Contacts of the helix formed by residues 105 - 116 (chain D) in PDB entry 1YCH
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 THR 105 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D VAL 4.8 0.2 + - - -
104D CYS* 1.3 82.6 - - - +
106D GLN* 1.3 60.8 + - - +
107D ARG* 4.3 4.0 - - - -
108D ALA* 3.0 14.9 + - - +
109D PHE* 3.0 24.1 + - - +
125D ILE* 4.1 2.2 - - - -
126D VAL 4.0 10.8 - - - +
143D GLU* 4.2 23.1 - - + +
150D PRO 5.7 0.2 - - - -
151D ASP* 2.9 24.8 + - - +
152D SER 4.4 2.5 - - - +
153D MET* 3.7 36.5 - - + -
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D THR* 1.3 71.5 - - - +
107D ARG* 1.3 74.6 + - + +
109D PHE* 3.1 11.8 + - - +
110D ASP* 3.0 50.2 + - - +
125D ILE* 3.2 38.5 - - + +
126D VAL 4.8 0.6 + - - -
127D LYS* 4.4 15.9 - - - +
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C TRP* 4.6 14.1 - - - +
105D THR* 3.4 2.9 - - - +
106D GLN* 1.3 84.1 - - + +
108D ALA* 1.3 57.3 + - - +
110D ASP* 3.2 17.4 + - - +
111D SER* 3.0 27.9 + - - -
150D PRO* 3.7 40.6 - - + +
151D ASP* 3.7 18.0 - - + +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D VAL* 4.5 7.4 - - + +
80D ASN 5.7 0.2 - - - +
82D THR* 3.7 11.2 - - + +
104D CYS* 3.8 12.8 - - + -
105D THR* 3.0 30.4 + - - +
106D GLN 3.1 0.2 - - - -
107D ARG* 1.3 76.0 - - - +
109D PHE* 1.3 59.0 + - - +
111D SER* 3.3 4.6 + - - -
112D LEU* 2.9 30.2 + - - +
151D ASP* 3.3 23.3 - - + +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D CYS* 3.6 11.4 - - - -
105D THR 3.0 14.1 + - - +
106D GLN* 3.1 19.3 + - - +
108D ALA* 1.3 77.4 - - - +
110D ASP* 1.3 69.8 + - - +
112D LEU* 3.6 5.0 - - - +
113D LYS* 2.8 61.6 + - + +
121D PHE* 3.6 31.0 - + - -
123D TYR* 3.6 48.5 - + + -
125D ILE* 4.2 12.6 - - + -
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C TRP* 5.4 1.1 - - - -
106D GLN* 3.0 41.8 + - - +
107D ARG* 3.6 20.1 + - - +
108D ALA 3.2 0.6 - - - -
109D PHE* 1.3 82.4 - - - +
111D SER* 1.3 56.8 + - - +
113D LYS* 3.2 25.5 + - - +
114D ALA* 3.0 27.5 + - - +
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Residues in contact with SER 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C TRP* 4.2 27.0 - - - +
82D THR* 2.8 34.0 + - - -
107D ARG 3.0 16.9 + - - -
108D ALA 3.5 2.5 - - - -
110D ASP* 1.3 73.4 - - - +
112D LEU* 1.3 56.1 + - - +
114D ALA* 2.9 2.6 + - - +
115D HIS* 2.7 54.8 + - - -
149D TRP* 4.7 0.2 - - - -
151D ASP* 4.3 4.7 - - - -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D VAL* 4.1 26.5 - - + -
82D THR* 3.2 22.0 - - + -
87D ALA* 4.5 7.4 - - + -
90D PHE* 4.1 30.5 - - + -
102D VAL* 4.4 11.2 - - + -
104D CYS* 4.5 9.2 - - - -
108D ALA 2.9 16.0 + - - +
109D PHE* 3.6 6.5 - - - +
111D SER* 1.3 76.7 + - - +
113D LYS* 1.3 61.4 + - - +
115D HIS* 5.8 0.2 - - + -
116D TYR* 3.1 54.9 + - + +
121D PHE* 4.6 13.9 - - + -
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PHE* 2.8 57.1 + - + +
110D ASP* 3.2 19.2 + - - +
112D LEU* 1.3 79.8 - - - +
114D ALA* 1.3 58.9 + - - +
117D SER* 3.0 35.4 + - - +
121D PHE* 4.9 9.6 - - + -
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C GLN 5.5 0.7 - - - +
376C TRP* 3.6 33.7 - - + -
377C VAL* 4.5 12.7 - - - +
379C ARG* 5.6 10.3 + - - +
110D ASP 3.0 12.5 + - - +
111D SER 2.9 7.7 + - - +
113D LYS* 1.3 79.9 - - - +
115D HIS* 1.3 61.8 + - - +
116D TYR 3.4 0.5 + - - -
117D SER* 4.1 6.2 + - - -
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Residues in contact with HIS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C TRP* 3.3 48.9 + + - +
377C VAL* 3.8 27.5 - - + +
721C FMN 5.2 1.4 + - - -
82D THR* 4.7 12.4 + - - +
83D GLU* 6.3 0.2 - - - -
84D SER* 6.1 4.9 - - - -
111D SER* 2.7 45.0 + - - +
114D ALA* 1.3 74.3 - - - +
116D TYR* 1.3 90.6 + + + +
149D TRP* 4.9 4.0 - + - -
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Residues in contact with TYR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D THR 5.1 2.5 + - - -
84D SER* 4.6 8.8 - - - -
87D ALA* 2.8 36.8 + - + +
88D GLY* 3.6 8.2 - - - -
90D PHE* 3.7 21.5 - + + -
91D PRO* 3.5 27.6 - - + -
112D LEU* 3.1 36.0 + - + +
114D ALA 3.2 0.4 - - - -
115D HIS* 1.3 108.4 - + + +
117D SER* 1.3 88.5 + - - +
118D HIS* 3.2 12.1 + - - +
119D ILE* 4.3 14.7 - - + +
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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