Contacts of the helix formed by residues 164 - 175 (chain B) in PDB entry 1YXJ
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 ASN 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE* 1.3 76.2 - - - +
165B TRP* 1.3 59.3 + - - +
166B GLU* 3.3 9.4 + - - +
167B LYS* 2.8 39.3 + - - +
168B SER* 2.9 29.8 + - - -
203B TRP* 3.5 0.4 - - - -
256B CYS 3.4 12.8 - - - +
257B ILE* 3.5 25.1 + - - +
258B LEU 3.1 10.3 + - - -
259B ALA* 4.3 1.4 - - - +
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Residues in contact with TRP 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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164B ASN* 1.3 71.7 - - - +
166B GLU* 1.3 74.2 + - - +
168B SER* 3.2 1.6 + - - -
169B GLN* 2.8 63.8 + - - +
179B LEU* 3.6 16.4 - - + +
203B TRP* 3.4 37.4 - + + +
204B MSE 2.9 21.2 + - - -
205B GLY 4.0 17.7 - - - -
206B LEU 4.1 2.0 + - - -
207B SER* 4.0 19.5 - - - -
218B GLU* 4.0 9.0 - - + -
243B CYS* 3.2 43.5 - - + +
256B CYS* 3.1 17.5 + - + +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASN* 3.3 9.8 + - - +
165B TRP* 1.3 90.9 - - - +
167B LYS* 1.3 57.7 + - - +
169B GLN* 3.2 27.6 + - - +
170B GLU* 3.0 27.6 + - + +
256B CYS* 4.7 1.2 + - - +
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Residues in contact with LYS 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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163B PHE* 3.7 44.0 - - + -
164B ASN* 2.8 23.1 + - - +
166B GLU* 1.3 70.8 - - - +
168B SER* 1.3 61.0 + - - +
170B GLU* 3.3 10.1 + - + +
171B LYS* 2.9 56.6 + - + +
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Residues in contact with SER 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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161B GLY 5.5 0.2 + - - -
163B PHE* 3.4 15.9 + - - +
164B ASN 2.9 21.2 + - - -
165B TRP* 3.5 5.2 - - - -
167B LYS* 1.3 73.5 - - - +
169B GLN* 1.3 65.9 + - - +
171B LYS* 3.3 8.4 + - - +
172B CYS* 3.1 26.9 + - - -
179B LEU* 4.5 5.6 - - - -
203B TRP* 3.4 18.7 - - - -
260B ALA 4.1 2.4 + - - -
262B SER* 3.8 27.4 + - - -
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Residues in contact with GLN 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 TRP* 2.8 32.8 + - + +
166B GLU* 3.2 36.0 - - - +
168B SER* 1.3 76.7 - - - +
170B GLU* 1.3 62.3 + - - +
172B CYS* 3.2 5.2 + - - +
173B LEU* 3.0 42.9 + - + +
179B LEU* 3.8 19.3 - - + +
218B GLU* 2.9 29.6 + - - +
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Residues in contact with GLU 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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166B GLU 3.0 13.5 + - - +
167B LYS* 3.5 13.5 - - + +
168B SER 3.3 0.2 - - - -
169B GLN* 1.3 79.0 - - - +
171B LYS* 1.3 63.5 + - + +
173B LEU* 3.2 19.7 + - - +
174B SER* 2.9 36.9 + - - -
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Residues in contact with LYS 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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163B PHE* 3.5 37.7 - - + -
167B LYS* 2.9 41.7 + - - +
168B SER* 3.7 7.0 - - - +
169B GLN 3.2 0.4 - - - -
170B GLU* 1.3 83.3 - - + +
172B CYS* 1.3 62.5 + - - +
174B SER* 2.6 26.5 + - - +
175B LEU* 3.5 15.5 + - + +
264B CYS* 4.8 1.8 - - - -
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Residues in contact with CYS 172 (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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168B SER 3.1 11.5 + - - -
169B GLN 3.2 6.9 + - - +
171B LYS* 1.3 75.2 - - - +
173B LEU* 1.3 62.7 + - - +
175B LEU* 3.0 9.6 + - - -
177B ALA* 2.9 27.3 + - - +
178B LYS* 3.7 22.0 - - - +
179B LEU* 3.5 31.6 - - - +
262B SER* 4.8 1.1 - - - -
264B CYS* 2.0 52.9 - - + -
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Residues in contact with LEU 173 (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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169B GLN* 3.0 38.6 + - + +
170B GLU* 3.5 22.9 - - - +
172B CYS* 1.3 78.2 - - - +
174B SER* 1.3 57.1 + - - +
175B LEU 3.1 0.2 - - - -
176B ASP* 3.0 19.1 + - - +
177B ALA 3.5 16.2 - - - +
178B LYS* 5.1 5.6 - - + -
218B GLU* 5.4 3.4 - - - +
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Residues in contact with SER 174 (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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170B GLU* 2.9 23.0 + - - -
171B LYS* 2.6 32.6 + - - +
173B LEU* 1.3 76.4 - - - +
175B LEU* 1.3 64.7 + - - +
176B ASP* 3.3 1.9 + - - +
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Residues in contact with LEU 175 (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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148B TRP* 4.0 21.1 - - + +
157B LEU* 3.6 31.6 - - + -
171B LYS* 3.5 18.2 - - + +
172B CYS* 3.0 11.0 + - - +
174B SER* 1.3 83.6 - - - +
176B ASP* 1.3 68.6 + - - +
177B ALA 3.1 0.8 + - - -
264B CYS* 4.9 1.8 - - - -
266B LYS* 3.1 24.1 + - - +
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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