Contacts of the helix formed by residues 159 - 171 (chain B) in PDB entry 1YLA
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 SER 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B GLN* 3.3 27.0 + - - +
147B LEU* 4.3 0.2 - - - -
158B SER* 1.3 75.4 + - - +
160B PRO* 1.3 76.6 - - - +
161B GLU* 3.1 3.1 - - - +
162B TYR* 3.2 41.2 + - - -
163B THR* 3.1 25.8 + - - +
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Residues in contact with PRO 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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159B SER* 1.3 86.5 - - - +
161B GLU* 1.3 60.4 + - - +
163B THR* 2.9 21.7 + - + +
164B LYS* 3.1 14.0 + - - +
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Residues in contact with GLU 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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159B SER* 3.1 2.2 - - - -
160B PRO* 1.3 80.3 - - - +
162B TYR* 1.3 83.8 - - + +
164B LYS* 3.4 7.1 + - - +
165B LYS* 3.2 55.1 + - + +
188B TRP* 4.8 1.6 - - - +
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Residues in contact with TYR 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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140B MET* 3.7 29.9 + - + +
143B GLN* 3.5 45.1 - - + +
144B THR 3.9 3.1 - - - -
147B LEU* 3.8 10.1 - - + -
159B SER* 3.2 25.9 + - - +
161B GLU* 1.3 98.5 - - + +
163B THR* 1.3 64.5 + - - +
165B LYS* 3.4 1.4 + - - -
166B ILE* 2.9 31.8 + - - +
188B TRP* 3.5 62.8 - + + -
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Residues in contact with THR 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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147B LEU* 3.9 17.9 - - + -
150B HIS* 6.0 4.5 - - + +
151B VAL* 6.2 2.0 - - + -
157B VAL* 6.1 4.0 - - + -
158B SER 4.2 3.8 - - - +
159B SER 3.1 15.7 - - - +
160B PRO* 2.9 22.5 + - + +
162B TYR* 1.3 76.7 - - - +
164B LYS* 1.3 57.3 + - - +
166B ILE* 3.4 9.9 + - + +
167B GLU* 2.9 47.8 + - - +
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Residues in contact with LYS 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 PRO 3.1 14.4 + - - +
161B GLU* 3.7 7.4 - - - +
162B TYR 3.3 0.2 - - - -
163B THR* 1.3 79.1 + - - +
165B LYS* 1.3 63.4 + - + +
167B GLU* 3.4 11.8 + - - +
168B ASN* 2.9 58.9 + - - +
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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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161B GLU* 3.2 46.6 + - - +
162B TYR 3.8 4.7 - - - +
164B LYS* 1.3 76.9 - - + +
166B ILE* 1.3 65.9 + - - +
168B ASN* 3.5 7.3 + - - +
169B LEU* 3.2 28.8 + - - +
183B LEU* 3.8 15.7 - - + -
188B TRP* 2.6 44.3 + - + +
189B ASP* 4.9 0.6 - - - +
190B VAL* 3.9 26.4 - - + +
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Residues in contact with ILE 166 (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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147B LEU* 3.6 32.1 - - + -
151B VAL* 5.6 2.9 - - + -
162B TYR 2.9 25.2 + - - +
163B THR* 3.6 9.6 - - + +
165B LYS* 1.3 77.0 - - - +
167B GLU* 1.3 58.7 + - + +
169B LEU 3.2 2.3 + - - -
170B CYS* 2.9 38.2 + - - -
176B ARG* 4.6 6.5 - - + +
179B VAL* 3.6 12.1 - - + +
180B ILE* 3.6 35.7 - - + -
183B LEU* 3.5 21.3 - - + -
188B TRP* 3.7 4.5 - - + -
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Residues in contact with GLU 167 (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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17A LEU* 4.5 7.5 - - + +
18A LYS* 4.0 42.8 + - + +
163B THR* 2.9 38.0 + - - +
164B LYS* 3.7 10.7 - - - +
166B ILE* 1.3 78.1 - - + +
168B ASN* 1.3 61.3 + - - +
170B CYS* 3.2 9.2 + - - +
171B ALA* 2.9 27.2 + - - +
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Residues in contact with ASN 168 (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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164B LYS* 2.9 52.1 + - - +
165B LYS* 3.9 7.5 - - - +
166B ILE 3.3 0.2 - - - -
167B GLU* 1.3 78.8 - - - +
169B LEU* 1.3 63.1 + - + +
171B ALA* 3.0 27.2 - - - +
172B MET* 3.6 10.5 + - - +
190B VAL* 6.5 0.9 - - + -
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Residues in contact with LEU 169 (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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165B LYS 3.2 13.0 + - - +
166B ILE 3.7 0.4 - - - +
168B ASN* 1.3 77.8 - - + +
170B CYS* 1.3 65.4 + - - +
172B MET* 3.1 35.0 + - + +
174B PHE* 3.2 22.0 - - - +
179B VAL* 3.3 30.3 - - + +
183B LEU* 3.9 24.5 - - + -
190B VAL* 4.3 14.1 - - + +
193B ALA* 4.6 5.8 - - + -
194B THR* 3.4 20.2 - - - +
197B LEU* 3.6 24.9 - - + -
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Residues in contact with CYS 170 (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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14A LYS* 6.6 0.4 - - + -
17A LEU* 5.6 2.2 - - - -
166B ILE* 2.9 22.2 + - - +
167B GLU* 3.2 11.6 + - - +
169B LEU* 1.3 71.8 - - - +
171B ALA* 1.3 54.5 + - - +
172B MET 2.8 5.4 - - - -
173B GLY* 2.7 25.8 + - - -
174B PHE 4.1 9.7 - - - +
176B ARG* 3.7 48.2 - - - -
179B VAL* 4.2 4.9 - - - -
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Residues in contact with ALA 171 (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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14A LYS* 6.3 3.1 - - - -
167B GLU 2.9 13.7 + - - +
168B ASN* 3.0 21.3 - - - +
170B CYS* 1.3 74.4 - - - +
172B MET* 1.3 60.4 + - + +
173B GLY 3.4 0.6 + - - -
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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