Contacts of the helix formed by residues 152 - 165 (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 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D ALA* 3.0 11.1 + - - -
150D ALA 3.4 0.2 - - - -
151D ALA* 1.3 78.9 - - - +
153D ALA* 1.3 60.0 + - - -
154D VAL 3.4 2.2 - - - -
155D GLY 4.0 1.3 - - - -
156D SER* 2.5 34.2 + - - -
321D ASN* 4.4 6.1 - - - -
323D GLY* 4.4 2.9 - - - -
701D NAP 3.3 27.8 - - - -
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Residues in contact with ALA 153 (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* 5.6 1.2 - - - -
121D THR* 5.2 0.9 + - - -
125D PRO* 4.1 11.8 - - + +
152D GLY* 1.3 73.4 - - - +
154D VAL* 1.3 63.2 + - - +
156D SER* 3.7 2.4 + - - -
157D VAL* 3.3 24.6 - - - +
323D GLY 4.3 1.4 - - - -
324D LYS* 3.5 49.1 - - + +
701D NAP 2.9 24.6 + - - +
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO* 3.7 32.1 - - + +
128D THR* 4.1 6.5 - - + -
129D ALA* 3.7 13.8 - - - +
153D ALA* 1.3 71.7 - - - +
155D GLY* 1.3 67.2 + - - +
157D VAL* 3.1 6.6 + - - +
158D VAL* 2.9 20.0 + - + +
215D PHE* 3.6 36.3 - - + -
217D ASN* 4.0 9.0 - - - +
239D CYS* 4.3 0.2 - - - -
701D NAP 2.8 48.5 + - + +
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Residues in contact with GLY 155 (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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147D VAL* 3.9 15.5 - - - +
149D ALA 3.4 20.6 + - - -
150D ALA* 3.5 8.9 - - - +
152D GLY 3.7 2.2 + - - -
153D ALA 3.6 0.2 - - - -
154D VAL* 1.3 77.6 - - - +
156D SER* 1.3 60.5 - - - +
158D VAL* 3.2 5.8 + - - +
159D GLY* 3.0 20.6 + - - -
187D PHE* 4.9 0.3 - - - -
217D ASN* 3.9 14.9 - - - +
701D NAP 4.4 1.0 + - - -
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Residues in contact with SER 156 (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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150D ALA 3.1 17.7 + - - -
151D ALA* 4.2 8.0 + - - -
152D GLY 2.5 25.3 + - - -
153D ALA* 3.7 5.4 + - - -
155D GLY* 1.3 75.0 - - - +
157D VAL* 1.3 66.0 + - - +
159D GLY 3.6 0.3 + - - -
160D GLN* 3.2 39.8 + - - +
181D TYR* 5.5 5.4 - - - -
182D LEU* 4.6 7.4 - - - -
185D LEU* 5.4 1.6 - - - -
187D PHE* 3.9 4.6 - - - -
323D GLY* 5.0 5.0 - - - -
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Residues in contact with VAL 157 (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 THR* 3.7 33.9 - - + +
126D GLY* 4.3 11.0 - - - +
129D ALA* 3.7 17.7 - - + -
153D ALA 3.3 17.3 - - - +
154D VAL 3.1 7.2 + - - +
156D SER* 1.3 78.9 + - - +
158D VAL* 1.3 65.9 + - - +
160D GLN* 3.2 8.3 + - - +
161D ILE* 3.0 41.3 + - + +
287D LEU* 4.3 5.4 - - + -
296D ILE* 4.1 15.5 - - + -
297D GLN 5.9 0.2 - - - +
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Residues in contact with VAL 158 (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* 3.4 17.0 - - + +
133D LEU* 3.3 27.0 - - + +
145D VAL* 4.9 3.1 - - + -
147D VAL* 4.1 12.8 - - + -
154D VAL* 2.9 19.4 + - + +
155D GLY* 3.2 8.0 + - - +
157D VAL* 1.3 77.3 - - - +
159D GLY* 1.3 65.0 + - - +
161D ILE* 4.8 1.1 - - - -
162D ALA* 3.0 19.4 + - - +
215D PHE* 3.3 61.0 - - + -
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Residues in contact with GLY 159 (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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147D VAL* 4.6 2.7 - - - +
155D GLY 3.0 12.5 + - - -
157D VAL 3.3 0.2 - - - -
158D VAL* 1.3 80.1 - - - +
160D GLN* 1.3 56.9 + - - +
162D ALA* 3.4 0.4 + - - -
163D LYS* 3.0 32.7 + - - +
169D VAL* 3.6 18.8 - - - +
187D PHE* 3.6 25.6 - - - -
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Residues in contact with GLN 160 (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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156D SER* 3.2 28.3 + - - +
157D VAL* 3.2 6.1 + - - +
159D GLY* 1.3 74.3 - - - +
161D ILE* 1.3 65.9 + - - +
163D LYS* 3.4 5.9 + - - +
164D LEU* 3.1 28.6 + - - +
181D TYR* 5.5 0.4 + - - -
185D LEU* 3.8 20.3 - - + +
187D PHE* 4.0 16.8 - - + -
295D LYS 4.0 12.3 - - - +
296D ILE* 3.5 17.1 - - + +
297D GLN* 2.7 53.3 + - - +
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Residues in contact with ILE 161 (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 4.8 1.3 - - - -
130D TYR* 4.1 24.7 - - + +
133D LEU* 3.7 15.3 - - + -
134D LEU* 4.3 24.0 - - + -
157D VAL* 3.0 35.0 + - + +
158D VAL 3.9 3.4 - - - +
160D GLN* 1.3 77.5 - - - +
162D ALA* 1.3 62.5 + - - +
164D LEU* 3.4 8.9 + - + +
165D LYS* 3.0 26.8 + - + +
287D LEU* 4.1 7.4 - - + -
290D TRP* 3.8 28.3 - - + -
296D ILE* 4.0 15.0 - - + -
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Residues in contact with ALA 162 (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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133D LEU* 3.5 17.2 - - + +
145D VAL* 4.4 10.5 - - + -
158D VAL 3.0 17.9 + - - +
159D GLY* 4.4 0.4 - - - -
161D ILE* 1.3 77.2 - - - +
163D LYS* 1.3 61.0 + - - +
165D LYS* 3.1 8.7 + - - -
166D GLY 3.2 0.3 + - - -
167D CYS* 2.9 44.5 + - + +
169D VAL* 3.7 21.8 - - + -
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Residues in contact with LYS 163 (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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159D GLY 3.0 19.8 + - - +
160D GLN* 3.6 7.4 - - - +
162D ALA* 1.3 76.5 - - - +
164D LEU* 1.3 57.9 + - - +
166D GLY* 2.9 20.1 + - - -
167D CYS 3.1 19.1 + - - +
168D LYS* 4.4 0.2 - - - +
169D VAL* 3.8 11.9 - - + -
185D LEU 5.8 1.6 - - - +
186D GLY 3.9 18.3 + - - +
187D PHE* 4.1 17.3 - - + -
188D ASP* 2.5 39.2 + - - +
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Residues in contact with LEU 164 (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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160D GLN 3.1 17.6 + - - +
161D ILE* 3.5 17.7 - - - +
163D LYS* 1.3 79.1 - - - +
165D LYS* 1.3 78.0 + - + +
166D GLY 3.2 0.8 + - - -
290D TRP* 4.2 34.3 - - + +
295D LYS* 3.8 48.7 - - + +
296D ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 165 (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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134D LEU* 4.2 25.8 - - + -
139D VAL* 4.8 6.1 - - + -
140D LYS 4.7 3.2 - - - +
141D GLY* 3.3 25.7 - - - +
161D ILE* 3.0 24.9 + - + +
162D ALA* 3.1 8.6 + - - +
164D LEU* 1.3 92.3 - - + +
166D GLY* 1.3 56.8 + - - +
167D CYS* 3.5 8.3 - - - -
290D TRP* 4.3 23.9 - - - -
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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