Contacts of the helix formed by residues 16 - 22 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13G ALA 4.9 0.2 - - - -
14G GLY 3.3 1.0 + - - -
15G PRO* 1.3 107.1 - - + +
17G VAL* 1.4 66.1 + - - +
18G HIS 2.9 3.4 - - - +
19G ILE* 2.8 36.1 + - + +
400H TRP* 3.7 10.9 + - - +
408H GLU* 3.1 40.2 - - + +
410H HIS* 3.3 27.6 - + + -
412H ASN* 3.4 43.3 + - + +
413H ASP* 3.6 24.1 + - + -
447H TYR* 5.9 3.1 - + - -
3550H DHB 6.2 0.4 - + - -
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Residues in contact with VAL 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ALA* 3.9 19.1 - - + -
14G GLY 3.3 15.6 + - - +
15G PRO 3.2 2.3 - - - +
16G TYR* 1.4 75.8 - - - +
18G HIS* 1.3 87.5 + - + +
19G ILE 3.0 1.0 + - - -
20G GLY* 3.0 4.0 + - - -
21G LEU* 2.9 48.3 + - + +
65G ASP 3.9 10.1 - - - +
67G PHE* 3.8 25.6 - - + -
132G ALA* 5.6 1.8 - - - -
400H TRP* 3.8 20.4 - - + +
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Residues in contact with HIS 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO 4.9 3.6 + - - -
16G TYR 2.8 1.4 + - - -
17G VAL* 1.3 85.9 - - + +
19G ILE* 1.3 60.6 - - - +
22G ALA* 2.7 58.9 + - + +
23G LEU* 3.3 0.7 + - - -
25G ALA 4.9 1.0 + - - -
26G ALA* 3.7 21.5 - - + +
64G ARG 4.6 0.9 - - - -
65G ASP* 3.7 24.9 + - + -
66G SER 3.1 21.0 + - - -
67G PHE* 4.6 3.8 - + + -
96G ALA* 3.6 8.7 - - + +
97G THR 3.5 21.5 - - - -
98G THR* 3.8 16.0 - - + +
410H HIS* 4.6 14.0 + - - +
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Residues in contact with ILE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G TYR* 2.8 27.8 + - + +
18G HIS* 1.3 76.2 - - - +
20G GLY* 1.3 58.8 + - - +
23G LEU* 3.0 22.6 - - - +
26G ALA* 4.1 7.2 - - + -
28G ASN* 4.1 11.6 + - - +
400H TRP* 3.8 20.4 - - + -
401H GLN 4.3 17.3 - - - +
408H GLU* 4.4 14.8 - - + +
409H ARG 3.7 36.1 - - - +
410H HIS* 3.8 14.8 - - + -
424H GLY 4.6 10.3 - - - +
425H GLY 4.9 0.9 - - - +
426H VAL* 3.2 18.6 - - + +
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Residues in contact with GLY 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL 3.0 4.6 + - - -
19G ILE* 1.3 80.6 - - - +
21G LEU* 1.3 71.7 + - - +
23G LEU* 3.3 10.4 - - - +
31G ARG* 4.3 5.7 + - - -
398H GLU* 4.3 7.8 - - - +
399H MET 4.6 0.7 - - - -
400H TRP* 3.7 31.5 - - - -
426H VAL* 3.9 14.9 - - - +
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G VAL* 2.9 25.8 + - + +
20G GLY* 1.3 87.4 - - - +
22G ALA* 1.4 59.4 + - - +
23G LEU* 3.9 4.9 - - - -
35G ILE 4.7 6.9 - - - +
36G TRP* 4.7 1.7 - - - -
67G PHE* 3.5 46.5 - - + -
69G GLU* 5.0 0.4 - - - +
94G ARG* 3.8 20.3 + - - +
398H GLU* 3.4 43.3 - - + +
400H TRP* 4.0 14.8 - - + -
464H GLY* 5.7 1.8 - - - -
473H LYS* 5.0 2.9 - - - +
475H ILE* 4.0 15.9 - - + -
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Residues in contact with ALA 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G HIS* 2.7 44.7 + - + +
21G LEU* 1.4 72.2 - - - +
23G LEU* 1.3 63.7 + - - +
24G GLU* 3.4 2.5 - - - -
25G ALA* 3.1 11.7 + - + -
26G ALA 3.0 17.0 + - - -
36G TRP* 3.6 29.8 - - + -
67G PHE* 4.7 4.3 - - + -
96G ALA* 4.5 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