Contacts of the helix formed by residues 164 - 174 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PHE* 1.3 74.9 - - - +
165A TRP* 1.3 64.5 + - - +
166A GLU* 3.3 10.1 + - - +
167A LYS* 2.8 28.7 + - - +
168A SER* 2.9 24.9 + - - -
203A TRP* 3.5 1.3 - - - -
256A CYS 3.5 6.1 - - - +
257A ILE* 3.4 32.6 + - - +
258A LEU 3.1 12.1 - - - +
259A ALA* 4.2 2.0 - - - +
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Residues in contact with TRP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASN* 1.3 74.2 - - - +
166A GLU* 1.3 70.6 + - + +
168A SER* 3.2 2.1 + - - -
169A GLN* 2.8 65.1 + - - +
179A LEU* 3.6 18.1 - - + +
203A TRP* 3.4 36.1 - + + +
204A MSE 3.0 21.2 + - - -
205A GLY 4.1 11.2 - - - -
206A LEU 4.1 2.4 + - - -
207A SER* 4.1 17.3 - - - -
218A GLU* 4.0 16.2 - - + -
243A CYS* 3.2 42.7 - - + +
256A CYS* 3.1 16.3 + - + +
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASN* 3.3 9.9 + - - +
165A TRP* 1.3 89.1 - - + +
167A LYS* 1.3 64.3 + - - +
169A GLN* 3.3 24.8 + - - +
170A GLU* 3.1 22.0 + - + +
256A CYS* 4.7 1.4 + - - +
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PHE* 3.6 44.1 - - + -
164A ASN* 2.8 23.4 + - - +
166A GLU* 1.3 71.5 - - - +
168A SER* 1.3 61.1 + - - +
170A GLU* 3.2 10.1 + - + +
171A LYS* 2.9 57.8 + - + +
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY 5.6 0.2 + - - -
163A PHE* 3.3 22.4 + - - +
164A ASN 2.9 20.7 + - - -
165A TRP 3.5 4.7 - - - -
167A LYS* 1.3 75.8 - - - +
169A GLN* 1.3 62.4 + - - +
171A LYS* 3.3 9.5 + - - +
172A CYS* 3.1 26.5 + - - -
179A LEU* 4.3 6.1 - - - -
203A TRP* 3.4 13.2 - - - -
260A ALA 4.0 3.3 + - - -
262A SER* 3.8 27.4 + - - -
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TRP* 2.8 35.1 + - + +
166A GLU* 3.4 31.7 - - - +
168A SER* 1.3 77.1 - - - +
170A GLU* 1.3 62.8 + - - +
172A CYS* 3.1 6.2 + - - +
173A LEU* 3.0 42.5 + - + +
179A LEU* 3.8 19.9 - - + +
218A GLU* 2.8 30.4 + - - +
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLU* 3.1 10.7 + - + +
167A LYS* 3.2 13.4 + - - +
169A GLN* 1.3 80.2 - - - +
171A LYS* 1.3 75.0 + - - +
173A LEU* 3.1 15.9 + - + +
174A SER* 2.9 37.7 + - - -
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PHE* 4.1 24.8 - - + -
167A LYS* 2.9 55.8 + - + +
168A SER* 3.5 10.5 - - - +
169A GLN 3.2 0.2 - - - -
170A GLU* 1.3 86.7 + - - +
172A CYS* 1.3 61.5 + - - +
174A SER* 2.6 27.4 + - - +
175A LEU* 3.5 13.4 - - + +
264A CYS* 4.8 2.7 - - - -
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Residues in contact with CYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A SER 3.1 10.1 + - - -
169A GLN 3.1 9.2 + - - +
171A LYS* 1.3 75.5 - - - +
173A LEU* 1.3 58.4 + - - +
175A LEU* 2.9 13.9 + - - -
177A ALA* 2.9 25.7 + - - +
178A LYS* 3.8 18.8 - - - +
179A LEU* 3.5 32.1 - - - +
262A SER* 4.7 1.3 - - - -
264A CYS* 2.0 55.9 - - + -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLN* 3.0 37.9 + - + +
170A GLU* 3.1 16.4 + - + +
172A CYS* 1.3 77.8 - - - +
174A SER* 1.3 57.0 + - - +
175A LEU 3.0 0.2 - - - -
176A ASP* 3.1 19.8 + - - +
177A ALA 3.4 18.8 - - - +
178A LYS* 4.8 7.2 - - + -
218A GLU* 5.3 2.9 - - - +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLU* 2.9 25.1 + - - -
171A LYS* 2.6 30.3 + - - +
173A LEU* 1.3 77.0 - - - +
175A LEU* 1.3 66.4 + - - +
176A ASP* 3.4 5.7 + - - +
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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