Contacts of the helix formed by residues 120 - 133 (chain D) in PDB entry 1Y3A
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 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LEU* 5.1 1.7 - - - +
119D MET* 1.3 79.8 - - - +
121D ALA* 1.3 61.1 + - - +
122D GLU* 3.6 17.4 + - - +
123D LEU* 3.0 25.8 + - - +
124D ALA* 2.8 29.8 + - - +
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Residues in contact with ALA 121 (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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120D THR* 1.3 72.6 - - - +
122D GLU* 1.3 56.9 + - - +
124D ALA* 3.4 7.8 + - - +
125D GLY* 2.9 28.1 + - - -
163D ALA* 6.3 0.2 - - - -
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Residues in contact with GLU 122 (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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106D GLN* 4.4 11.0 + - + +
110D LEU* 3.2 39.8 - - + +
120D THR* 3.6 13.8 + - - +
121D ALA* 1.3 80.7 - - - +
123D LEU* 1.3 59.8 + - - +
125D GLY* 3.4 1.4 + - - -
126D VAL* 3.3 23.1 + - + +
129D ARG* 5.3 0.7 + - - -
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Residues in contact with LEU 123 (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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78D ILE* 3.8 32.1 - - + -
107D LEU* 3.9 30.7 - - + +
110D LEU* 3.7 36.1 - - + +
111D ALA* 4.7 9.0 - - + +
119D MET* 4.2 18.6 - - - +
120D THR* 3.0 23.0 + - - +
122D GLU* 1.3 73.6 - - - +
124D ALA* 1.3 67.2 + - - +
126D VAL* 3.2 4.2 + - + +
127D ILE* 2.9 35.7 + - + +
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Residues in contact with ALA 124 (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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119D MET* 4.2 12.9 - - + -
120D THR 2.8 20.4 + - - +
121D ALA* 3.6 9.0 - - - +
123D LEU* 1.3 72.1 - - - +
125D GLY* 1.3 58.0 + - - +
127D ILE* 3.1 3.0 + - - +
128D LYS* 2.8 45.8 + - - +
159D LEU* 3.7 7.1 - - + +
163D ALA* 3.8 28.7 - - + -
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Residues in contact with GLY 125 (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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121D ALA 2.9 16.6 + - - -
122D GLU 3.9 1.6 - - - -
123D LEU 3.2 0.2 - - - -
124D ALA* 1.3 77.8 - - - +
126D VAL* 1.3 60.6 + - - +
128D LYS* 3.5 9.1 + - - +
129D ARG* 3.0 46.7 + - - +
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Residues in contact with VAL 126 (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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103D ASP* 3.3 29.3 - - - +
106D GLN* 3.8 26.5 - - + -
107D LEU* 3.8 25.4 - - + -
110D LEU* 4.0 3.1 - - + -
122D GLU* 3.3 14.1 + - + +
123D LEU* 3.2 11.3 + - + +
125D GLY* 1.3 76.0 - - - +
127D ILE* 1.3 64.1 + - - +
129D ARG* 3.8 21.1 - - - +
130D LEU* 3.2 29.5 + - + +
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Residues in contact with ILE 127 (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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77D THR* 4.9 3.6 - - + -
78D ILE* 4.5 8.1 - - + -
81D ILE* 4.2 22.4 - - + +
107D LEU* 4.2 17.5 - - + -
119D MET* 4.2 21.1 - - + -
123D LEU* 2.9 41.2 + - + +
124D ALA* 3.7 4.3 - - - +
126D VAL* 1.3 77.4 - - - +
128D LYS* 1.3 60.2 + - - +
130D LEU* 3.3 5.7 + - - +
131D TRP* 2.9 29.0 + - + +
156D LEU* 3.7 26.7 - - + -
159D LEU* 3.5 18.4 - - + -
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Residues in contact with LYS 128 (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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124D ALA* 2.8 35.3 + - - +
125D GLY* 4.0 7.7 - - - +
127D ILE* 1.3 72.9 - - - +
129D ARG* 1.3 63.0 + - + +
131D TRP* 3.8 6.8 - - - +
132D LYS* 3.1 24.3 + - - +
159D LEU* 3.4 22.0 - - + -
160D ASP* 2.8 45.6 + - - +
163D ALA* 4.8 5.9 - - - +
164D GLN* 5.5 3.2 - - - +
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Residues in contact with ARG 129 (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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100D ARG* 3.3 27.2 - - - +
103D ASP* 2.7 45.8 + - - +
122D GLU 5.3 0.4 + - - -
125D GLY* 3.0 36.3 + - - +
126D VAL* 3.8 18.2 - - - +
128D LYS* 1.3 78.8 - - + +
130D LEU* 1.3 61.0 + - - +
132D LYS* 3.4 6.8 + - - +
133D ASP 3.2 16.1 + - - -
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Residues in contact with LEU 130 (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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81D ILE* 4.2 13.5 - - + -
85D ILE* 4.3 10.1 - - + -
95D PHE* 3.8 28.9 - - + -
100D ARG* 3.8 27.1 - - + +
103D ASP* 4.0 6.5 - - + -
104D ALA* 4.0 18.8 - - + +
107D LEU* 4.1 18.6 - - + -
126D VAL* 3.2 39.8 + - + +
127D ILE* 3.8 3.4 - - - +
129D ARG* 1.3 73.9 - - - +
131D TRP* 1.3 65.8 + - - +
133D ASP 3.2 5.9 + - - -
136D VAL* 3.1 28.5 - - + +
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Residues in contact with TRP 131 (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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81D ILE* 4.4 6.2 - - + +
84D ILE* 3.9 20.4 - - + -
127D ILE* 2.9 18.2 + - + +
128D LYS* 3.8 7.0 - - - +
130D LEU* 1.3 77.2 - - - +
132D LYS* 1.3 62.4 + - + +
133D ASP 3.6 0.3 + - - +
136D VAL* 4.4 8.1 - - + +
137D GLN* 2.7 58.3 + - - +
140D PHE* 3.8 35.7 - + + -
153D ALA* 4.1 13.0 - - + -
156D LEU* 3.4 63.4 - - + +
157D ASN* 2.7 34.2 + - - -
159D LEU* 6.1 0.4 - - + -
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Residues in contact with LYS 132 (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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128D LYS 3.1 17.2 + - - +
129D ARG* 3.7 8.3 - - - +
130D LEU 3.1 0.2 - - - -
131D TRP* 1.3 79.6 - - + +
133D ASP* 1.3 64.6 + - - +
134D SER* 3.5 2.1 + - - -
137D GLN* 4.6 4.4 - - - +
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Residues in contact with ASP 133 (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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95D PHE* 3.4 7.0 - - - +
96D GLY* 2.7 35.1 + - - -
97D ASP* 3.0 16.6 + - - +
100D ARG* 3.3 29.7 + - + +
129D ARG 3.2 6.3 + - - +
130D LEU 3.2 14.7 + - - +
132D LYS* 1.3 78.5 - - - +
134D SER* 1.3 59.1 + - - +
135D GLY* 2.7 18.0 + - - -
136D VAL* 3.2 9.1 + - + +
137D GLN* 3.0 27.5 + - - +
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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