Contacts of the helix formed by residues 105 - 116 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A CYS* 1.3 82.5 - - - +
106A GLN* 1.3 58.9 + - - +
107A ARG* 3.6 2.6 + - - -
108A ALA* 3.0 24.4 + - - +
109A PHE* 2.9 24.6 + - - +
125A ILE* 4.3 2.4 - - - +
126A VAL 4.0 13.5 - - - +
143A GLU* 5.0 14.1 - - + +
150A PRO 5.7 0.2 - - - -
151A ASP* 3.1 26.1 + - - +
152A SER 4.1 3.1 - - - +
153A MET* 3.7 32.5 - - + +
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Residues in contact with GLN 106 (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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105A THR* 1.3 71.7 - - - +
107A ARG* 1.3 71.8 + - + +
109A PHE* 3.0 16.7 + - - +
110A ASP* 2.9 56.6 + - - +
125A ILE* 3.3 38.6 - - + +
126A VAL 4.7 0.4 + - - -
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Residues in contact with ARG 107 (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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105A THR* 3.4 2.1 + - - +
106A GLN* 1.3 82.5 - - + +
108A ALA* 1.3 62.4 + - - +
110A ASP* 3.4 16.6 + - - +
111A SER* 3.0 23.6 + - - -
150A PRO* 3.8 33.9 - - + +
151A ASP* 3.7 23.6 - - + +
346B GLY 5.4 0.6 + - - -
347B TRP* 4.1 22.6 - - - +
376B TRP* 6.1 2.4 - - - -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.4 5.8 - - + +
82A THR* 3.7 17.3 - - + +
104A CYS* 3.8 12.6 - - + -
105A THR* 3.0 34.3 + - - +
107A ARG* 1.3 74.8 - - - +
109A PHE* 1.3 56.1 + - - +
111A SER* 3.1 4.3 + - - -
112A LEU* 2.7 36.5 + - - +
151A ASP* 3.3 19.7 - - + +
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Residues in contact with PHE 109 (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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104A CYS* 3.6 11.8 - - - -
105A THR 2.9 13.7 + - - +
106A GLN* 3.0 18.4 + - - +
108A ALA* 1.3 76.2 - - - +
110A ASP* 1.3 72.1 + - - +
112A LEU* 3.4 6.4 + - - +
113A LYS* 3.1 67.2 + - + +
121A PHE* 4.0 13.7 - + - -
123A TYR* 3.2 60.3 - + - -
125A ILE* 4.1 10.8 - - + -
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Residues in contact with ASP 110 (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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106A GLN* 2.9 46.4 + - - +
107A ARG* 3.4 23.2 - - - +
108A ALA 3.2 0.2 - - - -
109A PHE* 1.3 81.3 - - - +
111A SER* 1.3 63.8 + - - +
113A LYS* 3.3 7.2 + - - +
114A ALA* 3.0 22.2 + - - +
376B TRP* 5.2 2.2 - - - +
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Residues in contact with SER 111 (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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82A THR* 2.6 32.2 + - - -
107A ARG 3.0 11.3 + - - -
108A ALA* 3.3 6.1 - - - -
110A ASP* 1.3 74.8 - - - +
112A LEU* 1.3 60.7 - - - +
114A ALA* 2.9 2.4 + - - +
115A HIS* 2.8 52.3 + - - -
151A ASP* 4.6 1.8 - - - -
376B TRP* 4.1 28.3 - - - +
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Residues in contact with LEU 112 (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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79A VAL* 4.0 27.8 - - + -
82A THR* 3.7 19.1 - - + -
87A ALA* 4.5 8.5 - - + -
90A PHE* 3.9 32.7 - - + -
102A VAL* 4.7 2.5 - - + -
104A CYS* 4.7 9.9 - - - -
108A ALA 2.7 23.1 + - - +
109A PHE* 3.6 7.0 - - - +
111A SER* 1.3 73.5 - - - +
113A LYS* 1.3 61.7 + - - +
115A HIS* 6.0 0.2 - - - +
116A TYR* 3.0 57.3 + - + +
117A SER 3.9 0.2 + - - -
121A PHE* 4.5 15.9 - - + -
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Residues in contact with LYS 113 (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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109A PHE* 3.1 60.6 + - + +
110A ASP* 3.8 6.7 - - - +
112A LEU* 1.3 75.5 - - - +
114A ALA* 1.3 57.9 + - - +
117A SER* 3.1 37.1 + - - +
119A ILE 4.1 11.0 + - - +
120A ASP* 4.2 15.6 + - - +
121A PHE* 3.8 32.0 + - + +
123A TYR* 5.2 2.4 - - - -
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Residues in contact with ALA 114 (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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110A ASP 3.0 12.1 + - - +
111A SER 2.9 8.3 + - - +
113A LYS* 1.3 79.9 - - - +
115A HIS* 1.3 63.1 + - - +
116A TYR 3.3 1.7 + - - -
117A SER* 5.0 2.4 + - - -
375B GLN 5.5 0.7 - - - +
376B TRP* 3.4 33.7 - - + -
377B VAL* 3.6 19.0 - - + +
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Residues in contact with HIS 115 (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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82A THR* 4.9 11.4 + - - -
84A SER* 5.4 8.2 + - - -
111A SER* 2.8 46.8 + - - +
112A LEU* 5.6 0.2 - - + -
114A ALA* 1.3 71.2 - - - +
116A TYR* 1.3 95.8 + + + +
149A TRP* 5.2 4.1 - + - -
376B TRP* 3.3 55.7 - + + +
377B VAL* 4.7 18.7 - - + +
711B FMN 5.3 1.4 + - - -
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Residues in contact with TYR 116 (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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82A THR 5.4 1.8 + - - -
84A SER* 5.2 5.0 - - - -
87A ALA* 3.0 34.5 + - + +
88A GLY* 3.7 8.2 - - - -
90A PHE* 3.9 16.2 - + + -
91A PRO* 3.8 25.6 - - + -
112A LEU* 3.0 43.1 + - + +
114A ALA 3.2 0.4 - - - -
115A HIS* 1.3 110.0 - - + +
117A SER* 1.3 83.6 + - - +
118A HIS* 3.3 7.1 + - - +
119A ILE* 4.1 15.9 - - + +
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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