Contacts of the helix formed by residues 16 - 28 (chain l) in PDB entry 6AH0
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 GLN 16 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14l MET 3.9 2.8 + - - -
15l VAL* 1.3 74.1 - - - +
17l PRO* 1.4 60.5 - - - +
18l ILE 3.3 2.7 - - - -
19l ASN* 2.9 23.5 + - - +
20l LEU 3.2 8.3 + - - -
34n PHE 4.8 11.4 - - - -
41n VAL* 6.1 0.2 - - - -
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Residues in contact with PRO 17 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15l VAL 3.8 2.6 - - - -
16l GLN* 1.4 69.3 - - - +
18l ILE* 1.3 61.9 + - - +
20l LEU* 3.2 11.8 + - - +
21l ILE* 3.3 9.0 + - - -
34n PHE* 5.1 9.7 - - - -
39n ASN 5.6 4.3 - - - +
40n LEU 4.9 13.7 - - - +
41n VAL* 5.0 8.3 - - - +
61n VAL* 6.0 4.4 - - - -
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Residues in contact with ILE 18 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16l GLN 3.2 0.8 + - - -
17l PRO* 1.3 75.7 - - - +
19l ASN* 1.3 57.2 + - - +
21l ILE* 3.4 3.3 + - - +
22l PHE* 3.0 21.8 + - - -
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Residues in contact with ASN 19 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16l GLN* 2.9 9.9 + - - +
18l ILE* 1.3 76.3 - - - +
20l LEU* 1.3 53.8 + - - +
22l PHE* 2.9 4.7 + - - +
23l ARG* 2.7 31.9 + - - -
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Residues in contact with LEU 20 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16l GLN 3.2 7.2 + - - -
17l PRO* 3.2 8.8 + - - -
19l ASN* 1.3 75.6 - - - +
21l ILE* 1.3 56.0 + - - +
23l ARG* 3.2 4.4 + - - +
24l TYR* 2.8 24.3 + - - -
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Residues in contact with ILE 21 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17l PRO 3.3 10.1 + - - -
18l ILE* 3.4 4.7 + - - +
19l ASN 3.1 0.4 - - - -
20l LEU* 1.3 74.2 - - - +
22l PHE* 1.3 58.9 + - - +
24l TYR* 2.8 5.0 + - - +
25l LEU* 2.8 28.1 + - - -
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Residues in contact with PHE 22 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18l ILE 3.0 10.8 + - - -
19l ASN* 2.9 9.3 + - - +
21l ILE* 1.3 73.8 - - - +
23l ARG* 1.3 55.8 + - - +
25l LEU* 3.4 2.1 + - - +
26l GLN* 3.0 24.8 + - - -
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Residues in contact with ARG 23 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19l ASN 2.7 12.9 + - - -
20l LEU* 3.4 5.8 - - - +
21l ILE 3.0 0.2 - - - -
22l PHE* 1.3 73.7 - - - +
24l TYR* 1.3 59.0 + - - +
26l GLN* 3.3 1.4 + - - +
27l ASN* 2.8 28.8 + - - -
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Residues in contact with TYR 24 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20l LEU 2.8 11.7 + - - -
21l ILE* 2.8 11.2 + - - +
23l ARG* 1.3 71.4 - - - +
25l LEU* 1.3 56.7 + - - +
27l ASN* 3.8 0.6 - - - +
28l ARG* 3.0 25.5 + - - -
29l SER* 3.6 14.8 + - - +
47l ILE* 4.7 4.2 + - - +
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Residues in contact with LEU 25 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21l ILE 2.8 15.5 + - - -
22l PHE* 3.7 4.9 - - - +
24l TYR* 1.3 74.9 - - - +
26l GLN* 1.3 61.8 + - - +
28l ARG* 3.4 7.3 + - - -
47l ILE* 3.7 24.7 - - - +
48l ILE 5.7 3.5 - - - +
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Residues in contact with GLN 26 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22l PHE 3.0 14.7 + - - -
23l ARG* 3.3 2.2 + - - +
25l LEU* 1.3 75.3 - - - +
27l ASN* 1.3 61.4 + - - +
28l ARG* 3.5 0.7 + - - -
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Residues in contact with ASN 27 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23l ARG 2.8 15.8 + - - -
24l TYR* 3.9 1.3 - - - +
26l GLN* 1.3 77.5 - - - +
28l ARG* 1.3 64.4 + - - +
29l SER* 3.1 4.5 + - - +
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Residues in contact with ARG 28 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24l TYR 3.0 9.3 + - - -
25l LEU 3.4 7.0 + - - -
26l GLN 3.3 3.6 - - - -
27l ASN* 1.3 77.8 - - - +
29l SER* 1.3 67.0 + - - +
30l ARG* 3.6 1.7 + - - -
46l CYS* 5.6 5.7 - - - +
47l ILE 5.3 4.3 - - - +
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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