Contacts of the helix formed by residues 151 - 165 (chain B) in PDB entry 1YYO
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 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B LYS* 3.4 7.3 + - - +
150B LYS* 1.3 73.4 - - - +
152B TYR* 1.3 64.6 + - + +
153B LYS* 3.4 20.1 - - - +
154B THR* 3.0 25.2 + - - -
155B ILE* 3.0 23.0 + - - +
207B GLN* 3.2 29.4 + - - +
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 3.9 26.6 + - + +
150B LYS 3.9 0.2 + - - -
151B ASP* 1.3 72.4 - - + +
153B LYS* 1.3 61.3 + - - +
155B ILE* 3.1 15.6 + - + +
156B LEU* 2.8 32.2 + - - +
207B GLN* 3.6 26.9 + - + +
208B ARG* 4.6 7.9 - - - -
210B ALA* 4.0 1.8 - - - -
211B GLU* 3.0 53.7 + - + +
214B ILE* 3.8 18.1 - - + +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 3.3 9.4 - - - +
152B TYR* 1.3 78.1 - - - +
154B THR* 1.3 61.7 + - - +
156B LEU* 3.7 2.6 + - - +
157B GLN* 3.3 22.0 + - - +
168B PRO* 5.7 0.2 - - - +
170B TYR* 3.8 30.1 + - - +
203B LYS* 4.5 10.4 - - + +
206B GLU* 3.2 42.2 + - + -
207B GLN* 3.2 39.2 + - + +
210B ALA* 3.9 8.5 - - + -
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LYS* 3.2 22.2 - - + +
151B ASP* 3.0 28.2 + - - -
152B TYR 3.1 0.6 - - - -
153B LYS* 1.3 76.0 - - - +
155B ILE* 1.3 66.3 + - - +
157B GLN* 3.4 12.3 + - - +
158B GLU* 3.0 46.1 + - - +
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LYS* 5.7 3.4 - - + +
150B LYS* 3.4 43.3 - - + +
151B ASP 3.0 12.9 + - - +
152B TYR* 3.1 20.8 + - + +
154B THR* 1.3 76.5 - - - +
156B LEU* 1.3 62.4 + - - +
158B GLU* 3.2 6.2 + - - +
159B ILE* 3.0 44.0 + - + +
214B ILE* 3.8 16.8 - - + -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR 2.8 19.5 + - - +
153B LYS 3.8 3.1 - - - +
155B ILE* 1.3 71.9 - - - +
157B GLN* 1.3 57.8 + - - +
159B ILE* 3.3 4.9 + - + +
160B THR* 2.9 53.6 + - + +
168B PRO* 3.5 15.0 - - + -
170B TYR* 3.3 24.5 - - + +
210B ALA* 3.5 23.8 - - + +
213B LEU* 3.7 35.7 - - + -
214B ILE* 4.0 17.9 - - + +
217B LEU* 4.1 8.7 - - + -
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Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS 3.3 11.7 + - - +
154B THR* 3.5 15.7 - - - +
155B ILE 3.2 0.4 - - - -
156B LEU* 1.3 80.7 - - - +
158B GLU* 1.3 59.6 + - + +
160B THR* 3.1 7.1 + - - -
161B GLN* 2.9 55.0 + - - +
167B ARG* 3.3 34.1 - - + +
168B PRO* 4.2 10.2 - - + +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B LYS* 3.4 27.9 + - - +
154B THR* 3.0 38.2 + - - +
155B ILE* 3.7 5.5 - - - +
157B GLN* 1.3 81.7 - - + +
159B ILE* 1.3 58.2 + - + +
161B GLN* 4.1 11.7 - - - +
162B LYS* 3.0 29.5 + - - +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ILE* 3.0 37.8 + - + +
156B LEU* 3.5 9.6 - - - +
158B GLU* 1.3 74.1 - - + +
160B THR* 1.3 66.4 + - - +
162B LYS* 3.1 16.1 + - - +
163B ARG* 3.1 37.4 + - - +
214B ILE* 4.0 22.4 - - + +
217B LEU* 4.3 20.6 - - + -
218B GLU* 6.2 1.1 - - + -
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU* 2.9 43.7 + - + +
157B GLN* 3.1 9.9 + - - -
159B ILE* 1.3 73.6 - - - +
161B GLN* 1.3 58.7 + - - +
163B ARG* 4.8 0.4 - - - -
164B TRP* 3.0 34.8 + - + +
165B LYS 3.4 2.3 + - - -
166B GLU 2.9 27.2 + - - +
168B PRO* 3.7 7.7 - - + +
190B ILE* 3.5 32.8 - - + -
217B LEU* 4.0 10.8 - - + -
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Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B GLN* 2.9 37.6 + - - +
158B GLU* 4.1 10.8 - - - +
160B THR* 1.3 75.5 + - - +
162B LYS* 1.3 67.7 + - - +
165B LYS* 3.1 29.5 + - - +
166B GLU 3.8 17.3 - - - +
167B ARG* 3.2 30.6 - - + +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU 3.0 20.0 + - - +
159B ILE* 3.1 7.8 + - - +
161B GLN* 1.3 80.2 - - - +
163B ARG* 1.3 62.1 + - - +
165B LYS* 3.9 13.2 + - - +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ILE* 3.1 32.6 + - - +
160B THR* 4.2 0.9 - - - +
162B LYS* 1.3 83.8 - - + +
164B TRP* 1.3 113.2 + - + +
165B LYS* 3.5 11.7 + - - +
217B LEU* 3.7 30.9 + - - +
220B SER* 4.2 14.1 + - - -
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Residues in contact with TRP 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B THR* 3.0 25.8 + - + +
163B ARG* 1.3 111.9 - - + +
165B LYS* 1.3 73.6 + - - +
166B GLU* 2.9 20.3 + - + +
190B ILE* 3.4 38.8 - - + -
191B LYS* 3.2 44.4 - - + +
193B TYR* 4.2 13.9 - + - -
217B LEU* 3.8 26.7 - - + -
220B SER* 5.9 1.1 - - - -
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B THR 3.4 0.4 + - - -
161B GLN* 3.1 31.6 + - - +
162B LYS 3.9 13.8 + - - -
163B ARG 4.0 9.2 + - - +
164B TRP* 1.3 79.2 - - - +
166B GLU* 1.3 62.5 + - - +
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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