Contacts of the helix formed by residues 10 - 26 (chain D) 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 SER 10 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C GLU* 2.9 44.7 + - - +
59C PHE* 6.2 1.8 - - - -
63C THR* 5.9 6.4 - - - +
66C ASP* 5.6 1.6 + - - -
67C LYS* 5.7 5.7 + - - -
11D PRO* 1.4 77.2 - - - +
12D GLU 3.0 29.2 + - - +
13D ARG 3.8 0.5 + - - -
14D LEU* 3.4 19.3 + - - +
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Residues in contact with PRO 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C THR* 5.7 3.4 - - + +
66C ASP* 3.8 43.7 - - + +
67C LYS* 4.5 17.0 - - + +
70C ALA* 5.2 2.5 - - + -
10D SER* 1.4 94.1 - - - +
12D GLU* 1.3 51.3 + - - +
14D LEU* 3.3 5.7 - - + +
15D ALA* 2.7 32.8 + - - +
59D PHE* 3.1 34.7 - - + -
63D THR* 5.4 3.6 - - + +
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 5.5 3.6 + - - +
10D SER* 3.0 27.7 + - - +
11D PRO* 1.3 77.2 - - - +
13D ARG* 1.3 59.5 + - + +
15D ALA* 4.3 7.0 - - + +
16D ALA* 5.4 2.5 - - + +
63D THR* 5.6 2.5 - - + -
67D LYS* 5.0 15.9 - - - +
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D SER 3.8 1.2 + - - -
12D GLU* 1.3 70.5 + - + +
14D LEU* 1.3 55.2 + - - +
15D ALA 3.3 1.3 - - - -
16D ALA* 3.6 20.2 - - + -
17D ALA* 2.8 31.4 + - - +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D SER* 3.4 16.7 + - - +
11D PRO* 3.3 15.6 + - + +
12D GLU 3.4 0.2 - - - -
13D ARG* 1.3 74.5 - - - +
15D ALA* 1.3 65.8 + - - +
17D ALA* 3.3 8.2 + - + +
18D LEU* 3.1 20.8 + - + +
56D MSE 5.0 17.4 - - + +
59D PHE* 3.4 29.8 - - + -
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO 2.7 20.7 + - - +
12D GLU* 4.7 3.6 - - + -
14D LEU* 1.3 73.7 - - - +
16D ALA* 1.3 61.2 + - - +
18D LEU* 3.1 16.1 + - - +
19D PHE* 3.2 24.5 + - + -
59D PHE* 3.6 12.0 - - + -
60D ALA* 4.9 5.8 - - - +
63D THR* 3.7 37.2 - - + +
67D LYS* 5.9 1.6 - - - +
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 5.1 2.6 - - + +
13D ARG* 3.4 26.0 + - + +
14D LEU 3.3 0.4 - - - -
15D ALA* 1.3 79.0 - - - +
17D ALA* 1.3 55.9 + - - +
19D PHE* 3.5 9.7 + - - +
20D ASP* 3.1 28.5 + - - +
67D LYS* 6.2 1.8 - - - +
102D GLU* 5.8 2.5 - - - +
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG 2.8 21.6 + - - +
14D LEU* 3.5 9.4 - - + +
15D ALA 3.2 0.2 - - - -
16D ALA* 1.3 70.8 - - - +
18D LEU* 1.3 66.6 + - - +
20D ASP* 3.4 5.1 + - - +
21D VAL* 3.0 34.1 + - + +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.1 12.3 + - + +
15D ALA* 3.1 11.7 + - - +
17D ALA* 1.3 78.3 - - - +
19D PHE* 1.3 60.7 + - + +
21D VAL* 3.7 7.3 - - + -
22D ALA* 2.8 43.6 + - + +
56D MSE 3.1 68.0 - - + +
57D PHE* 3.9 23.8 - - + +
59D PHE* 5.6 2.2 - - + -
60D ALA* 3.7 15.5 - - + -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 3.2 28.4 + - + -
16D ALA* 4.0 7.4 - - - +
17D ALA 3.3 0.2 - - - -
18D LEU* 1.3 76.6 - - + +
20D ASP* 1.3 53.5 + - - +
22D ALA* 4.6 1.1 - - - -
23D ALA* 2.8 38.1 + - - +
57D PHE* 6.2 1.3 - + - -
60D ALA* 3.8 44.0 - - + -
61D LEU* 4.2 9.6 - - + -
63D THR* 5.8 0.7 - - + -
64D LEU* 4.6 13.2 - - + -
101D ARG* 5.0 3.4 - - + -
102D GLU* 3.7 41.1 - - + +
105D VAL* 3.5 34.4 - - + +
106D MSE 4.2 21.1 - - + -
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Residues in contact with ASP 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA 3.1 18.8 + - - +
17D ALA* 3.8 7.2 - - - +
18D LEU 3.2 0.2 - - - -
19D PHE* 1.3 76.2 - - - +
21D VAL* 1.3 62.9 + - + +
23D ALA* 3.4 6.3 + - - +
24D GLU* 3.1 24.4 + - - +
101D ARG* 4.5 25.4 + - - +
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ALA* 3.0 24.2 + - + +
18D LEU* 3.8 7.6 - - + +
20D ASP* 1.3 74.5 - - + +
22D ALA* 1.3 62.8 + - + +
24D GLU* 3.2 6.0 + - - +
25D SER* 2.9 44.7 + - - +
26D GLY 5.9 0.2 - - - +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 2.8 32.8 + - + +
21D VAL* 1.3 76.4 - - - +
23D ALA* 1.3 63.3 + - - +
26D GLY* 3.0 33.2 + - - +
27D LEU* 4.0 14.4 + - + +
57D PHE* 4.3 4.5 - - + -
105D VAL* 3.6 28.5 - - + +
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE 2.8 24.3 + - - +
20D ASP 3.5 6.1 - - - +
21D VAL 3.2 0.2 - - - -
22D ALA* 1.3 75.2 - - - +
24D GLU* 1.3 60.6 + - + +
26D GLY* 4.4 1.4 + - - -
101D ARG* 3.2 38.4 - - + +
104D HIS* 4.2 22.7 + - - +
105D VAL* 3.3 11.4 - - + +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASP 3.1 13.6 + - - +
21D VAL* 3.9 4.3 - - - +
23D ALA* 1.3 81.6 - - - +
25D SER* 1.3 61.6 + - - +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 2.9 28.2 + - - +
24D GLU* 1.3 80.0 - - - +
26D GLY* 1.3 67.4 + - - +
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Residues in contact with GLY 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 5.9 0.2 - - - +
22D ALA* 3.0 25.5 + - - +
23D ALA 4.4 1.6 + - - -
24D GLU 3.6 1.6 - - - -
25D SER* 1.3 88.2 + - - +
27D LEU* 1.3 67.2 + - - +
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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