Contacts of the helix formed by residues 123 - 135 (chain D) in PDB entry 2Y05
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 GLY 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D ALA 3.5 15.3 - - - -
120D GLY 2.9 8.4 + - - -
121D THR 3.3 0.8 + - - -
122D VAL* 1.3 79.5 - - - +
124D MET* 1.3 61.6 + - - -
126D GLY 3.0 1.7 + - - -
127D LEU* 2.8 36.1 + - - +
280D ARG* 6.2 0.4 - - - -
284D LEU* 4.2 6.1 - - - +
287D LEU* 4.9 0.4 - - - +
1331D EDO 3.9 7.6 - - - -
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Residues in contact with MET 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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47D ASP* 4.2 15.3 - - + +
49D TYR* 4.1 24.9 - - + -
66D GLN* 4.8 13.6 + - - +
118D ALA 4.4 3.8 + - - -
119D LEU 4.6 1.0 + - - +
123D GLY* 1.3 69.9 - - - +
125D PRO* 1.3 72.1 - - + +
127D LEU* 3.4 10.8 + - - +
128D THR* 2.7 37.8 + - - -
272D VAL* 3.6 22.6 - - + +
273D TYR* 3.9 29.2 - - + +
701D NAP 3.7 21.8 - - + -
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Residues in contact with PRO 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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47D ASP* 4.6 6.3 - - - +
119D LEU 3.1 25.1 - - - +
120D GLY* 3.5 14.4 - - - +
124D MET* 1.3 103.2 - - + +
126D GLY* 1.3 59.4 + - - +
128D THR* 3.3 7.5 + - - +
129D ALA* 3.2 21.0 + - - +
153D ALA* 4.1 17.3 - - + +
154D VAL* 3.7 27.3 - - + +
324D LYS* 3.9 15.0 - - + -
701D NAP 4.9 2.9 - - + +
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Residues in contact with GLY 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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120D GLY 3.0 12.3 + - - -
121D THR* 3.3 27.8 - - - +
123D GLY 3.5 0.7 - - - -
125D PRO* 1.3 75.5 - - - +
127D LEU* 1.3 56.4 + - - +
128D THR 3.4 0.2 + - - -
129D ALA* 3.4 4.2 + - - +
130D TYR* 3.0 28.2 + - - +
157D VAL* 4.4 12.1 - - - -
287D LEU* 3.6 11.9 - - - +
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Residues in contact with LEU 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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123D GLY 2.8 25.4 + - - +
124D MET* 3.7 4.5 - - - +
126D GLY* 1.3 71.2 - - - +
128D THR* 1.3 59.5 + - - +
130D TYR* 4.2 1.6 - - - -
131D PHE* 2.9 45.4 + - + +
272D VAL* 3.5 20.1 - - + +
275D TRP 5.9 0.4 - - - +
280D ARG* 3.9 34.1 - - + +
283D ALA* 3.5 31.0 - - + -
284D LEU* 3.7 33.2 - - + +
287D LEU* 3.8 6.9 - - + +
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Residues in contact with THR 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 MET 2.7 19.8 + - - -
125D PRO 3.4 9.4 - - - -
126D GLY 3.3 0.4 - - - -
127D LEU* 1.3 76.6 - - - +
129D ALA* 1.3 56.9 + - - +
131D PHE* 5.3 0.2 - - - -
132D GLY* 2.9 28.2 + - - -
154D VAL* 4.1 8.1 - - + -
215D PHE* 3.9 1.3 - - - -
239D CYS* 3.4 33.2 - - - -
270D PHE* 3.6 14.0 - - + -
272D VAL* 3.2 19.8 - - - +
701D NAP 3.3 28.5 - - + -
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Residues in contact with ALA 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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125D PRO 3.2 7.0 + - - +
126D GLY 3.5 9.0 - - - +
128D THR* 1.3 77.2 - - - +
130D TYR* 1.3 59.6 + - - +
133D LEU* 2.9 35.3 + - - +
154D VAL* 3.7 12.5 - - + +
157D VAL* 3.7 24.0 - - + -
158D VAL* 3.4 29.7 - - + +
161D ILE* 4.8 1.8 - - - -
215D PHE* 3.8 1.7 - - - -
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Residues in contact with TYR 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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126D GLY 3.0 14.7 + - - +
127D LEU* 3.7 7.9 - - - +
129D ALA* 1.3 77.8 - - - +
131D PHE* 1.3 80.1 + + - +
133D LEU* 5.1 0.2 - - - -
134D LEU* 2.9 53.6 + - + +
135D GLU* 5.7 2.0 - - + -
161D ILE* 4.1 12.5 - - + +
279D ALA 5.5 0.2 - - - -
282D LYS* 4.7 6.9 - - - +
283D ALA* 3.5 32.6 + - + -
286D ASP* 2.6 42.3 + - + -
287D LEU* 4.2 12.1 - - + -
290D TRP* 3.8 24.6 - + - -
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Residues in contact with PHE 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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127D LEU* 2.9 42.8 + - + +
128D THR* 4.6 1.1 - - - +
130D TYR* 1.3 90.1 - + - +
132D GLY* 1.3 58.9 + - - +
135D GLU* 3.0 51.7 + - + +
136D ILE* 3.2 11.5 + - - +
270D PHE* 5.5 0.2 - - + -
272D VAL* 5.1 2.2 - - + -
275D TRP* 3.6 68.6 - + + -
279D ALA* 3.4 30.5 - - + -
280D ARG* 4.5 3.4 - - + -
283D ALA* 3.6 19.5 - - + -
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Residues in contact with GLY 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 THR 2.9 20.0 + - - -
131D PHE* 1.3 78.3 - - - +
133D LEU* 1.3 55.8 + - - +
136D ILE* 3.4 8.2 + - - +
137D CYS* 2.9 28.6 + - - +
215D PHE* 3.7 15.3 - - - -
237D ALA* 3.8 2.9 - - - +
270D PHE* 3.7 20.3 - - - -
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Residues in contact with LEU 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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129D ALA 2.9 16.9 + - - +
130D TYR 4.2 0.9 - - - +
132D GLY* 1.3 76.8 - - - +
134D LEU* 1.3 58.5 + - + +
137D CYS* 3.3 15.1 - - + +
138D GLY 3.0 23.4 + - - -
139D VAL* 3.4 37.3 + - + -
145D VAL* 3.9 23.8 - - + -
158D VAL* 3.3 38.4 - - + +
161D ILE* 3.7 17.9 - - + -
162D ALA* 3.5 24.2 - - + +
215D PHE* 3.7 3.5 - - + -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D TYR* 2.9 55.0 + - + +
133D LEU* 1.3 77.7 - - + +
135D GLU* 1.3 64.9 + - + +
138D GLY* 3.3 15.7 - - - -
139D VAL* 3.7 30.6 - - + +
161D ILE* 4.3 24.2 - - + -
165D LYS* 4.2 26.2 - - + -
290D TRP* 4.7 2.0 - - + -
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Residues in contact with GLU 135 (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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130D TYR* 5.7 1.9 - - + -
131D PHE* 3.0 43.7 + - + +
134D LEU* 1.3 85.8 - - + +
136D ILE* 1.3 67.8 + - + +
138D GLY* 3.8 6.1 + - - -
266D ARG* 5.5 2.1 + - - -
275D TRP* 4.3 20.7 + - + +
279D ALA* 6.0 0.9 - - - +
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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