Contacts of the helix formed by residues 9 - 27 (chain E) in PDB entry 2NVX
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 ILE 9 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E ASN* 3.3 19.7 - - - +
6E GLU* 2.8 27.2 + - - +
8E ASN* 1.3 88.1 - - + +
10E SER* 1.3 54.0 + - - +
11E ARG 3.2 1.1 - - - -
12E LEU* 2.9 10.8 + - + +
13E TRP* 2.4 41.1 + - + +
39E LEU* 5.2 8.1 - - + -
42E PHE* 4.5 20.1 - - + -
43E LYS* 5.6 6.7 - - + -
47E CYS* 5.8 3.6 - - - -
51E GLY 4.2 7.0 - - - +
52E ARG* 4.1 39.5 - - + +
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Residues in contact with SER 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320A PRO* 5.7 10.3 - - - -
6E GLU* 2.9 27.3 + - - -
7E ARG* 4.2 8.3 - - - -
9E ILE* 1.3 77.9 - - - +
11E ARG* 1.3 61.4 + - - +
13E TRP* 3.8 15.4 - - - +
14E ARG* 3.3 33.2 + - - +
39E LEU* 5.0 5.4 - - - +
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Residues in contact with ARG 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1315A GLU* 4.1 18.9 + - - -
1318A THR* 2.9 58.1 + - - +
1319A VAL* 5.1 3.2 - - - +
1320A PRO* 5.5 8.3 - - + +
7E ARG* 3.4 32.8 + - + +
8E ASN* 5.1 3.6 - - - +
9E ILE 3.2 0.4 - - - -
10E SER* 1.3 77.4 - - - +
12E LEU* 1.3 59.0 + - - +
14E ARG* 3.4 4.5 + - - +
15E ALA* 3.0 29.0 + - - +
138E ALA* 4.9 8.7 - - - +
141E VAL* 3.8 32.4 - - + +
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ASN 3.4 21.2 + - - +
9E ILE* 2.9 15.1 + - + +
11E ARG* 1.3 80.2 - - - +
13E TRP* 1.3 56.4 + - - +
15E ALA* 3.6 6.5 - - + +
16E PHE* 3.1 28.2 + - + +
42E PHE* 4.3 10.0 - - + -
52E ARG 5.0 7.9 - - - +
53E PRO* 5.6 2.5 - - + -
55E ARG* 3.6 40.6 - - + +
58E MET* 4.0 27.6 - - + -
82E PHE* 4.7 11.9 - - + -
137E GLU* 4.0 17.3 - - - +
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Residues in contact with TRP 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE 2.4 25.4 + - - +
10E SER* 4.0 12.6 - - - +
11E ARG 3.3 0.2 - - - -
12E LEU* 1.3 73.7 - - - +
14E ARG* 1.3 82.9 + - + +
16E PHE* 3.4 9.1 - + + +
17E ARG* 3.4 33.4 + - + +
37E LEU* 3.1 33.1 + - + +
38E PRO* 3.9 9.3 + - + -
39E LEU* 3.6 42.2 - - + -
42E PHE* 3.7 40.4 - + + +
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Residues in contact with ARG 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317A MET 4.7 0.6 + - - -
1318A THR* 3.4 31.3 + - - +
1319A VAL 4.3 9.9 + - - +
1320A PRO* 4.7 10.3 - - - +
1324A PRO* 4.9 5.8 - - - +
10E SER* 3.3 19.4 + - - +
11E ARG* 3.4 6.8 + - - +
12E LEU 3.3 0.2 - - - -
13E TRP* 1.3 94.7 - - + +
15E ALA* 1.3 63.1 + - - +
16E PHE 3.2 0.7 - - - -
17E ARG* 3.7 9.6 + - - +
18E THR* 3.3 20.3 + - - -
141E VAL* 3.1 53.5 + - - +
142E VAL* 3.7 22.8 - - - +
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Residues in contact with ALA 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ARG 3.0 18.5 + - - +
12E LEU* 3.6 11.7 - - + +
13E TRP 3.3 0.2 - - - -
14E ARG* 1.3 75.3 - - - +
16E PHE* 1.3 60.3 - - - +
18E THR 4.2 0.2 - - - -
19E VAL* 2.9 27.9 + - - +
82E PHE* 4.4 5.9 - - + -
137E GLU* 4.4 21.8 - - + +
140E LEU* 3.2 26.7 - - + +
141E VAL* 4.0 6.1 - - + +
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Residues in contact with PHE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU* 3.1 12.4 + - + +
13E TRP* 3.4 15.3 - + - +
15E ALA* 1.3 75.7 - - - +
17E ARG* 1.3 68.7 + - - +
19E VAL* 2.8 21.0 + - + +
20E LYS* 3.2 42.2 + - + +
34E GLU 5.5 2.9 - - - -
37E LEU* 5.1 11.0 - - + -
42E PHE* 4.5 16.4 - + + -
46E TYR* 3.7 32.8 - + - -
58E MET* 4.4 30.3 - - + -
60E PHE* 4.1 19.3 - + - -
82E PHE* 4.3 19.0 - + + -
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Residues in contact with ARG 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E TRP* 3.4 25.4 + - + +
14E ARG* 3.8 12.6 - - - +
16E PHE* 1.3 79.6 - - - +
18E THR* 1.3 56.2 + - - +
20E LYS* 2.6 33.8 + - - +
21E GLU* 3.1 37.3 + - - +
35E VAL* 4.2 23.8 - - + +
36E GLU* 3.8 37.0 + - - +
37E LEU 5.7 0.6 + - - -
146E HIS* 5.7 1.8 + - - -
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Residues in contact with THR 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ARG 3.3 10.9 + - - -
15E ALA 4.3 0.4 - - - -
16E PHE 3.3 0.6 - - - -
17E ARG* 1.3 76.8 - - - +
19E VAL* 1.3 57.5 + - - +
21E GLU* 3.7 10.6 + - - -
22E MET* 3.1 25.4 + - - +
140E LEU* 3.3 40.1 + - + +
141E VAL 3.9 0.2 + - - -
142E VAL* 3.6 5.0 - - - +
143E ASN* 3.3 48.8 + - - +
187E TYR* 4.9 4.0 - - + -
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Residues in contact with VAL 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA 2.9 21.5 - - - +
16E PHE* 2.8 10.9 + - + +
18E THR* 1.3 76.1 - - - +
20E LYS* 1.3 62.2 + - - +
22E MET* 3.5 13.8 + - - +
23E VAL* 3.0 40.1 + - + +
60E PHE* 4.6 6.5 - - + -
80E VAL* 4.0 26.9 - - + -
82E PHE* 3.7 22.0 - - + -
109E ILE* 5.3 8.1 - - + -
111E VAL* 5.4 2.7 - - + -
140E LEU* 4.5 19.1 - - + -
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Residues in contact with LYS 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PHE* 3.2 46.6 + - + +
17E ARG* 2.6 18.2 + - - +
19E VAL* 1.3 68.2 - - - +
21E GLU* 1.3 59.7 + - - +
23E VAL* 2.9 20.1 + - - +
24E LYS* 3.2 12.0 + - - +
30E ILE* 4.0 27.6 - - + +
34E GLU* 2.9 40.0 + - + +
35E VAL* 4.0 28.5 - - + +
46E TYR* 4.9 4.2 + - - -
60E PHE* 4.0 33.6 - - + +
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Residues in contact with GLU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 3.1 38.1 + - - +
18E THR* 3.7 8.0 + - - -
20E LYS* 1.3 76.0 - - - +
22E MET* 1.3 61.2 + - - +
24E LYS* 3.5 12.8 - - + +
25E ASP* 3.2 31.7 + - - +
35E VAL* 3.9 16.7 - - + +
143E ASN* 2.7 43.2 + - - +
146E HIS* 3.3 28.9 + - + -
187E TYR* 3.6 3.6 - - - +
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Residues in contact with MET 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E THR 3.1 17.6 + - - +
19E VAL* 3.5 15.0 - - - +
20E LYS 3.1 0.2 - - - -
21E GLU* 1.3 79.6 - - - +
23E VAL* 1.3 59.4 + - + +
25E ASP* 3.2 3.5 + - - +
26E ARG* 2.9 69.3 + - + +
109E ILE* 4.6 13.0 - - + -
135E PHE* 3.9 26.0 - - + -
140E LEU* 4.5 19.7 - - - -
187E TYR* 3.5 44.6 + - + +
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E VAL* 3.0 21.0 + - + +
20E LYS 2.9 8.2 + - - +
22E MET* 1.3 78.4 - - + +
24E LYS* 1.3 65.8 + - - +
26E ARG* 3.3 17.8 + - + +
28E TYR* 3.2 41.9 + - + -
30E ILE* 3.7 21.5 - - + -
60E PHE* 4.8 2.9 - - + -
62E ALA* 3.8 13.9 - - + -
78E LEU* 4.5 6.5 - - + -
80E VAL* 4.3 23.1 - - + -
109E ILE* 6.3 0.4 - - + -
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Residues in contact with LYS 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LYS 3.2 8.4 + - - +
21E GLU* 3.5 20.9 - - + +
23E VAL* 1.3 76.7 - - - +
25E ASP* 1.3 66.7 + - - +
27E GLY* 3.0 21.1 + - - -
28E TYR 3.5 19.9 + - - +
30E ILE* 3.9 31.0 + - + +
32E GLN* 2.6 34.0 + - - +
35E VAL* 4.7 11.2 - - + -
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Residues in contact with ASP 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLU* 3.2 21.4 + - - +
22E MET 3.5 4.3 - - - +
23E VAL 3.2 0.2 - - - -
24E LYS* 1.3 81.4 - - - +
26E ARG* 1.3 67.7 + - - +
27E GLY* 3.0 3.4 + - - -
145E THR* 4.9 3.6 + - - -
187E TYR* 3.5 29.0 + - + +
188E LEU* 4.3 14.1 - - + +
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Residues in contact with ARG 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E MET* 2.9 54.9 + - + +
23E VAL* 3.3 13.5 - - + +
25E ASP* 1.3 77.0 - - - +
27E GLY* 1.3 57.1 + - - +
28E TYR* 3.7 22.4 - - + -
75E MET* 4.1 22.8 - - + +
78E LEU* 4.0 16.4 - - + +
107E THR* 4.1 5.7 - - - +
109E ILE* 3.7 10.5 - - - +
133E GLU* 2.9 42.8 + - - -
135E PHE* 4.2 0.8 - - - -
155E ARG* 5.4 8.3 + - - +
186E LEU 3.5 6.1 + - - -
187E TYR 3.8 8.3 + - - +
188E LEU* 3.8 32.2 + - - +
189E GLY* 4.1 1.8 + - - -
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Residues in contact with GLY 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LYS 3.0 9.5 + - - -
25E ASP 3.0 1.5 - - - -
26E ARG* 1.3 79.8 - - - +
28E TYR* 1.3 69.3 + - - +
64E PRO* 4.2 2.4 - - - +
65E THR* 3.7 6.8 + - - -
68E SER* 2.8 32.8 + - - -
75E MET* 4.8 6.4 - - - +
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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