Contacts of the helix formed by residues 234 - 242 (chain A) in PDB entry 3SMZ
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 ASP 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A PHE* 3.3 27.9 - - + -
233A ASN* 1.3 76.0 - - - +
235A VAL* 1.3 64.1 + - - +
236A ASP* 3.5 18.9 + - - +
237A ALA* 4.0 9.6 + - + +
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Residues in contact with VAL 235 (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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233A ASN* 3.2 13.1 + - - +
234A ASP* 1.3 72.0 + - - +
236A ASP* 1.3 70.2 + - - +
238A LEU* 3.1 16.1 + - - +
239A CYS* 3.3 21.9 + - - -
251A CYS 3.4 25.1 - - - +
252A GLN* 4.3 1.3 - - + -
253A LEU* 3.8 39.5 - - + +
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Residues in contact with ASP 236 (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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234A ASP* 3.5 14.3 - - - +
235A VAL* 1.3 79.1 - - - +
237A ALA* 1.4 60.6 + - - +
239A CYS* 3.8 7.2 + - - +
240A ARG* 3.2 57.2 + - - +
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Residues in contact with ALA 237 (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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232A PHE* 4.9 7.6 - - + -
234A ASP* 4.0 11.5 + - + +
235A VAL 3.3 1.4 + - - -
236A ASP* 1.4 74.8 - - - +
238A LEU* 1.3 60.0 + - - +
240A ARG* 3.6 12.9 + - - +
241A ALA* 3.0 28.2 + - - +
287A LEU* 4.3 9.2 - - + +
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Residues in contact with LEU 238 (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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225A VAL* 3.8 8.7 - - + -
228A LEU* 3.8 19.7 - - + -
232A PHE* 3.7 20.8 - - + -
235A VAL 3.1 9.0 + - - +
237A ALA* 1.3 75.3 - - - +
239A CYS* 1.3 59.5 + - - +
241A ALA* 3.1 7.7 + - - +
242A LEU* 3.0 43.7 + - + +
251A CYS* 4.4 12.3 - - - -
253A LEU* 3.7 27.6 - - + -
265A ALA* 3.8 19.3 - - + -
267A LEU* 4.6 1.6 - - + -
287A LEU* 4.6 4.7 - - + -
292A LEU* 3.7 29.4 - - + -
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Residues in contact with CYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A VAL* 3.3 25.7 + - - +
236A ASP* 4.0 6.5 - - - +
238A LEU* 1.3 74.3 - - - +
240A ARG* 1.4 52.9 + - + +
242A LEU* 3.2 8.1 + - - +
243A SER* 2.8 34.2 + - - -
248A PRO* 4.3 5.7 - - + +
251A CYS* 2.0 62.8 - - + -
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Residues in contact with ARG 240 (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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236A ASP* 3.2 55.0 + - - +
237A ALA* 3.9 9.5 - - - +
239A CYS* 1.4 74.6 - - + +
241A ALA* 1.4 58.3 + - - +
243A SER* 3.1 29.5 + - - +
244A ALA* 3.9 1.7 + - - +
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Residues in contact with ALA 241 (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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237A ALA 3.0 18.2 + - - +
238A LEU* 3.1 5.8 + - - +
240A ARG* 1.4 75.4 - - - +
242A LEU* 1.3 61.0 + - + +
243A SER 3.3 1.2 + - - -
244A ALA* 4.0 15.6 - - - +
281A GLN* 4.3 5.5 + - - -
282A ALA* 4.9 3.3 - - - +
285A LEU* 4.4 19.2 - - + +
287A LEU* 3.8 22.4 - - + -
292A LEU* 5.7 1.8 - - + -
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Residues in contact with LEU 242 (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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223A LEU* 4.7 4.7 - - + -
225A VAL* 3.8 22.9 - - + -
238A LEU* 3.0 39.7 + - + +
239A CYS 3.2 7.6 + - - +
240A ARG 3.2 0.4 - - - -
241A ALA* 1.3 77.8 - - + +
243A SER* 1.4 55.5 + - - +
244A ALA* 3.4 4.4 + - - -
245A VAL 5.0 0.3 + - - -
246A HIS 3.1 12.6 + - - +
248A PRO* 4.1 1.4 - - + +
267A LEU* 3.9 18.4 - - + -
269A TYR* 3.2 30.2 + - - +
278A ALA* 4.6 7.1 - - - +
281A GLN* 5.2 2.2 - - - +
282A ALA* 3.8 27.6 - - + -
292A LEU* 5.2 4.5 - - + -
294A VAL* 4.2 21.3 - - + -
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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