Contacts of the helix formed by residues 16 - 22 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14I GLY* 3.2 1.2 - - - -
15I PRO* 1.3 105.3 - - + +
17I VAL* 1.4 56.8 + - - +
18I HIS 3.0 3.1 - - - +
19I ILE* 2.8 43.5 + - + +
400J TRP* 3.7 8.1 + - - +
408J GLU* 3.3 43.3 - - + +
410J HIS* 3.4 30.3 - + + -
412J ASN* 3.3 41.0 + - + +
413J ASP* 3.7 23.3 + - + -
447J TYR* 5.8 2.5 - + - -
4550J DHB 5.8 0.4 - + - -
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ALA* 3.6 27.3 + - + +
14I GLY 3.3 17.2 + - - +
15I PRO 3.2 3.8 - - - +
16I TYR* 1.4 77.2 - - - +
18I HIS* 1.3 88.6 + - + +
20I GLY* 3.1 12.6 + - - -
21I LEU* 3.1 29.8 + - + +
65I ASP 4.1 12.1 - - - +
67I PHE* 4.3 19.7 - - + -
132I ALA* 5.6 1.8 - - - -
400J TRP* 3.8 22.6 - - + +
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Residues in contact with HIS 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I PRO 5.3 3.1 + - - -
16I TYR 3.0 1.4 + - - -
17I VAL* 1.3 89.8 - - + +
19I ILE* 1.3 67.2 + - - +
21I LEU 4.8 0.2 - - - -
22I ALA* 2.8 61.6 + - + +
23I LEU 3.3 0.3 + - - -
25I ALA* 4.9 2.2 + - + -
26I ALA* 3.6 15.6 - - + +
65I ASP* 3.9 16.9 + - + -
66I SER 3.3 21.4 + - - -
67I PHE* 4.7 4.3 - + - -
96I ALA* 3.7 7.6 - - + +
97I THR 3.4 20.2 - - - -
98I THR* 3.6 21.6 - - + +
410J HIS* 4.7 14.4 + - + -
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Residues in contact with ILE 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I TYR* 2.8 26.5 + - + +
18I HIS* 1.3 79.6 - - - +
20I GLY* 1.3 59.1 + - - +
23I LEU* 3.3 15.8 - - - +
26I ALA* 3.9 6.1 - - - -
28I ASN* 4.2 11.6 + - - +
400J TRP* 3.6 17.7 - - + -
401J GLN 4.2 11.9 - - - +
408J GLU* 5.5 4.5 - - + +
409J ARG* 3.7 28.7 - - + +
410J HIS* 3.8 24.7 - - + -
424J GLY 4.2 7.9 - - - +
425J GLY 3.6 25.6 - - - +
426J VAL* 3.3 23.7 - - + +
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL 3.1 5.1 + - - -
19I ILE* 1.3 82.6 - - - +
21I LEU* 1.3 72.3 + - - +
23I LEU* 3.6 9.6 - - - +
31I ARG* 4.3 4.2 + - - -
398J GLU* 4.3 8.1 - - - +
399J MET 4.7 0.4 - - - +
400J TRP* 3.6 31.0 - - - -
426J VAL* 3.9 14.9 - - - +
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 3.1 26.6 + - + +
20I GLY* 1.3 90.4 - - - +
22I ALA* 1.4 60.5 + - - +
23I LEU* 3.9 4.7 - - - -
31I ARG* 5.9 0.2 - - - +
34I GLU* 6.0 0.4 - - - -
35I ILE 4.8 2.8 - - - +
36I TRP* 4.2 6.9 - - - -
67I PHE* 3.5 44.6 - - + -
69I GLU* 5.3 0.2 - - - +
94I ARG* 3.7 18.1 + - - +
398J GLU* 3.4 42.8 - - + +
400J TRP* 3.8 20.6 - - + -
464J GLY* 5.7 1.6 - - - -
473J LYS* 5.4 2.9 - - - +
475J ILE* 3.9 11.0 - - + -
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Residues in contact with ALA 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I HIS* 2.8 41.9 + - + +
21I LEU* 1.4 73.8 - - - +
23I LEU* 1.3 60.4 + - - +
24I GLU* 3.2 3.8 + - - -
25I ALA* 3.3 6.1 + - + -
26I ALA* 2.8 25.6 + - - +
36I TRP* 3.6 33.2 - - + -
67I PHE* 4.4 5.4 - - + -
96I ALA* 4.6 0.2 - - + -
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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