Contacts of the helix formed by residues 16 - 22 (chain A) in PDB entry 1YKN
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 TYR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 3.3 1.4 - - - -
15A PRO* 1.3 106.6 - - + +
17A VAL* 1.3 66.0 + - - +
18A HIS 3.0 2.9 - - - +
19A ILE* 2.8 27.3 + - + +
400B TRP* 3.6 13.7 + - + -
408B GLU* 3.4 43.3 - - + +
410B HIS* 3.3 35.0 - + + -
412B ASN* 3.3 43.3 + - + +
413B ASP* 3.6 19.7 + - + -
447B TYR* 5.6 3.6 - + - -
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Residues in contact with VAL 17 (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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13A ALA* 3.8 27.6 - - + +
14A GLY 3.5 11.0 + - - +
15A PRO 3.4 2.3 - - - +
16A TYR* 1.3 78.1 - - - +
18A HIS* 1.3 76.6 + - + +
19A ILE 3.1 0.4 + - - -
20A GLY* 3.3 2.5 + - - -
21A LEU* 2.9 47.6 + - + +
65A ASP 4.2 10.3 - - - +
67A PHE* 3.9 21.8 - - + -
132A ALA* 5.4 2.0 - - - -
400B TRP* 3.6 28.9 - - + +
475B ILE* 4.8 0.2 - - + -
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Residues in contact with HIS 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 PRO 5.1 4.2 + - - -
16A TYR 2.9 1.4 + - - -
17A VAL* 1.3 86.0 - - + +
19A ILE* 1.4 62.8 + - - +
22A ALA* 2.9 46.7 + - + +
23A LEU 3.6 0.3 + - - -
25A ALA 5.1 0.6 + - - -
26A ALA* 3.5 25.4 - - + +
65A ASP* 3.8 21.3 + - + +
66A SER 3.0 24.9 + - - -
67A PHE* 4.2 5.8 - + + +
96A ALA* 3.3 19.1 - - + +
97A THR 3.0 24.5 - - - -
98A THR* 4.2 13.2 - - + +
410B HIS* 4.6 14.5 + - - +
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Residues in contact with ILE 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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16A TYR* 2.8 18.5 + - + +
18A HIS* 1.4 78.8 - - - +
20A GLY* 1.3 57.7 + - - +
23A LEU* 3.2 18.1 - - - +
26A ALA* 4.1 6.1 - - + -
28A ASN* 4.1 11.3 + - - +
400B TRP* 3.8 22.9 - - + -
401B GLN 4.5 13.5 - - - +
408B GLU* 4.9 9.0 - - + +
409B ARG 3.4 38.8 - - - +
410B HIS* 3.8 24.9 - - + -
424B GLY 4.7 8.1 - - - +
425B GLY 4.7 3.4 - - - +
426B VAL* 3.3 17.9 - - + +
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Residues in contact with GLY 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 VAL 3.3 3.4 + - - -
19A ILE* 1.3 80.9 - - - +
21A LEU* 1.4 74.8 + - - +
23A LEU* 3.3 12.5 - - - +
31A ARG* 4.2 5.9 + - - -
398B GLU* 4.5 5.2 - - - +
399B MET 4.7 0.4 - - - +
400B TRP* 3.6 25.5 - - - -
426B VAL* 3.6 18.8 - - - +
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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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17A VAL* 2.9 21.3 + - + +
20A GLY* 1.4 92.6 - - - +
22A ALA* 1.3 59.7 + - - +
23A LEU* 4.0 3.1 - - - -
31A ARG* 6.0 0.2 - - - -
34A GLU* 6.1 0.4 - - - -
35A ILE 4.8 2.3 - - - +
36A TRP* 4.3 5.7 - - - -
67A PHE* 3.6 47.6 - - + -
94A ARG* 3.7 17.4 + - - +
398B GLU* 3.4 43.7 - - + +
400B TRP* 3.7 17.3 - - + -
464B GLY* 5.6 2.2 - - - -
473B LYS* 5.1 3.4 - - - +
475B ILE* 3.8 23.1 - - + -
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Residues in contact with ALA 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 HIS* 2.9 42.2 + - + +
21A LEU* 1.3 71.1 - - - +
23A LEU* 1.3 59.2 + - - +
24A GLU* 3.5 2.5 - - - -
25A ALA* 3.5 6.6 + - + -
26A ALA* 2.9 21.5 + - - +
36A TRP* 3.2 41.3 - - + -
67A PHE* 4.7 3.1 - - + -
96A ALA* 4.5 1.1 - - + -
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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