Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 3N9Y
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 ASN 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY 3.4 1.4 - - - -
17A ASP* 1.3 76.7 - - - +
19A GLY* 1.3 52.2 + - - +
20A TRP* 2.9 16.6 + - - +
21A LEU* 2.9 40.7 + - + +
22A ASN* 2.8 38.5 + - - +
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Residues in contact with GLY 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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17A ASP 3.3 7.7 + - - -
18A ASN* 1.3 73.8 + - - +
20A TRP* 1.3 58.4 + - - +
22A ASN* 3.7 1.4 - - - +
23A LEU* 3.0 21.8 + - - +
53A LYS* 3.4 26.3 - - - +
55A GLY 3.0 35.8 + - - -
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Residues in contact with TRP 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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18A ASN* 2.9 11.5 + - - +
19A GLY* 1.3 74.0 - - - +
21A LEU* 1.3 61.7 + - - +
23A LEU* 3.3 18.9 + - + +
24A TYR* 2.9 28.6 + - - +
55A GLY* 3.6 35.3 + - - -
56A ASN* 4.1 6.1 - - + -
210A ASN 4.4 0.4 - - - -
211A LEU* 4.3 9.9 - - + -
212A PRO* 3.8 26.5 - - + -
215A LEU* 3.9 21.1 - - + -
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Residues in contact with LEU 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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18A ASN* 2.9 35.4 + - + +
20A TRP* 1.3 75.4 - - - +
22A ASN* 1.3 67.3 + - - +
24A TYR* 3.2 18.9 + - + +
25A HIS* 3.1 48.6 + - + +
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Residues in contact with ASN 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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15A PRO* 3.7 36.4 - - + +
16A GLY* 2.9 25.9 + - - +
18A ASN 2.8 23.9 + - - +
19A GLY 3.7 0.4 - - - +
20A TRP 3.3 0.2 - - - -
21A LEU* 1.3 75.6 - - - +
23A LEU* 1.3 58.0 + - - +
25A HIS* 3.4 8.5 + - - +
26A PHE* 3.0 28.8 + - - +
52A GLU* 4.5 7.9 - - - +
53A LYS* 3.1 33.4 + - - +
54A LEU* 3.9 8.0 - - + +
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Residues in contact with LEU 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 GLY 3.0 16.5 + - - +
20A TRP* 3.5 13.9 - - + +
22A ASN* 1.3 74.0 - - - +
24A TYR* 1.3 66.4 + - - +
26A PHE* 3.3 6.4 + - + +
27A TRP* 3.0 74.7 + - + +
54A LEU* 3.8 15.2 - - + +
55A GLY* 3.9 21.5 - - - +
210A ASN* 3.7 37.2 - - + +
211A LEU* 4.0 11.9 - - + -
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Residues in contact with TYR 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 TRP 2.9 14.4 + - - +
21A LEU* 3.2 22.2 + - + +
23A LEU* 1.3 76.8 - - - +
25A HIS* 1.3 74.0 + + - +
27A TRP* 3.5 10.0 + + + +
28A ARG* 3.0 71.2 + - + +
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Residues in contact with HIS 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 LEU* 3.1 47.5 + - + +
22A ASN* 4.0 7.6 - - - +
24A TYR* 1.3 84.4 - + - +
26A PHE* 1.3 65.1 + - - +
28A ARG* 3.1 42.8 + - - -
29A GLU* 3.0 41.2 + - - +
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Residues in contact with PHE 26 (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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22A ASN 3.0 17.2 + - - +
23A LEU* 3.3 11.9 + - + +
25A HIS* 1.3 76.7 - - - +
27A TRP* 1.3 80.0 + + - +
29A GLU* 5.3 0.2 - - - -
30A THR* 3.0 19.6 + - - +
31A GLY 2.9 47.0 + - - -
32A THR* 3.9 10.5 - - + -
35A VAL* 3.7 29.6 - - + -
38A HIS* 3.6 53.6 - + + +
54A LEU* 4.2 14.6 - - + -
210A ASN* 4.5 13.7 - - - -
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Residues in contact with TRP 27 (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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23A LEU* 3.0 58.3 + - + +
24A TYR* 4.0 7.6 - + + +
26A PHE* 1.3 90.6 - + - +
28A ARG* 1.3 63.6 + - - +
31A GLY* 3.5 18.7 + - - +
32A THR* 3.2 34.7 - - + +
207A PRO 5.2 1.6 - - - -
210A ASN* 4.9 5.3 - - + +
211A LEU* 4.4 14.6 - - + -
220A ARG* 3.9 35.7 - - - -
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Residues in contact with ARG 28 (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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24A TYR* 3.0 50.2 + - + +
25A HIS* 3.1 32.5 + - - +
27A TRP* 1.3 78.3 - - - +
29A GLU* 1.3 94.7 + - - +
30A THR 5.4 0.2 - - - -
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Residues in contact with GLU 29 (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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25A HIS* 3.0 27.7 + - - +
26A PHE* 5.3 0.2 - - - -
28A ARG* 1.3 113.2 + - - +
30A THR* 1.3 68.5 + - - +
45A LYS* 5.3 6.6 + - - -
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Residues in contact with THR 30 (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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26A PHE* 3.0 17.7 + - - -
27A TRP 4.4 0.7 - - - -
28A ARG 5.4 0.2 - - - -
29A GLU* 1.3 86.6 + - - +
31A GLY* 1.3 60.0 + - - +
34A LYS* 3.4 47.2 - - + +
37A LEU* 4.2 7.6 - - + -
38A HIS* 3.8 21.6 + - + +
41A GLN* 3.3 22.7 + - - +
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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