Contacts of the helix formed by residues 11 - 25 (chain A) in PDB entry 2NP2
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 LYS 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 1.3 71.8 - - - +
12A SER* 1.3 58.8 + - - +
14A ILE* 3.9 2.3 - - - +
15A VAL* 2.9 43.6 + - + +
35A ARG* 5.8 0.9 - - - +
38A ILE* 4.2 18.1 - - + +
39A ASP* 3.4 25.1 + - - +
42A PHE* 4.6 11.1 - - + -
56B GLU 3.7 5.3 + - - -
57B PHE* 3.9 23.4 - - + +
58B ARG 5.4 4.4 + - - -
233D A 3.0 40.1 + - - +
234D A 2.7 33.5 + - - -
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Residues in contact with SER 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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10A THR* 2.8 12.4 + - - -
11A LYS* 1.3 79.6 - - - +
13A ASP* 1.3 63.9 + - - -
15A VAL* 3.1 8.4 + - - +
16A ASP* 2.6 38.0 + - - +
35A ARG* 5.4 7.3 + - - +
233D A 3.9 5.5 + - - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS 4.0 5.2 - - - +
9A VAL* 3.6 20.0 - - + +
10A THR* 2.8 36.9 + - - +
12A SER* 1.3 74.8 - - - +
14A ILE* 1.3 66.1 + - - +
16A ASP* 2.8 19.8 + - - +
17A GLN* 2.8 25.2 + - + +
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.3 17.7 - - + -
10A THR 3.0 15.1 + - - +
11A LYS* 3.9 5.8 - - - +
13A ASP* 1.3 74.9 - - - +
15A VAL* 1.3 59.0 + - + +
17A GLN* 3.0 7.9 + - - +
18A ILE* 2.8 48.1 + - + +
38A ILE* 5.9 0.9 - - + -
41B PHE* 4.1 20.6 - - + +
44B GLU* 4.6 12.1 - - + +
45B LEU* 4.9 4.5 - - + +
48B ASN* 3.2 30.7 - - + +
55B ILE* 3.9 22.7 - - + -
57B PHE* 4.3 5.4 - - + -
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Residues in contact with VAL 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 LYS* 2.9 37.0 + - + +
12A SER* 3.1 8.5 + - - +
14A ILE* 1.3 76.4 - - + +
16A ASP* 1.3 65.9 + - - +
18A ILE* 3.5 4.3 + - - +
19A ALA* 3.1 19.2 + - - +
31A LYS* 4.1 12.8 - - + +
34A ILE* 4.0 20.3 - - + +
35A ARG* 3.5 48.2 - - + +
38A ILE* 4.3 17.9 - - + -
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 2.6 35.0 + - - +
13A ASP* 2.8 12.6 + - - +
15A VAL* 1.3 76.7 - - - +
17A GLN* 1.3 61.9 + - + +
19A ALA* 2.9 28.3 + - - +
20A LEU* 3.0 13.2 + - + +
31A LYS* 3.4 26.6 - - - +
35A ARG* 5.8 0.9 + - - -
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Residues in contact with GLN 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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9A VAL* 4.4 4.5 - - - +
13A ASP* 2.8 28.9 + - + +
14A ILE* 3.5 7.9 - - - +
16A ASP* 1.3 73.8 - - + +
18A ILE* 1.3 61.1 + - - +
20A LEU* 3.0 15.3 + - + +
21A ASN* 2.7 30.5 + - - +
44B GLU* 3.0 30.6 + - + +
47B SER* 5.1 0.4 + - - -
48B ASN* 3.0 36.2 + - - +
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Residues in contact with ILE 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 ILE* 2.8 26.6 + - + +
15A VAL 3.7 4.7 - - - +
17A GLN* 1.3 76.3 - - - +
19A ALA* 1.3 63.4 + - - +
21A ASN* 3.9 6.9 - - - +
22A ILE* 2.9 39.0 + - + +
34A ILE* 3.7 16.8 - - + -
38A ILE* 4.0 13.9 - - + -
37B VAL* 4.2 7.9 - - + +
40B ALA* 3.6 21.1 - - + +
41B PHE* 3.5 49.6 - - + +
44B GLU* 4.0 4.9 - - + -
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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 VAL 3.1 12.2 + - - +
16A ASP* 2.9 18.5 + - - +
18A ILE* 1.3 79.8 - - - +
20A LEU* 1.3 63.0 + - + +
22A ILE* 3.3 4.0 + - - +
23A LYS* 3.1 31.2 + - - +
29A LEU 5.3 3.6 - - - +
31A LYS* 4.2 22.7 - - + +
34A ILE* 3.7 19.1 - - + -
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Residues in contact with LEU 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 ASP* 3.0 16.0 + - + +
17A GLN* 3.0 15.9 + - + +
19A ALA* 1.3 73.0 - - + +
21A ASN* 1.3 69.0 + - - +
23A LYS* 2.7 21.2 + - + +
24A ASN* 2.8 26.8 + - - +
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Residues in contact with ASN 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 GLN 2.7 14.8 + - - +
18A ILE* 3.9 7.2 - - - +
20A LEU* 1.3 73.1 - - - +
22A ILE* 1.3 64.1 + - - +
24A ASN* 3.4 12.3 + - - +
25A ASN* 3.3 27.8 + - - +
36B LEU* 6.1 0.5 - - - +
40B ALA* 3.6 16.7 - - - +
43B GLU* 2.6 37.5 + - - +
44B GLU* 3.1 29.6 + - + +
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Residues in contact with ILE 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 ILE* 2.9 43.8 + - + +
19A ALA* 3.5 5.4 - - - +
20A LEU 2.8 0.8 + - - -
21A ASN* 1.3 79.0 - - - +
23A LYS* 1.3 61.0 + - + +
25A ASN* 3.4 8.8 + - - -
27A LEU* 3.3 43.3 - - + +
29A LEU* 4.2 29.8 - - + +
34A ILE* 4.3 7.6 - - + -
36B LEU* 3.7 36.8 - - + -
37B VAL* 4.3 5.8 - - + -
40B ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 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* 3.1 22.2 + - - +
20A LEU* 2.7 17.3 + - + +
22A ILE* 1.3 70.5 - - + +
24A ASN* 1.3 53.1 + - - +
25A ASN 2.8 5.8 - - - -
26A ASN* 2.7 26.9 + - - +
27A LEU 3.2 20.4 - - - +
28A LYS* 4.6 17.7 - - + +
29A LEU 4.7 14.8 - - - +
31A LYS* 5.6 6.5 - - - +
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Residues in contact with ASN 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 LEU* 2.8 37.3 + - - +
21A ASN* 3.6 10.6 - - - +
22A ILE 3.3 0.2 - - - -
23A LYS* 1.3 74.2 - - - +
25A ASN* 1.3 70.3 + - - +
26A ASN* 3.4 7.4 + - - +
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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 ASN* 3.3 20.7 + - - +
22A ILE* 3.4 7.2 + - - +
23A LYS 2.8 1.0 - - - -
24A ASN* 1.3 93.4 + - - +
26A ASN* 1.3 69.2 + - - +
27A LEU* 2.8 25.7 - - + +
43B GLU* 5.7 0.9 - - - +
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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