Contacts of the helix formed by residues 120 - 128 (chain C) in PDB entry 1YIT
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 ASP 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C VAL* 5.6 1.9 - - + +
116C ALA 4.7 2.2 - - - +
117C ALA 3.7 12.6 - - - +
118C THR 3.2 4.0 - - - -
119C ALA* 1.3 78.4 - - - +
121C ALA* 1.3 63.3 + - - +
122C ASP* 2.9 22.8 + - - +
123C LEU* 3.0 36.9 + - + +
124C VAL* 3.1 12.7 + - - +
136C VAL* 3.9 2.5 - - - -
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Residues in contact with ALA 121 (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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119C ALA 3.9 1.0 + - - -
120C ASP* 1.3 70.7 + - - +
122C ASP* 1.3 64.2 + - - +
124C VAL* 3.7 6.0 + - - +
125C ALA* 3.2 22.2 + - - +
131C PHE* 3.8 13.4 - - + -
133C ARG 5.0 1.8 - - - +
134C ASP* 3.5 29.2 - - - +
136C VAL* 3.3 18.8 - - + +
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Residues in contact with ASP 122 (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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120C ASP* 2.9 11.1 + - - +
121C ALA* 1.3 77.0 - - - +
123C LEU* 1.3 67.4 + - - +
125C ALA* 3.1 7.3 + - - +
126C ASP* 2.9 30.0 + - - +
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Residues in contact with LEU 123 (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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26C VAL* 3.7 37.2 - - + -
117C ALA* 4.0 23.3 - - + +
120C ASP* 3.0 31.5 + - + +
122C ASP* 1.3 74.4 - - - +
124C VAL* 1.3 53.5 + - - +
126C ASP* 2.7 19.9 + - + +
127C ARG* 2.6 35.1 + - - +
229C PRO* 4.8 7.7 - - + +
230C GLY* 4.5 6.7 - - - -
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Residues in contact with VAL 124 (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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117C ALA 4.1 4.0 - - - +
118C THR* 3.7 22.2 - - - +
120C ASP 3.1 14.3 + - - +
121C ALA* 3.7 8.3 - - - +
123C LEU* 1.3 78.4 - - - +
125C ALA* 1.3 59.0 + - - +
127C ARG* 3.5 0.9 + - - +
128C GLY 3.5 3.6 + - - -
129C HIS* 3.4 21.8 + - + +
131C PHE* 3.9 18.6 - - + -
136C VAL* 4.3 7.0 - - + -
230C GLY 3.2 22.4 + - - +
231C ARG 4.6 2.9 - - - +
232C LEU* 3.7 38.4 - - + +
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Residues in contact with ALA 125 (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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121C ALA 3.2 13.1 + - - +
122C ASP* 3.1 11.0 + - - +
123C LEU 3.1 0.8 - - - -
124C VAL* 1.3 74.1 - - - +
126C ASP* 1.3 66.4 + - - +
128C GLY* 3.0 15.4 + - - -
129C HIS 4.1 6.3 - - - +
131C PHE* 4.0 17.7 - - + -
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Residues in contact with ASP 126 (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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13090 U 5.6 1.2 + - - -
122C ASP* 2.9 25.3 + - - +
123C LEU* 2.7 27.1 + - + +
125C ALA* 1.3 68.6 - - - +
127C ARG* 1.3 63.4 + - - +
128C GLY* 2.9 7.6 + - - -
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Residues in contact with ARG 127 (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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13080 A 2.9 22.2 + - - -
13090 U 2.9 55.5 + - - +
123C LEU 2.6 11.7 + - - +
124C VAL 3.7 4.3 - - - +
126C ASP* 1.3 71.9 - - - +
128C GLY* 1.3 57.3 + - - +
129C HIS* 3.4 22.6 + - - +
168C ARG* 4.7 1.0 - - - +
190C ALA 4.6 0.2 + - - -
225C PRO* 2.8 47.6 + - - +
228C ALA* 2.9 27.5 + - + +
229C PRO 3.0 24.7 - - - +
230C GLY 3.2 30.1 - - - +
231C ARG 3.8 0.9 - - - +
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Residues in contact with GLY 128 (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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13090 U 4.1 2.9 - - - -
13100 U 3.6 14.2 + - - -
124C VAL 3.5 0.4 + - - -
125C ALA 3.0 10.1 + - - -
126C ASP 2.9 6.6 + - - -
127C ARG* 1.3 79.6 - - - +
129C HIS* 1.3 66.0 + - - +
130C GLU* 4.4 5.2 - - - +
168C ARG* 3.4 24.4 + - - -
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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