Contacts of the helix formed by residues 15 - 33 (chain F) in PDB entry 1N33
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 ASP 15 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F LEU* 1.3 76.5 - - - +
16F GLN* 1.3 70.3 + - - +
17F SER* 2.7 15.0 + - - -
18F GLN* 2.5 54.1 + - - +
19F LEU* 3.1 16.8 + - - +
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Residues in contact with GLN 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASP* 1.3 79.2 + - - +
17F SER* 1.3 61.8 + - - +
19F LEU* 2.9 38.3 + - - +
20F ALA* 3.3 8.5 + - - +
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Residues in contact with SER 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASP* 2.7 10.6 + - - -
16F GLN* 1.3 78.7 - - - +
18F GLN* 1.3 60.7 + - - -
19F LEU 3.4 0.5 + - - -
20F ALA* 3.7 17.9 + - - +
21F LEU* 3.9 6.4 + - - +
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Residues in contact with GLN 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ASN 4.1 8.1 + - - +
14F LEU* 3.1 36.8 - - + +
15F ASP* 2.5 54.9 + - - +
17F SER* 1.3 74.2 - - - +
19F LEU* 1.3 61.8 + - - +
21F LEU* 3.9 14.2 + - - +
22F GLU* 4.0 8.5 - - - +
84F ASN* 5.1 1.0 + - - -
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 5.9 1.8 - - + -
14F LEU* 4.0 19.7 - - + +
15F ASP 3.1 9.2 + - - +
16F GLN* 2.9 27.8 + - - +
18F GLN* 1.3 73.9 - - - +
20F ALA* 1.3 79.2 + - + +
21F LEU 3.0 2.5 - - - -
22F GLU* 2.6 30.8 + - + +
23F LYS* 3.2 37.3 + - + -
42F GLU* 5.0 0.7 - - - +
59F TYR* 4.0 35.0 - - + +
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Residues in contact with ALA 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLN* 3.3 8.6 + - - +
17F SER* 3.8 13.9 - - - +
19F LEU* 1.3 91.0 - - + +
21F LEU* 1.3 62.5 + - - +
23F LYS* 3.6 3.4 + - - +
24F GLU* 3.0 26.1 + - - +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F SER 3.9 6.0 + - - +
18F GLN* 3.9 11.4 + - - +
19F LEU 2.8 4.4 + - - -
20F ALA* 1.3 76.8 - - - +
22F GLU* 1.3 59.3 + - - +
24F GLU* 2.9 10.1 - - + +
25F ILE* 2.8 53.2 + - + +
82F ARG* 3.5 26.9 - - - +
84F ASN* 5.7 0.9 - - - +
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Residues in contact with GLU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 4.1 19.7 - - + -
14F LEU* 4.3 8.7 - - + -
18F GLN 4.0 8.9 - - - +
19F LEU* 2.6 15.7 + - + +
21F LEU* 1.3 73.3 - - - +
23F LYS* 1.3 52.5 + - + +
24F GLU 2.8 5.4 + - - -
25F ILE* 3.0 5.2 + - - +
26F ILE* 2.7 40.8 + - + +
82F ARG* 3.0 38.9 + - - -
84F ASN* 2.6 47.7 + - + +
85F VAL* 3.8 11.7 - - + +
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 5.7 1.6 - - + -
19F LEU* 3.2 36.8 + - + -
20F ALA* 4.1 6.3 - - - +
22F GLU* 1.3 79.0 - - + +
24F GLU* 1.3 63.2 + - - +
26F ILE* 3.8 16.8 - - + -
27F GLN* 3.2 38.4 + - - +
42F GLU* 2.8 40.5 + - - +
59F TYR* 6.1 0.7 - - + -
61F LEU* 4.8 9.2 - - + -
63F TYR* 4.6 13.9 - - - +
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Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ALA 3.0 16.0 + - - +
21F LEU* 2.9 20.9 - - + +
22F GLU 2.8 1.2 + - - -
23F LYS* 1.3 74.7 - - - +
25F ILE* 1.3 59.6 + - + +
26F ILE 2.9 4.2 + - - -
27F GLN* 3.0 4.3 + - - +
28F ARG* 2.7 68.4 + - - +
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Residues in contact with ILE 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 2.8 48.6 + - + +
22F GLU 3.8 5.2 - - - +
24F GLU* 1.3 81.9 - - + +
26F ILE* 1.3 57.6 + - + +
28F ARG* 3.9 19.0 - - - +
29F ALA* 2.8 32.5 + - + +
78F GLU* 5.4 9.2 - - + +
79F LEU* 5.2 6.7 - - + -
82F ARG* 4.0 37.5 - - + +
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Residues in contact with ILE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 4.1 23.3 - - + -
10F LEU* 4.3 11.7 - - + -
22F GLU* 2.7 29.1 + - + +
23F LYS* 3.6 14.4 - - - +
24F GLU 2.9 0.2 + - - -
25F ILE* 1.3 79.1 - - + +
27F GLN* 1.3 58.9 + - + +
29F ALA* 3.3 3.6 - - - +
30F LEU* 2.8 42.3 + - + +
61F LEU* 3.6 19.3 - - + -
63F TYR* 3.5 39.3 - - + +
79F LEU* 4.0 12.5 - - + +
85F VAL* 5.5 7.2 - - + -
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Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LYS* 3.2 28.6 - - - +
24F GLU* 3.0 3.3 + - - +
26F ILE* 1.3 79.2 - - + +
28F ARG* 1.3 58.4 + - - +
29F ALA 2.9 5.2 - - - -
30F LEU* 4.0 13.2 - - + -
31F GLU* 2.9 34.4 + - + +
37F VAL* 5.8 8.9 - - + +
63F TYR* 4.6 14.5 - - + +
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Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F GLU* 2.7 54.8 + - - +
25F ILE* 4.0 18.4 - - - +
27F GLN* 1.3 72.3 - - - +
29F ALA* 1.3 56.5 + - - +
31F GLU* 5.1 1.7 - - - +
32F ASN* 2.8 28.8 + - - +
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Residues in contact with ALA 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ILE* 2.8 22.5 + - + +
26F ILE 3.3 4.7 - - - +
27F GLN 2.9 0.6 - - - -
28F ARG* 1.3 78.3 - - - +
30F LEU* 1.3 69.8 + - - +
32F ASN* 2.7 16.8 + - - +
33F TYR* 3.0 19.1 + - + -
75F LEU* 4.3 5.6 - - + -
78F GLU* 4.4 20.4 - - + -
79F LEU* 4.2 15.0 - - + -
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Residues in contact with LEU 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 5.5 10.1 - - + -
26F ILE* 2.8 43.4 + - + +
27F GLN* 3.9 9.6 - - + +
29F ALA* 1.3 72.1 - - - +
31F GLU* 1.3 65.3 + - - +
33F TYR* 2.9 14.4 + - - +
35F ALA* 3.1 36.7 + - + +
37F VAL* 4.3 20.0 - - + -
63F TYR* 4.5 22.4 - - + -
65F VAL* 4.9 8.3 - - + -
67F MET* 5.9 0.4 - - - -
75F LEU* 4.1 27.8 - - + -
79F LEU* 4.6 11.4 - - + -
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F GLN* 2.9 19.6 + - + +
28F ARG* 5.1 1.8 - - - +
30F LEU* 1.3 73.3 - - - +
32F ASN* 1.3 59.8 + - - +
33F TYR 3.3 0.7 + - - -
34F GLY* 3.7 9.2 + - - -
35F ALA 4.1 12.3 + - - +
37F VAL* 5.7 1.5 - - + +
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Residues in contact with ASN 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ARG* 2.8 26.4 + - - +
29F ALA* 2.7 10.8 + - - +
31F GLU* 1.3 80.7 - - - +
33F TYR* 1.3 65.1 + - + -
34F GLY 3.4 0.4 - - - -
71F ARG* 3.4 10.7 + - - -
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Residues in contact with TYR 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ALA* 3.0 14.0 + - - -
30F LEU 2.9 4.6 + - - +
32F ASN* 1.3 85.9 - - + +
34F GLY* 1.3 61.0 + - - +
35F ALA 3.5 1.1 - - - +
67F MET* 4.2 6.7 - - + +
68F PRO* 4.3 3.1 - - - +
71F ARG* 3.2 55.9 + - + +
74F ASP* 3.7 27.4 + - + -
75F LEU* 3.4 60.6 - - + -
77F ARG* 5.7 1.2 - - - -
78F GLU* 3.7 40.0 + - + +
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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