Contacts of the helix formed by residues 8 - 30 (chain A) in PDB entry 2NSG
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 PRO 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASP 4.4 1.8 - - - +
7A LEU* 1.3 91.8 - - + +
9A LEU* 1.3 66.1 + - - +
10A GLU* 4.5 6.3 - - + +
11A GLU* 3.1 46.8 + - + +
12A ARG* 3.1 9.6 + - - -
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Residues in contact with LEU 9 (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 LEU 3.6 1.2 + - - -
8A PRO* 1.3 72.2 - - - +
10A GLU* 1.3 64.9 + - + +
12A ARG* 3.0 30.6 + - - +
13A LEU* 2.9 28.8 + - - +
120A TRP* 3.8 52.3 - - + +
135A SER* 4.1 5.2 - - - -
138A LEU* 3.3 31.6 - - + +
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Residues in contact with GLU 10 (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 PRO* 3.2 4.5 + - + +
9A LEU* 1.3 82.1 - - + +
11A GLU* 1.3 60.2 + - + +
13A LEU* 3.4 21.7 + - - +
14A THR* 3.0 32.0 + - - -
17A ARG* 5.5 1.4 + - - -
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Residues in contact with GLU 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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7A LEU* 3.8 21.8 - - + +
8A PRO* 3.1 41.3 + - + +
10A GLU* 1.3 76.5 - - + +
12A ARG* 1.3 60.1 + - - +
14A THR* 3.4 7.1 + - - -
15A LEU* 3.0 35.3 + - + +
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Residues in contact with ARG 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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4A PHE* 3.5 59.1 + - + +
5A HIS* 4.2 18.0 + - - +
7A LEU* 3.2 30.6 + - + -
8A PRO 3.1 11.2 + - - +
9A LEU* 3.0 33.8 + - - +
11A GLU* 1.3 75.6 - - - +
13A LEU* 1.3 63.4 + - - +
15A LEU* 3.4 1.1 + - - -
16A ALA* 3.1 22.3 + - - +
133A PRO* 5.7 1.0 - - - +
135A SER* 3.2 36.8 + - - -
136A GLU* 5.0 1.0 - - - +
138A LEU* 3.7 15.0 - - + +
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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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9A LEU 2.9 15.5 + - - +
10A GLU* 3.7 22.9 - - - +
12A ARG* 1.3 74.7 - - - +
14A THR* 1.3 65.0 + - - +
16A ALA* 3.2 3.4 + - - +
17A ARG* 2.9 73.3 + - - +
112A TRP* 3.5 44.4 - - + -
113A ARG* 5.2 3.6 - - + +
120A TRP* 5.7 4.7 - - + -
138A LEU* 3.9 15.9 - - + +
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Residues in contact with THR 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 GLU* 3.0 18.1 + - - +
11A GLU* 3.7 8.2 - - - -
12A ARG 3.3 0.2 - - - -
13A LEU* 1.3 78.9 - - - +
15A LEU* 1.3 57.8 + - + +
17A ARG* 3.3 11.2 + - - +
18A LEU* 2.8 48.6 + - + +
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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
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4A PHE* 3.7 20.9 - - + -
7A LEU* 3.6 31.2 - - + -
11A GLU* 3.0 18.5 + - + +
12A ARG 3.7 4.3 - - - +
13A LEU 3.3 0.2 - - - -
14A THR* 1.3 74.5 - - + +
16A ALA* 1.3 60.2 + - - +
18A LEU* 3.8 14.6 - - + +
19A GLY 2.9 22.7 + - - -
142A SER* 3.9 1.8 - - - -
146A TRP* 3.1 13.4 + - + +
162A PRO* 4.0 32.1 - - + -
164A VAL* 3.8 15.7 - - + -
165A ILE* 4.2 7.6 - - + -
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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 ARG 3.1 13.6 + - - +
13A LEU* 3.2 9.2 + - - +
15A LEU* 1.3 76.3 - - - +
17A ARG* 1.3 57.4 + - - +
19A GLY* 3.4 1.6 + - - -
20A THR* 2.9 32.8 + - - -
112A TRP* 4.0 28.0 - - + -
138A LEU* 4.0 10.1 - - + +
141A ARG* 4.9 1.6 - - + -
142A SER* 3.3 24.6 + - - +
145A VAL* 4.2 3.1 - - - +
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Residues in contact with ARG 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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10A GLU* 5.5 1.2 + - - -
13A LEU* 2.9 54.3 + - + +
14A THR* 3.7 9.5 + - - +
16A ALA* 1.3 74.6 - - + +
18A LEU* 1.3 64.4 + - + +
20A THR* 3.3 8.2 + - - -
21A SER* 3.0 28.4 + - - +
109A ASP* 2.8 31.6 + - - +
112A TRP* 5.4 2.5 - - + -
113A ARG* 3.2 35.0 - - - +
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Residues in contact with LEU 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 THR* 2.8 43.2 + - + +
15A LEU* 3.8 17.7 - - + +
17A ARG* 1.3 76.7 - - + +
19A GLY* 1.3 58.5 + - - +
21A SER* 3.4 7.2 + - - +
22A HIS* 2.9 29.1 + - - +
25A ARG* 4.8 2.6 + - - -
146A TRP* 3.7 14.8 - - + -
162A PRO* 6.0 1.8 - - + -
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Residues in contact with GLY 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 2.9 11.6 + - - -
18A LEU* 1.3 79.0 - - - +
20A THR* 1.3 55.5 + - - +
22A HIS* 3.3 2.9 + - - +
23A TYR* 2.8 29.8 + - - +
145A VAL* 3.5 17.1 - - - +
146A TRP* 3.1 34.1 - - - -
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Residues in contact with THR 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 21.9 + - - -
17A ARG* 3.6 7.7 - - - -
18A LEU 3.3 0.2 - - - -
19A GLY* 1.3 73.5 - - - +
21A SER* 1.3 60.7 + - - +
23A TYR* 3.2 2.5 + - - +
24A SER* 2.7 40.1 + - - +
101A HIS* 4.8 3.6 - - + -
105A VAL* 3.6 43.6 - - + +
112A TRP* 5.9 1.9 - - - -
141A ARG* 4.5 8.6 + - - +
145A VAL* 3.7 21.6 - - + +
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Residues in contact with SER 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 ARG* 3.0 17.5 + - - +
18A LEU* 3.8 9.4 - - - -
20A THR* 1.3 75.6 - - - +
22A HIS* 1.3 57.4 + - - +
24A SER* 3.4 7.3 + - - -
25A ARG* 2.9 49.5 + - - +
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Residues in contact with HIS 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 LEU 2.9 18.0 + - - +
19A GLY 3.4 4.5 - - - +
20A THR 3.2 0.2 - - - -
21A SER* 1.3 76.9 - - - +
23A TYR* 1.3 59.9 + - - +
25A ARG* 3.2 36.0 + - - +
26A GLN* 3.3 26.1 + - - +
146A TRP* 3.4 35.4 + + + -
149A ALA* 3.6 22.1 - - + +
156A ALA* 3.5 24.9 - - + +
157A THR 4.8 1.6 + - - -
160A ASP* 3.6 37.3 - - + +
161A ILE* 5.7 0.2 - - - +
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY 2.8 16.8 + - - +
20A THR* 3.5 4.5 - - - +
22A HIS* 1.3 77.3 - - - +
24A SER* 1.3 62.0 + - - +
26A GLN* 3.0 6.6 + - - +
27A LEU* 3.0 24.7 + - + +
49A LEU* 4.6 0.6 - - + +
50A ILE* 3.6 26.2 + - - +
53A VAL* 3.4 36.1 - - + +
101A HIS* 3.3 42.2 - + - -
145A VAL* 3.8 22.7 - - + +
148A HIS* 3.9 12.8 - - + -
149A ALA* 3.7 29.6 - - - -
152A LEU* 3.5 25.2 - - + +
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Residues in contact with SER 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 THR* 2.7 27.0 + - - +
21A SER* 3.7 7.6 - - - -
23A TYR* 1.3 73.9 - - - +
25A ARG* 1.3 59.9 + - - +
27A LEU* 3.3 7.1 + - - +
28A SER* 3.0 28.8 + - - -
101A HIS* 2.9 27.7 + - - -
105A VAL* 5.2 0.3 - - - +
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Residues in contact with ARG 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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18A LEU 4.8 2.2 + - - -
21A SER* 2.9 33.8 + - - +
22A HIS* 3.5 38.4 + - - +
23A TYR 3.2 0.4 - - - -
24A SER* 1.3 76.7 - - - +
26A GLN* 1.3 68.9 + - - +
28A SER* 3.4 8.6 + - - -
29A LEU* 3.2 27.2 + - + +
146A TRP* 6.1 0.2 - - - -
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Residues in contact with GLN 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 HIS* 3.4 23.9 + - - +
23A TYR 3.0 7.1 + - - +
25A ARG* 1.3 82.0 + - - +
27A LEU* 1.3 64.2 + - - +
29A LEU* 3.0 17.4 + - - +
30A VAL* 3.2 15.9 + - - +
149A ALA* 3.7 13.0 + - + +
152A LEU* 3.9 15.5 - - + -
154A ALA* 3.0 14.5 - - + +
155A VAL* 2.8 46.1 - - - +
156A ALA* 3.1 30.5 + - + +
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Residues in contact with LEU 27 (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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23A TYR* 3.0 18.2 + - + +
24A SER* 3.3 9.4 + - - +
26A GLN* 1.3 75.8 - - - +
28A SER* 1.3 63.3 + - - +
30A VAL* 3.1 18.3 + - + +
35A PHE* 3.9 13.9 - - + -
50A ILE* 3.4 41.1 - - + -
98A ARG* 3.0 33.4 + - + +
101A HIS* 3.6 40.2 - - + +
152A LEU* 3.7 13.4 - - + +
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Residues in contact with SER 28 (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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24A SER 3.0 17.5 + - - -
25A ARG* 3.4 10.3 - - - -
27A LEU* 1.3 79.0 - - - +
29A LEU* 1.3 62.1 + - - +
30A VAL 3.5 5.9 + - - +
31A ASP* 5.3 1.0 - - - +
98A ARG* 4.0 9.5 + - - +
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Residues in contact with LEU 29 (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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25A ARG* 3.2 15.5 + - + +
26A GLN* 3.0 20.7 + - - +
28A SER* 1.3 78.4 - - - +
30A VAL* 1.3 63.3 + - - +
31A ASP* 3.5 10.8 + - - +
34A GLU* 4.3 2.6 - - - +
154A ALA* 4.1 10.3 - - + -
155A VAL* 3.8 31.9 - - + -
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Residues in contact with VAL 30 (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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26A GLN 3.5 14.6 - - - +
27A LEU* 3.1 16.7 + - + +
28A SER 3.7 3.6 - - - +
29A LEU* 1.3 78.0 - - - +
31A ASP* 1.3 67.4 + - - +
34A GLU* 3.7 12.8 - - + +
35A PHE* 3.8 14.6 - - + -
46A ARG* 3.5 40.6 - - - +
50A ILE* 5.6 0.7 - - + -
98A ARG* 2.6 29.6 + - - -
152A LEU* 4.1 17.9 - - + +
154A ALA* 4.7 7.4 - - + -
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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
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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