Contacts of the helix formed by residues 9 - 26 (chain A) in PDB entry 2NP5
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 THR 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A SER* 1.3 73.0 + - - +
11A PRO* 4.0 7.6 - - + -
12A GLU* 2.7 39.4 + - - +
13A ARG* 3.0 48.9 + - - +
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Residues in contact with SER 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 1.3 76.8 - - - +
11A PRO* 1.4 72.7 - - - +
13A ARG* 3.1 21.5 + - - +
14A LEU* 3.1 28.6 + - - +
41A VAL* 6.0 2.3 - - - +
49A HIS* 3.6 25.0 - - - -
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Residues in contact with PRO 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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9A THR* 4.0 7.0 - - + -
10A SER* 1.4 93.6 - - - +
12A GLU* 1.3 68.2 + - - +
14A LEU* 3.1 9.9 + - + +
15A ALA* 2.8 24.8 + - - +
49A HIS* 3.7 22.4 - - + +
50A PHE* 4.0 20.3 - - + -
59A PHE* 3.6 31.3 - - + -
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Residues in contact with GLU 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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9A THR* 2.7 61.1 - - - +
11A PRO* 1.3 86.4 - - - +
13A ARG* 1.3 55.3 + - - +
15A ALA* 3.3 5.1 + - - +
16A ALA* 3.0 28.4 + - - +
59A PHE* 3.8 24.7 - - + -
63A THR* 5.4 9.7 - - + +
602A NDS 4.6 8.0 + - - -
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Residues in contact with ARG 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 THR* 3.0 50.1 + - - +
10A SER* 3.1 19.9 + - - +
12A GLU* 1.3 75.3 - - - +
14A LEU* 1.3 65.7 + - + +
16A ALA* 3.4 7.5 + - - +
17A ALA* 3.1 22.5 + - - +
39A ALA* 4.6 6.2 - - + +
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Residues in contact with LEU 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 SER* 3.1 12.9 + - - +
11A PRO* 3.1 9.3 + - + +
13A ARG* 1.3 76.9 - - + +
15A ALA* 1.3 58.7 + - - +
17A ALA* 3.2 5.6 + - - +
18A LEU* 2.8 30.3 + - - +
35A VAL* 3.7 12.8 - - + +
39A ALA* 3.7 24.2 - - + -
41A VAL* 3.9 20.9 - - + -
45A ALA 4.5 1.6 - - - +
46A VAL* 4.0 24.5 - - + -
49A HIS* 4.0 23.6 - - + +
50A PHE* 3.7 29.8 - - + -
56A MSE 5.8 1.8 - - + -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO 2.8 13.5 + - - +
12A GLU 3.6 8.7 - - - +
14A LEU* 1.3 74.7 - - - +
16A ALA* 1.3 57.9 + - - +
18A LEU* 3.3 4.7 + - - +
19A PHE* 3.0 28.8 + - - +
50A PHE* 5.5 0.6 - - - -
56A MSE 6.6 0.2 - - - -
59A PHE* 4.0 7.2 - - + -
60A ALA* 3.9 26.9 - - - +
63A THR* 3.9 31.9 - - + +
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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 GLU 3.0 15.9 + - - +
13A ARG* 3.6 8.3 - - - +
14A LEU 3.2 0.2 - - - -
15A ALA* 1.3 75.4 - - - +
17A ALA* 1.3 64.0 + - - +
19A PHE* 3.4 8.5 + - - +
20A ASP* 3.0 23.2 + - - +
63A THR* 5.8 0.2 - - - +
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Residues in contact with ALA 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 ARG 3.1 13.4 + - - +
14A LEU 3.2 8.0 + - - +
16A ALA* 1.3 73.8 - - - +
18A LEU* 1.3 66.7 + - - +
20A ASP* 3.2 7.9 + - - +
21A VAL* 2.9 28.9 + - - +
35A VAL* 3.8 9.6 - - + +
38A ARG* 4.2 8.5 - - + +
39A ALA* 3.7 36.3 - - + +
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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 LEU 2.8 12.3 + - - +
15A ALA* 3.3 11.2 + - - +
17A ALA* 1.3 77.7 - - - +
19A PHE* 1.3 60.1 + - - +
21A VAL* 3.3 2.5 + - - +
22A ALA* 2.9 29.7 + - + +
27A LEU* 3.9 23.3 - - + -
30A ALA* 4.1 6.2 - - + +
35A VAL* 4.0 18.7 - - + +
56A MSE 3.8 28.9 - - + +
57A PHE* 3.7 28.7 - - + -
60A ALA* 4.0 23.1 - - + -
109A PHE* 4.1 8.5 - - + -
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Residues in contact with PHE 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 ALA 3.0 15.9 + - - +
16A ALA* 3.7 8.1 - - - +
17A ALA 3.2 0.2 - - - -
18A LEU* 1.3 80.7 - - + +
20A ASP* 1.3 57.5 + - - +
22A ALA* 3.7 3.8 - - - +
23A ALA* 2.8 34.0 + - + +
60A ALA* 6.3 0.7 - - + -
64A LEU* 3.9 24.2 - - + -
98A ALA 5.0 0.2 - - - -
101A ARG* 3.4 42.6 - - + -
102A GLU* 3.7 37.2 - - + -
105A VAL* 3.8 30.6 - - + +
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Residues in contact with ASP 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 3.0 14.1 + - - +
17A ALA* 3.2 11.9 + - - +
19A PHE* 1.3 76.6 - - - +
21A VAL* 1.3 61.4 + - - +
23A ALA* 3.6 2.6 + - - +
24A GLU* 3.2 30.5 + - - +
38A ARG* 2.6 36.0 + - + +
101A ARG* 2.6 33.9 + - - +
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Residues in contact with VAL 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 ALA 2.9 19.2 + - - +
18A LEU* 3.8 4.9 - - - +
20A ASP* 1.3 76.4 - - - +
22A ALA* 1.3 56.3 + - - +
24A GLU* 3.0 8.1 + - - +
25A SER* 2.9 38.9 + - - +
29A GLY 3.0 36.6 - - - +
30A ALA* 3.9 7.4 - - - -
34A GLU* 4.0 18.8 - - + +
35A VAL* 4.7 1.8 - - + -
38A ARG* 3.6 42.2 - - + +
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Residues in contact with ALA 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 21.1 + - + +
19A PHE 3.8 3.1 - - - +
21A VAL* 1.3 70.1 - - - +
23A ALA* 1.3 62.6 + - - +
26A GLY* 2.8 39.7 + - - +
27A LEU* 3.8 29.2 - - + +
30A ALA* 4.9 0.9 - - + -
104A HIS* 3.4 7.3 + - - -
105A VAL* 3.9 21.1 - - + +
108A ALA* 5.9 0.7 - - + -
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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 PHE* 2.8 18.7 + - + +
22A ALA* 1.3 76.8 - - - +
24A GLU* 1.3 60.2 + - + +
101A ARG* 4.0 44.6 - - + +
104A HIS* 3.1 21.2 + - - -
105A VAL* 3.6 16.1 - - + +
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Residues in contact with GLU 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 ASP* 3.2 13.2 + - - +
21A VAL* 3.0 8.3 + - - +
23A ALA* 1.3 81.5 - - + +
25A SER* 1.3 64.0 + - - +
26A GLY 3.7 0.4 - - - -
38A ARG* 2.8 43.8 + - - -
101A ARG* 5.5 2.5 - - - +
115C THR* 3.7 14.2 - - - +
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Residues in contact with SER 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 VAL* 2.9 20.4 + - - +
24A GLU* 1.3 80.2 + - - +
26A GLY* 1.3 62.4 + - - +
28A GLU* 3.4 16.5 - - - +
29A GLY* 3.7 22.8 + - - -
115C THR* 4.1 14.6 + - - +
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Residues in contact with GLY 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 ALA* 2.8 30.3 + - - -
24A GLU 3.7 0.4 - - - -
25A SER* 1.3 79.2 + - - +
27A LEU* 1.3 64.1 + - - -
28A GLU* 3.2 11.0 - - - -
29A GLY* 3.1 14.6 + - - -
30A ALA 3.9 1.4 + - - -
104A HIS* 4.0 17.4 - - - -
108A ALA* 5.4 2.7 - - - -
111C VAL* 5.9 1.8 - - - -
115C THR* 5.2 1.3 - - - -
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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