Contacts of the helix formed by residues 9 - 26 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER* 1.3 70.0 + - - -
11B PRO* 3.3 10.7 - - - +
12B GLU* 2.4 37.9 + - - +
13B ARG* 3.1 46.6 + - - +
49B HIS* 4.7 6.3 + - - -
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Residues in contact with SER 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 1.3 78.8 - - - +
11B PRO* 1.4 60.0 - - - +
13B ARG* 3.1 13.8 + - - +
14B LEU* 2.7 37.0 + - - +
41B VAL* 3.7 30.0 - - - +
45B ALA* 4.9 2.5 - - - +
49B HIS* 3.6 27.3 - - - -
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Residues in contact with PRO 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.5 14.8 - - - +
10B SER* 1.4 90.6 - - - +
12B GLU* 1.3 62.4 + - - +
14B LEU* 3.2 3.8 + - + +
15B ALA* 2.8 24.3 + - - +
49B HIS* 3.5 33.6 - - + -
50B PHE* 3.9 22.4 - - + -
59B PHE* 3.4 31.5 - - + -
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 2.4 39.9 + - - +
11B PRO* 1.3 81.1 - - - +
13B ARG* 1.3 65.5 + - + +
15B ALA* 3.3 5.2 + - - +
16B ALA* 3.0 23.9 + - - +
59B PHE* 3.8 24.7 - - + -
63B THR* 5.5 7.8 - - + +
603B NDS 5.0 5.0 + - - -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.1 47.5 + - - +
10B SER* 3.6 14.1 + - - +
12B GLU* 1.3 76.3 - - + +
14B LEU* 1.3 58.4 + - - +
16B ALA* 3.3 7.3 + - - +
17B ALA* 3.0 28.2 + - - +
39B ALA* 3.8 14.5 - - + +
41B VAL* 4.4 17.7 - - + -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER* 2.7 34.7 + - - +
11B PRO* 3.6 3.6 - - + +
13B ARG* 1.3 72.9 - - - +
15B ALA* 1.3 55.9 - - - +
17B ALA* 3.2 0.9 + - - -
18B LEU* 2.9 30.7 + - - +
35B VAL* 3.6 15.2 - - + +
36B ALA* 4.1 11.7 - - - -
39B ALA* 4.1 18.4 - - + -
41B VAL* 4.2 10.3 - - + -
45B ALA 4.8 2.2 - - - +
46B VAL* 3.9 40.4 - - + +
49B HIS* 5.0 1.8 - - + -
50B PHE* 3.6 31.9 - - + -
56B MSE 5.0 6.1 - - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO 2.8 19.4 + - - +
12B GLU* 3.3 5.4 + - - +
14B LEU* 1.3 71.6 - - - +
16B ALA* 1.3 57.4 + - - +
18B LEU* 3.4 3.0 + - - +
19B PHE* 3.0 27.4 + - - +
50B PHE* 5.7 0.2 - - - -
56B MSE 5.8 1.1 - - - -
59B PHE* 3.8 7.6 - - + -
60B ALA* 3.8 29.2 - - - +
63B THR* 3.7 33.2 - - + +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU 3.0 17.3 + - - +
13B ARG* 3.8 6.5 - - - +
15B ALA* 1.3 73.7 - - - +
17B ALA* 1.3 61.8 + - - +
19B PHE* 3.3 8.3 + - - +
20B ASP* 3.0 37.8 + - - +
63B THR* 5.6 1.3 - - + +
67B LYS* 6.6 0.4 - - - -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG 3.0 17.4 + - - +
14B LEU 3.7 4.0 - - - +
16B ALA* 1.3 73.1 - - - +
18B LEU* 1.3 61.7 + - - +
20B ASP* 3.3 5.5 + - - +
21B VAL* 2.9 34.6 + - - +
35B VAL* 3.5 26.9 - - + +
38B ARG* 3.9 12.6 - - + -
39B ALA* 3.6 19.1 - - + +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 2.9 16.9 + - - +
15B ALA 3.7 4.3 - - - +
16B ALA 3.3 0.2 - - - -
17B ALA* 1.3 78.2 - - - +
19B PHE* 1.3 67.0 + - - +
21B VAL* 3.3 1.3 + - - +
22B ALA* 2.9 22.7 + - + +
27B LEU* 3.8 24.2 - - + -
30B ALA* 5.5 2.2 - - + -
35B VAL* 3.8 21.3 - - + +
56B MSE 4.1 13.9 - - + +
57B PHE* 3.6 40.8 - - + -
60B ALA* 3.8 27.8 - - + -
109B PHE* 3.9 11.0 - - + -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 3.0 14.6 + - - +
16B ALA* 3.3 11.4 - - - +
18B LEU* 1.3 81.7 - - - +
20B ASP* 1.3 70.2 + - - +
22B ALA* 4.6 2.0 - - - -
23B ALA* 2.8 32.2 + - + +
64B LEU* 3.8 32.3 - - + -
98B ALA 4.9 0.7 - - - -
101B ARG* 3.7 27.1 - - + -
102B GLU* 3.7 34.8 - - + -
105B VAL* 3.5 31.7 - - + +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.0 23.3 + - - +
17B ALA* 3.3 9.2 + - - +
19B PHE* 1.3 88.0 - - - +
21B VAL* 1.3 62.3 + - - +
23B ALA* 3.3 1.6 + - - +
24B GLU* 3.1 31.3 + - - +
38B ARG* 3.5 34.7 + - - +
101B ARG* 3.4 18.7 + - - +
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 2.9 25.9 + - - +
18B LEU* 3.9 4.0 - - - +
20B ASP* 1.3 70.3 - - - +
22B ALA* 1.3 58.8 + - - +
24B GLU* 3.2 3.2 + - - -
25B SER* 2.9 46.4 + - - +
26B GLY 3.7 1.0 + - - +
30B ALA* 3.7 26.5 - - + -
34B GLU* 4.1 26.0 - - + +
35B VAL* 4.6 5.4 - - + -
38B ARG* 3.9 33.0 - - + +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 2.9 17.4 + - + +
19B PHE 3.8 3.1 - - - +
21B VAL* 1.3 76.5 - - - +
23B ALA* 1.3 58.8 + - - +
26B GLY* 2.9 35.5 + - - -
27B LEU* 3.7 34.7 + - + +
30B ALA* 5.0 1.3 - - + +
104B HIS* 3.3 9.0 + - - -
105B VAL* 4.0 20.1 - - + -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 2.8 20.8 + - + +
20B ASP 3.7 4.7 - - - +
21B VAL 3.2 0.2 - - - -
22B ALA* 1.3 76.3 - - - +
24B GLU* 1.3 59.7 + - - +
101B ARG* 4.0 41.4 - - + +
104B HIS* 2.8 25.3 + - - +
105B VAL* 3.6 17.0 - - + +
115D THR* 5.1 0.2 - - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP 3.1 14.2 + - - +
21B VAL* 4.0 3.4 - - - +
23B ALA* 1.3 80.4 - - - +
25B SER* 1.3 60.8 + - - +
26B GLY 3.8 0.2 - - - -
38B ARG* 2.7 39.3 + - - -
101B ARG* 2.7 38.1 + - - +
115D THR* 3.9 11.3 - - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 2.9 26.7 + - - +
24B GLU* 1.3 80.4 - - - +
26B GLY* 1.3 64.9 + - - +
29B GLY* 5.2 3.6 + - - -
34B GLU* 5.4 1.4 + - - -
112D ARG* 5.8 0.5 + - - -
115D THR* 4.0 15.4 + - - +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL 4.0 1.6 - - - +
22B ALA* 2.9 25.2 + - - -
24B GLU 3.8 0.6 - - - -
25B SER* 1.3 84.5 + - - +
27B LEU* 1.3 66.3 + - - +
28B GLU* 3.4 4.5 - - - -
29B GLY* 4.0 1.9 + - - -
30B ALA* 4.0 12.3 + - - +
104B HIS* 3.9 16.1 - - - -
108B ALA* 5.7 0.2 - - - -
111D VAL* 5.9 2.5 - - - -
115D THR* 4.6 3.1 - - - -
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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