Contacts of the helix formed by residues 222 - 226 (chain A) in PDB entry 1WSQ
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 THR 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ARG 4.6 0.6 + - - -
176A ASP* 2.7 28.3 + - - -
178A LYS* 3.9 15.7 + - + +
221A THR* 1.3 74.6 - - - +
223A LEU* 1.3 68.4 + - - +
224A SER* 4.2 7.2 - - - +
225A TYR* 3.0 42.8 + - + +
226A ARG* 3.1 12.7 + - - +
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Residues in contact with LEU 223 (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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222A THR* 1.3 71.7 - - - +
224A SER* 1.3 64.8 + - - +
226A ARG* 3.0 58.6 + - - +
231A VAL* 4.8 0.7 - - + -
264A GLU* 3.8 48.9 - - + +
266A GLN* 3.7 33.9 - - + +
269A ILE* 3.5 15.5 - - + +
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Residues in contact with SER 224 (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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222A THR* 3.2 6.4 + - - +
223A LEU* 1.3 79.0 - - - +
225A TYR* 1.3 63.7 + - - +
226A ARG 4.9 0.2 - - - +
250A CYS* 3.7 16.2 - - - +
260A LEU* 3.7 33.7 - - - +
261A PRO* 5.3 0.2 - - - +
262A PHE* 4.6 8.5 + - - -
263A GLY 3.1 28.2 + - - +
264A GLU* 3.4 17.9 + - - +
269A ILE* 4.7 4.6 - - - +
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Residues in contact with TYR 225 (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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176A ASP* 6.1 0.7 - - - +
177A LEU 3.2 18.2 - - - +
178A LYS* 3.4 30.6 - - + +
179A VAL* 3.3 21.1 + - - +
180A GLU* 4.4 3.1 + - - -
222A THR* 3.0 31.9 + - + +
224A SER* 1.3 79.6 - - - +
226A ARG* 1.3 63.6 + - - +
227A ALA 3.6 1.0 + - - -
230A MET* 5.8 0.2 - - - +
243A ALA 4.8 1.6 - - - +
246A TRP* 3.4 15.8 - - - -
247A ALA* 3.7 32.6 + - + +
250A CYS* 3.7 10.3 - - + -
251A LEU* 3.9 17.5 - - + -
254A LYS* 3.6 22.2 - - - +
260A LEU* 3.5 29.8 - - + -
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Residues in contact with ARG 226 (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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217A ILE* 3.6 22.6 + - - +
218A LYS* 3.8 34.0 + - - +
221A THR* 2.8 46.4 + - - +
222A THR 3.1 6.0 + - - +
223A LEU* 3.0 48.8 + - - +
224A SER 4.9 0.2 - - - +
225A TYR* 1.3 76.2 - - - +
227A ALA* 1.3 62.5 + - - +
230A MET* 3.6 29.8 - - + -
231A VAL* 3.9 20.4 - - + +
246A TRP* 3.4 10.8 + - - -
266A GLN* 5.4 3.2 + - - -
269A ILE* 3.4 18.4 - - - +
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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