Contacts of the helix formed by residues 227 - 232 (chain B) 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 ALA 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B TYR 3.5 3.2 + - - -
226B ARG* 1.3 77.0 - - - +
228B PRO* 1.4 71.1 - - + +
229B GLU* 3.1 26.9 - - + +
230B MET* 2.9 25.7 + - - +
231B VAL* 3.0 10.8 + - - +
243B ALA* 4.1 15.7 + - + +
246B TRP* 3.6 24.2 - - + -
301B ARG* 4.1 0.2 - - - +
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Residues in contact with PRO 228 (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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226B ARG 3.9 0.4 - - - -
227B ALA* 1.4 88.5 - - + +
229B GLU* 1.3 60.9 + - - +
231B VAL* 4.4 7.4 - - + -
232B ASN* 2.8 34.3 + - - +
235B SER* 5.4 1.1 - - - -
246B TRP* 3.6 31.0 - - + -
269B ILE* 3.6 24.9 - - + +
270B CYS* 4.1 18.4 - - - +
296B PRO* 3.8 25.1 - - + +
301B ARG* 4.0 0.7 - - - +
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Residues in contact with GLU 229 (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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205B PRO* 5.3 0.3 - - - +
227B ALA* 3.5 15.6 - - + +
228B PRO* 1.3 74.8 - - - +
230B MET* 1.3 61.9 + - + +
232B ASN 3.5 11.3 - - - +
233B LEU* 3.3 19.1 - - - +
235B SER* 4.2 4.2 + - - -
237B LYS* 3.8 30.2 - - + +
238B ILE 4.3 7.2 - - - +
239B ILE* 3.7 24.9 - - + +
240B THR 5.3 1.0 + - - -
242B LYS* 4.6 0.2 - - - +
243B ALA* 3.6 12.0 + - - +
296B PRO 3.8 0.7 + - - +
298B PRO* 3.5 21.0 - - + +
301B ARG* 3.0 42.0 + - - -
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Residues in contact with MET 230 (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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173B ILE* 5.4 0.2 - - + -
175B ARG* 4.1 22.0 - - + -
217B ILE* 3.9 29.8 - - + +
221B THR* 4.0 24.9 - - + -
226B ARG* 3.5 27.9 - - + -
227B ALA* 2.9 19.7 + - + +
229B GLU* 1.3 79.1 - - + +
231B VAL* 1.3 64.0 + - - +
232B ASN 3.5 0.2 - - - -
233B LEU* 3.4 21.5 - - - +
239B ILE* 3.7 25.1 - - + -
243B ALA* 3.7 27.6 - - + +
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Residues in contact with VAL 231 (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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223B LEU* 4.5 4.9 - - + -
226B ARG* 4.0 24.7 - - + +
227B ALA 3.0 12.9 + - - +
228B PRO* 3.9 5.4 - - + +
230B MET* 1.3 78.9 - - - +
232B ASN* 1.3 58.2 + - - +
233B LEU* 3.8 3.5 + - - +
266B GLN* 3.4 38.0 - - + +
269B ILE* 3.9 26.5 - - + -
270B CYS* 3.5 22.9 - - - -
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Residues in contact with ASN 232 (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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228B PRO* 2.8 18.1 + - + +
229B GLU 3.5 8.9 - - - +
231B VAL* 1.3 73.1 - - + +
233B LEU* 1.3 57.8 + - - +
234B TYR* 3.0 29.6 + - - +
235B SER* 3.1 40.5 + - - +
270B CYS* 4.0 17.4 - - - +
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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