8 1.8 - - - +
14A GLU 3.3 0.2 - - - -
15A PHE* 1.3 81.2 - - + +
17A LEU* 1.3 59.2 + - + +
20A HIS* 2.9 28.4 + - - +
34A TRP* 3.3 12.0 - - - -
36A PRO* 3.7 32.3 - - + -
352A ILE* 3.8 19.5 - - + -
355A LEU* 4.1 1.3 - - + -
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Residues in contact with LEU 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 LEU* 3.0 28.9 + - + +
14A GLU 4.4 0.4 - - - +
16A ALA* 1.3 80.5 - - + +
18A HIS* 1.3 66.8 + - + +
20A HIS* 3.8 6.6 - - + +
21A ARG* 3.2 28.1 + - - +
234A VAL* 6.0 0.2 - - - +
235A PRO* 3.5 41.6 - - + +
236A THR* 4.1 2.0 - - - -
237A ALA* 3.8 26.0 - - + +
240A LEU* 3.6 30.7 - - + -
352A ILE* 4.1 4.3 - - + -
355A LEU* 4.0 20.9 - - + -
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Residues in contact with HIS 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 GLU* 3.0 48.0 + - + +
15A PHE* 3.9 5.2 - - - +
17A LEU* 1.3 78.9 - - + +
19A LEU* 1.3 61.5 + - - +
21A ARG* 3.1 41.4 + - - +
22A ARG* 3.5 24.2 + - - +
61A LEU* 6.0 6.1 - - + -
237A ALA* 6.4 0.4 - - + -
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Residues in contact with LEU 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 PHE* 3.1 33.1 + - + +
18A HIS* 1.3 72.9 - - - +
20A HIS* 1.3 65.8 + - - +
22A ARG* 3.1 6.9 + - - +
23A LEU* 3.0 29.2 + - + +
34A TRP* 3.7 33.0 - - + -
39A VAL* 4.4 5.8 - - + -
61A LEU* 5.1 5.3 - - + +
267A LEU* 5.3 3.8 - - + -
270A VAL* 3.7 31.4 - - + +
271A LEU* 4.3 19.7 - - + -
274A ALA* 3.9 25.4 - - + -
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Residues in contact with HIS 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 ALA 2.9 19.6 + - - +
17A LEU* 3.8 9.2 - - + +
18A HIS 3.3 0.2 - - - -
19A LEU* 1.3 77.0 - - - +
21A ARG* 1.3 55.8 + - - +
23A LEU* 3.2 3.3 + - - +
24A ALA* 2.8 31.9 + - + +
32A VAL* 4.1 21.8 - - + +
34A TRP* 2.9 27.3 + - - +
234A VAL* 4.0 19.1 - - + -
235A PRO* 4.9 8.0 - - + +
343A HIS* 4.8 0.4 + - - -
355A LEU* 3.5 44.2 - - + +
356A GLY 4.3 1.4 + - - -
357A SER* 2.8 30.9 + - - -
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Residues in contact with ARG 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 LEU* 3.2 13.7 + - - +
18A HIS* 3.1 43.7 + - - +
20A HIS* 1.3 79.1 - - - +
22A ARG* 1.3 61.8 + - + +
24A ALA* 3.4 1.4 + - - +
25A GLU* 3.0 52.6 + - + +
234A VAL* 4.5 21.2 - - + +
235A PRO 5.2 3.7 + - - +
236A THR* 4.6 21.5 - - - +
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Residues in contact with ARG 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 HIS* 3.6 20.7 + - - +
19A LEU* 3.1 6.2 + - - +
21A ARG* 1.3 80.5 - - + +
23A LEU* 1.3 64.1 + - - +
25A GLU* 3.5 8.6 + - - +
26A ALA* 3.3 22.0 + - - +
270A VAL* 3.4 37.9 - - + +
273A GLU* 3.5 44.4 + - - +
274A ALA* 3.6 20.2 + - - +
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Residues in contact with LEU 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 LEU* 3.0 22.3 + - + +
20A HIS 3.6 5.6 - - - +
22A ARG* 1.3 76.6 - - - +
24A ALA* 1.3 61.8 + - - +
26A ALA* 3.2 19.2 + - + +
27A VAL* 3.8 6.6 - - - +
32A VAL* 3.7 21.9 - - + +
34A TRP* 3.7 50.0 - - + +
265A HIS* 4.4 20.2 - - + +
266A GLN 6.1 0.2 - - - +
267A LEU* 4.3 13.2 - - + -
270A VAL* 4.1 26.9 - - + -
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Residues in contact with ALA 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 HIS* 2.8 21.5 + - + +
21A ARG 3.8 4.0 - - - +
23A LEU* 1.3 76.0 - - - +
25A GLU* 1.3 58.9 + - + +
26A ALA 3.3 0.3 + - - -
27A VAL 3.0 24.6 + - - +
30A GLY* 3.4 24.5 - - - +
32A VAL* 3.5 14.1 - - + +
234A VAL* 4.2 28.7 - - + -
357A SER* 5.2 0.4 - - - +
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Residues in contact with GLU 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 ARG* 3.0 43.9 + - + +
22A ARG* 4.0 8.1 - - - +
23A LEU 3.3 0.4 - - - -
24A ALA* 1.3 77.4 - - + +
26A ALA* 1.3 60.6 + - - +
27A VAL 3.2 4.3 + - - +
234A VAL* 6.2 3.4 - - + -
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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 ARG 3.3 12.4 + - - +
23A LEU* 3.2 16.3 + - + +
24A ALA 3.1 1.0 - - - -
25A GLU* 1.3 77.1 - - - +
27A VAL* 1.3 62.6 + - + +
28A PRO* 4.6 1.6 - - - +
270A VAL* 6.4 1.3 - - + -
273A GLU* 6.0 1.8 - - - +
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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