Contacts of the helix formed by residues 105 - 116 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C VAL 4.8 0.4 + - - +
104C CYS* 1.3 80.5 - - - +
106C GLN* 1.3 59.6 + - - +
107C ARG* 3.8 2.5 + - - +
108C ALA* 3.2 15.2 + - - +
109C PHE* 2.9 26.5 + - - +
125C ILE* 4.3 2.0 - - - +
126C VAL 4.0 10.5 - - - +
143C GLU* 4.3 19.7 - - + -
150C PRO 5.7 0.4 - - - -
151C ASP* 3.1 24.6 + - - +
152C SER 4.3 2.5 - - - +
153C MET* 3.5 41.5 - - + -
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C THR* 1.3 72.3 - - - +
107C ARG* 1.3 71.3 + - + +
109C PHE* 3.0 18.7 + - - +
110C ASP* 3.0 48.1 + - - +
125C ILE* 3.5 35.8 - - + +
126C VAL 4.7 0.8 + - - -
127C LYS* 4.2 13.1 + - - +
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C THR* 3.5 2.4 + - - +
106C GLN* 1.3 81.8 - - + +
108C ALA* 1.3 61.9 + - - +
110C ASP* 3.2 18.1 + - - +
111C SER* 3.0 23.4 + - - -
150C PRO* 3.0 42.8 - - + +
151C ASP* 3.7 20.6 - - + +
346D GLY 5.3 1.8 + - - -
347D TRP* 4.2 24.1 - - - +
376D TRP* 5.7 4.6 - - - -
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 4.5 7.0 - - + +
80C ASN 5.6 0.4 - - - +
82C THR* 3.8 14.4 - - + +
104C CYS* 3.9 10.5 - - + -
105C THR* 3.2 33.0 + - - +
106C GLN 3.1 0.6 - - - -
107C ARG* 1.3 75.1 - - - +
109C PHE* 1.3 53.9 + - - +
111C SER* 3.1 4.0 + - - -
112C LEU* 2.7 37.3 + - - +
151C ASP* 3.2 23.1 - - + +
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C CYS* 4.0 13.6 - - - -
105C THR 2.9 13.9 + - - +
106C GLN* 3.3 24.5 - - - +
108C ALA* 1.3 77.0 - - - +
110C ASP* 1.3 62.7 + - - +
112C LEU* 3.4 5.1 + - - +
113C LYS* 3.1 61.1 + - + +
121C PHE* 3.7 30.7 - + - -
123C TYR* 3.5 49.8 - + - -
125C ILE* 4.0 14.1 - - + -
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLN* 3.0 41.6 + - - +
107C ARG* 3.5 24.6 - - - +
108C ALA 3.1 0.2 - - - -
109C PHE* 1.3 81.8 - - - +
111C SER* 1.3 61.3 + - - +
113C LYS* 3.3 17.9 + - - +
114C ALA* 3.1 21.5 + - - +
376D TRP* 5.5 0.9 - - - +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR* 2.9 27.4 + - - -
107C ARG 3.0 13.2 + - - -
108C ALA 3.5 4.3 - - - -
110C ASP* 1.3 72.9 - - - +
112C LEU* 1.3 62.3 + - - +
114C ALA* 3.0 6.0 + - - +
115C HIS* 2.8 60.1 + - - -
149C TRP* 4.8 0.2 - - - -
151C ASP* 4.4 5.2 - - - -
376D TRP* 4.3 20.2 - - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 4.3 17.9 - - + -
82C THR* 3.3 21.5 - - + -
87C ALA* 4.6 4.0 - - + -
90C PHE* 4.0 30.0 - - + -
102C VAL* 4.2 24.9 - - + -
104C CYS* 4.3 12.8 - - - -
108C ALA 2.7 20.0 + - - +
109C PHE* 3.6 6.7 - - - +
111C SER* 1.3 74.0 - - - +
113C LYS* 1.3 60.8 + - - +
115C HIS* 4.9 0.7 - - - -
116C TYR* 3.2 52.2 + - + +
117C SER 3.8 0.3 + - - -
121C PHE* 4.5 13.9 - - + -
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Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 3.1 56.4 + - + +
110C ASP* 3.7 17.1 + - - +
111C SER 3.2 0.2 - - - -
112C LEU* 1.3 76.6 - - - +
114C ALA* 1.3 59.3 + - - +
117C SER* 2.9 36.5 + - - +
121C PHE* 5.0 9.6 - - + -
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ASP 3.1 12.5 + - - +
111C SER 3.0 7.3 + - - +
113C LYS* 1.3 79.3 - - - +
115C HIS* 1.3 62.4 + - - +
116C TYR* 3.3 2.1 + - - -
117C SER* 4.6 3.5 + - - -
375D GLN 5.4 0.7 - - - +
376D TRP* 3.7 32.5 - - + -
377D VAL* 4.5 11.8 - - - +
379D ARG* 5.9 5.6 - - - +
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Residues in contact with HIS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR* 4.5 14.2 + - - -
83C GLU* 6.0 0.8 - - - -
84C SER* 6.3 2.9 - - - -
111C SER* 2.8 47.1 + - - +
112C LEU* 4.9 0.4 - - - -
114C ALA* 1.3 72.0 - - - +
116C TYR* 1.3 97.8 + + + +
149C TRP* 4.8 4.6 - + - -
376D TRP* 3.2 44.3 + + + +
377D VAL* 3.9 27.3 - - + +
731D FMN 5.2 2.0 + - - -
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Residues in contact with TYR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR* 5.2 2.6 + - - -
84C SER* 5.1 6.8 + - - -
87C ALA* 2.8 37.1 + - + +
88C GLY* 3.7 8.4 + - - -
90C PHE* 3.8 21.8 - + + -
91C PRO* 3.6 26.0 - - + -
112C LEU* 3.2 33.3 + - + +
114C ALA 3.2 0.8 - - - -
115C HIS* 1.3 109.0 - + + +
117C SER* 1.3 85.3 + - - +
118C HIS* 3.4 6.6 + - - +
119C ILE* 4.6 13.5 - - + +
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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