Contacts of the helix formed by residues 16 - 22 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K ALA 4.9 0.4 + - - -
14K GLY 3.4 1.2 - - - -
15K PRO* 1.3 105.0 - - + +
17K VAL* 1.4 53.7 + - - +
18K HIS 3.1 5.6 - - - -
19K ILE* 2.9 38.6 + - + +
400L TRP* 3.7 9.1 + - - +
408L GLU* 3.1 43.3 - - + +
410L HIS* 3.3 44.9 - + + -
412L ASN* 3.4 15.7 + - + +
413L ASP* 3.2 39.0 + - + +
447L TYR* 5.5 2.2 - + - -
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Residues in contact with VAL 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K ALA* 3.8 27.9 + - + +
14K GLY 3.5 12.1 + - - +
15K PRO 3.7 2.4 + - - +
16K TYR* 1.4 73.3 - - - +
18K HIS* 1.3 70.8 + - + +
20K GLY* 2.8 7.6 + - - -
21K LEU* 2.8 56.7 + - + +
65K ASP 4.2 9.4 - - - +
67K PHE* 3.9 26.9 - - + -
132K ALA* 5.5 1.3 - - - -
400L TRP* 3.8 19.2 - - + -
475L ILE* 4.7 0.2 - - + -
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Residues in contact with HIS 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K PRO 5.3 2.5 + - - -
16K TYR 3.0 0.4 + - - -
17K VAL* 1.3 83.0 - - + +
19K ILE* 1.4 65.8 + - - +
20K GLY 3.0 1.3 - - - -
22K ALA* 2.8 63.6 + - + +
23K LEU* 3.3 1.4 + - - -
25K ALA* 4.4 4.9 - - + +
26K ALA* 3.8 14.3 - - + +
64K ARG 4.6 0.9 - - - -
65K ASP* 3.9 22.2 + - + -
66K SER 3.5 19.4 + - - -
67K PHE* 4.6 4.9 - + + -
96K ALA* 3.6 9.3 - - + +
97K THR 3.5 19.3 - - - -
98K THR* 3.7 17.6 - - + +
410L HIS* 4.5 15.4 + - - +
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Residues in contact with ILE 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K TYR* 2.9 22.8 + - + +
18K HIS* 1.4 78.1 - - - +
20K GLY* 1.4 60.5 + - - +
23K LEU* 3.5 13.4 - - - +
26K ALA* 3.9 8.1 - - + -
28K ASN* 3.9 13.6 + - - +
400L TRP* 3.8 22.0 - - + -
401L GLN 4.4 14.6 - - - +
408L GLU* 4.6 7.0 - - + +
409L ARG* 3.1 40.2 - - + +
410L HIS* 3.6 27.6 - - + -
425L GLY* 5.3 3.1 - - - +
426L VAL* 3.1 25.6 - - + +
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Residues in contact with GLY 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K VAL 2.8 7.2 + - - -
19K ILE* 1.4 81.7 - - - +
21K LEU* 1.3 72.8 + - - +
23K LEU* 3.4 12.3 - - - +
31K ARG* 4.2 5.5 + - - -
398L GLU* 4.7 5.7 - - - +
399L MET 4.7 0.8 - - - +
400L TRP* 3.6 28.8 - - - -
426L VAL* 3.9 12.4 - - - +
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Residues in contact with LEU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K VAL* 2.8 22.6 + - + +
20K GLY* 1.3 86.8 - - - +
22K ALA* 1.3 59.8 + - - +
23K LEU* 3.9 4.3 - - - -
31K ARG* 5.6 0.7 - - - +
34K GLU* 5.9 0.9 - - - -
35K ILE 4.7 2.9 - - - +
36K TRP* 4.0 7.4 - - - -
67K PHE* 3.8 31.9 - - + -
94K ARG* 3.5 17.1 + - - +
398L GLU* 3.3 48.0 - - + +
400L TRP* 3.6 30.5 - - + -
464L GLY* 5.6 1.8 - - - -
473L LYS* 5.2 3.8 - - - +
475L ILE* 3.9 17.0 - - + -
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Residues in contact with ALA 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K HIS* 2.8 45.9 + - + +
21K LEU* 1.3 75.6 - - - +
23K LEU* 1.3 65.4 + - - +
24K GLU* 3.3 2.7 - - - -
25K ALA* 3.2 6.9 + - + -
26K ALA 3.1 15.9 + - - -
36K TRP* 3.6 33.9 - - + -
67K PHE* 4.7 4.0 - - + -
96K ALA* 4.6 1.6 - - + -
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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