Contacts of the helix formed by residues 17 - 26 (chain A) in PDB entry 1SNL
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 4.5 16.2 - - - +
16A PHE* 1.3 83.0 + - - +
18A PRO* 1.3 64.0 - - - +
19A LYS* 3.0 24.2 + - - +
20A THR* 2.7 37.2 + - - -
21A PHE* 4.2 2.1 + - - +
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Residues in contact with PRO 18 (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 ARG* 5.7 4.0 - - - +
16A PHE* 3.7 12.8 - - + +
17A ASN* 1.3 88.3 - - - +
19A LYS* 1.3 66.9 + - + +
20A THR 3.2 0.2 - - - -
21A PHE* 3.2 36.6 + - + -
22A PHE* 3.3 2.4 + - - +
90A PHE* 5.2 12.1 - - + -
91A LEU* 5.4 9.4 - - + -
94A THR* 5.3 11.4 - - + +
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Residues in contact with LYS 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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15A ARG* 6.2 0.7 - - - +
17A ASN* 3.0 17.2 - - - +
18A PRO* 1.3 82.0 - - + +
20A THR* 1.3 63.5 + - - +
22A PHE* 3.3 15.3 + - - +
23A ILE* 3.4 26.4 + - + +
87A LEU* 5.1 20.4 - - + -
90A PHE* 6.5 0.2 - - - -
91A LEU* 5.5 8.8 - - + +
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Residues in contact with THR 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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17A ASN* 2.7 29.9 + - - -
18A PRO 3.2 1.2 - - - -
19A LYS* 1.3 74.5 - - - +
21A PHE* 1.3 68.8 + - - +
22A PHE 3.0 2.0 - - - -
23A ILE* 2.8 28.9 + - + +
24A LEU* 3.0 20.4 + - + +
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Residues in contact with PHE 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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17A ASN 4.2 1.4 + - - +
18A PRO* 3.2 24.4 + - + +
20A THR* 1.3 80.2 - - - +
22A PHE* 1.3 89.4 + + + +
24A LEU* 3.7 5.7 + - - +
25A HIS* 3.2 69.4 + + + +
33A LEU* 5.8 4.5 - - + -
90A PHE* 3.6 33.9 - + - -
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Residues in contact with PHE 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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18A PRO 3.3 3.6 + - - +
19A LYS* 3.3 12.5 + - - +
20A THR 3.0 0.2 - - - -
21A PHE* 1.3 97.4 - + + +
23A ILE* 1.3 55.0 + - + +
25A HIS* 3.6 3.3 + - - +
26A ASP* 2.4 72.6 + - - +
31A GLY* 3.5 27.1 - - - -
32A VAL* 4.2 4.9 - - - -
33A LEU* 4.1 26.5 - - + -
85A VAL* 4.5 6.3 - - + -
86A THR 4.7 0.4 - - - -
87A LEU* 3.9 34.5 - - + -
90A PHE* 3.9 40.2 - + + -
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Residues in contact with ILE 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 LYS* 3.5 29.6 - - + +
20A THR* 2.8 20.4 + - + +
22A PHE* 1.3 75.6 - - + +
24A LEU* 1.3 59.6 + - - +
26A ASP* 2.5 44.3 + - + +
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Residues in contact with LEU 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 THR* 3.0 17.3 + - + +
21A PHE* 4.1 5.8 - - - +
23A ILE* 1.3 81.4 - - - +
25A HIS* 1.3 73.7 + - + +
26A ASP 3.3 3.8 + - - +
27A ILE* 4.9 4.2 - - - +
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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 PHE* 3.2 54.5 + + + +
22A PHE* 4.0 4.7 - - - +
23A ILE 3.0 1.2 - - - -
24A LEU* 1.3 92.1 - - + +
26A ASP* 1.3 60.6 + - - +
27A ILE* 3.0 11.2 + - - +
33A LEU* 3.9 20.6 - - + +
37A GLU* 3.3 17.8 - - - +
41A LEU* 3.8 30.4 - - + +
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Residues in contact with ASP 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 PHE* 2.4 55.6 - - - +
23A ILE* 2.5 27.2 + - + +
24A LEU 4.4 2.4 - - - +
25A HIS* 1.3 69.1 - - - +
27A ILE* 1.3 63.5 + - - +
28A ASN 3.6 1.1 - - - -
29A SER* 3.7 20.3 + - - +
30A ASP* 4.8 7.4 - - - +
31A GLY* 4.3 8.5 + - - -
33A LEU* 3.3 22.1 - - - +
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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