Contacts of the helix formed by residues 10 - 26 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PRO* 1.4 72.2 - - - +
12C GLU* 3.3 3.7 - - - +
13C ARG* 3.2 43.7 + - - +
14C LEU* 2.8 37.5 + - - +
41C VAL* 5.1 10.4 - - - +
45C ALA* 5.7 4.9 - - - +
49C HIS* 3.3 27.4 + - - -
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Residues in contact with PRO 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C SER* 1.4 93.4 - - - +
12C GLU* 1.3 58.3 + - + +
14C LEU* 3.4 12.4 + - + +
15C ALA* 3.0 22.3 + - - +
49C HIS* 3.7 27.6 - - + +
50C PHE* 4.1 14.6 - - + -
59C PHE* 3.2 33.6 - - + -
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C SER 3.3 2.2 - - - +
11C PRO* 1.3 79.4 - - + +
13C ARG* 1.3 64.3 + - - +
15C ALA* 3.0 6.4 + - - +
16C ALA* 3.0 23.5 + - - +
59C PHE* 4.3 13.9 - - + -
63C THR* 5.5 8.1 - - + +
10D SER* 2.9 48.3 + - - +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C SER* 3.2 41.5 + - - +
12C GLU* 1.3 78.4 - - - +
14C LEU* 1.3 55.6 + - - +
16C ALA* 3.4 7.5 + - - +
17C ALA* 3.0 28.8 + - - +
39C ALA* 3.8 31.1 + - + +
40C GLY* 5.6 0.6 - - - -
41C VAL* 4.6 13.2 - - + +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER* 2.8 32.0 + - - +
11C PRO* 3.6 6.7 - - + +
12C GLU 3.2 0.2 - - - -
13C ARG* 1.3 71.4 - - + +
15C ALA* 1.3 57.4 + - - +
17C ALA* 3.3 3.0 + - - -
18C LEU* 2.8 30.1 + - - +
35C VAL* 3.6 22.9 - - + +
39C ALA* 4.1 5.2 - - + -
41C VAL* 3.8 29.8 - - + -
45C ALA* 4.8 0.9 - - + +
46C VAL* 3.9 32.5 - - + +
49C HIS* 4.4 9.9 - - + -
50C PHE* 3.5 32.1 - - + -
56C MSE 5.4 2.9 - - + +
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PRO 3.0 14.0 + - - +
12C GLU* 3.0 8.7 + - - +
14C LEU* 1.3 73.2 - - - +
16C ALA* 1.3 60.6 + - - +
18C LEU* 3.5 2.6 + - - +
19C PHE* 3.0 27.9 + - - +
50C PHE* 5.7 0.2 - - - -
59C PHE* 4.0 11.4 - - + -
60C ALA* 4.0 19.7 - - - +
63C THR* 3.8 35.4 - - + +
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU 3.0 11.9 + - - +
13C ARG* 3.7 10.5 - - - +
15C ALA* 1.3 77.6 - - - +
17C ALA* 1.3 58.0 + - - +
19C PHE* 3.3 8.2 + - - +
20C ASP* 3.0 34.2 + - - +
63C THR* 5.7 0.4 - - - +
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Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG 3.0 18.1 + - - +
14C LEU 3.7 4.0 - - - +
16C ALA* 1.3 74.2 - - - +
18C LEU* 1.3 65.6 + - - +
20C ASP* 3.2 5.5 + - - +
21C VAL* 3.0 28.1 + - - +
35C VAL* 3.7 17.3 - - + +
38C ARG* 3.8 22.3 - - + +
39C ALA* 3.6 21.5 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU 2.8 20.7 + - - +
15C ALA 3.7 4.5 - - - +
16C ALA 3.4 0.2 - - - -
17C ALA* 1.3 73.2 - - - +
19C PHE* 1.3 65.2 + - - +
21C VAL* 3.2 2.8 + - - +
22C ALA* 2.9 23.9 + - + +
27C LEU* 3.9 13.7 - - + -
30C ALA* 4.0 9.0 - - + -
35C VAL* 3.9 13.8 - - + +
56C MSE 3.8 25.8 - - + -
57C PHE* 3.7 31.0 - - + -
60C ALA* 3.8 27.6 - - + -
109C PHE* 3.9 19.7 - - + -
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ALA 3.0 17.6 + - - +
16C ALA* 3.3 7.8 + - - +
18C LEU* 1.3 80.5 - - + +
20C ASP* 1.3 69.8 + - - +
22C ALA* 3.5 4.0 + - - +
23C ALA* 2.9 31.0 + - + +
60C ALA* 6.2 0.9 - - + -
64C LEU* 3.7 33.4 - - + -
98C ALA 4.9 0.4 - - - -
101C ARG* 3.8 23.8 - - + -
102C GLU* 3.6 40.2 - - + -
105C VAL* 3.7 23.6 - - + +
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Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ALA* 3.0 17.3 + - - +
17C ALA* 3.4 12.7 - - - +
19C PHE* 1.3 90.7 - - - +
21C VAL* 1.3 61.3 + - - +
23C ALA* 3.6 4.2 + - - +
24C GLU* 3.2 28.9 + - - +
38C ARG* 3.5 25.4 + - + +
101C ARG* 6.0 1.6 - - - -
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ALA 3.0 21.0 + - - +
18C LEU* 3.7 4.5 - - - +
20C ASP* 1.3 75.3 - - - +
22C ALA* 1.3 52.9 - - - +
24C GLU* 3.1 10.4 + - - +
25C SER* 2.7 45.3 + - - +
29C GLY* 3.4 35.4 - - - +
30C ALA* 3.9 6.7 - - + +
34C GLU* 3.8 32.8 - - + +
35C VAL* 4.8 2.7 - - + -
38C ARG* 3.8 23.3 - - + +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 2.9 17.8 + - + +
19C PHE 3.7 3.6 - - - +
21C VAL* 1.3 74.5 - - - +
23C ALA* 1.3 61.1 + - - +
26C GLY* 2.7 41.0 + - - +
27C LEU* 4.0 27.8 - - + +
30C ALA* 4.9 1.5 - - + +
104C HIS* 3.4 6.8 - - - -
105C VAL* 3.9 22.1 - - + +
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 4.8 1.4 - - - +
19C PHE* 2.9 25.3 + - + +
20C ASP* 3.9 5.4 - - - +
22C ALA* 1.3 73.1 - - - +
24C GLU* 1.3 63.3 + - + +
101C ARG* 3.9 40.9 - - + +
104C HIS* 3.1 21.9 + - - -
105C VAL* 3.6 12.5 - - + +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 4.0 13.0 - - - +
20C ASP* 3.2 10.4 + - - +
21C VAL* 3.1 8.3 + - - +
23C ALA* 1.3 82.1 - - + +
25C SER* 1.3 62.0 + - - +
26C GLY 3.7 0.2 - - - -
38C ARG* 2.7 45.3 + - - -
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 4.9 8.2 + - - -
21C VAL* 2.7 24.5 + - - +
24C GLU* 1.3 76.8 - - - +
26C GLY* 1.3 60.8 + - - +
28C GLU* 3.3 21.1 - - - +
29C GLY* 3.3 23.8 + - - -
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Residues in contact with GLY 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 6.2 1.6 - - - -
115A THR* 5.4 1.1 - - - -
22C ALA* 2.7 36.8 + - - -
24C GLU 3.7 0.8 - - - -
25C SER* 1.3 81.7 + - - +
27C LEU* 1.3 64.8 + - - -
28C GLU* 3.2 10.3 - - - -
29C GLY* 3.1 8.0 + - - -
30C ALA 4.1 1.0 + - - -
104C HIS* 4.1 17.8 - - - -
108C ALA* 5.6 2.2 - - - -
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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