Contacts of the helix formed by residues 232 - 241 (chain A) in PDB entry 1LWW
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 SER 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A SER* 1.3 75.8 - - - +
233A TYR* 1.3 53.3 + - - +
234A GLU* 3.6 16.3 + - - +
235A GLU* 2.7 38.4 + - - +
236A ALA* 2.7 32.9 + - - +
261A LYS* 4.2 2.0 - - - -
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Residues in contact with TYR 233 (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 SER* 1.3 71.2 - - - +
234A GLU* 1.3 77.5 + - - +
237A HIS* 2.8 48.9 + + + +
252A ASP* 2.4 32.2 + - - -
255A CYS* 3.9 15.7 - - + -
261A LYS* 3.6 22.8 - - + +
263A GLN* 3.5 36.4 - - + +
264A ALA* 3.4 25.7 - - + -
265A VAL 5.2 0.2 + - - -
304A ARG* 3.8 35.7 + - - -
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Residues in contact with GLU 234 (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 SER* 3.7 18.0 + - - +
233A TYR* 1.3 98.9 + - - +
235A GLU* 1.3 67.5 + - + +
237A HIS* 4.1 4.2 - - - +
238A LYS* 3.4 19.9 + - - +
263A GLN* 4.8 5.4 + - - -
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Residues in contact with GLU 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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228A LEU* 6.1 0.4 - - - -
231A SER* 3.9 11.0 - - - -
232A SER* 2.7 41.5 + - - +
234A GLU* 1.3 74.7 - - - +
236A ALA* 1.3 66.7 + - - +
238A LYS* 3.2 7.3 + - - +
239A ALA* 3.1 23.1 + - - +
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Residues in contact with ALA 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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228A LEU* 4.0 29.0 - - + +
231A SER* 4.5 0.6 - - - -
232A SER 2.7 12.3 + - - +
233A TYR 3.8 1.8 - - - +
235A GLU* 1.3 74.3 - - - +
237A HIS* 1.3 62.7 + - - +
239A ALA* 3.4 1.9 + - - +
240A LEU* 3.1 27.0 + - - +
255A CYS* 3.9 12.3 - - - -
259A LEU* 4.3 3.4 - - + -
261A LYS* 3.5 33.0 - - - -
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Residues in contact with HIS 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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233A TYR* 2.8 37.6 + + + +
234A GLU* 4.1 3.8 - - - +
236A ALA* 1.3 74.0 - - - +
238A LYS* 1.3 65.5 + - - +
240A LEU* 3.5 2.3 + - - +
241A CYS* 3.3 44.5 + - - -
248A THR* 3.2 37.6 + - + +
251A ALA* 3.7 13.5 - - + +
252A ASP* 3.1 32.2 + - - -
255A CYS* 3.8 6.4 - - - -
297A LYS* 6.4 0.4 - - - -
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Residues in contact with LYS 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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234A GLU 3.4 11.2 + - - +
235A GLU* 3.2 10.6 + - - +
237A HIS* 1.3 80.2 + - - +
239A ALA* 1.3 66.6 + - - +
241A CYS* 3.3 18.2 + - + +
242A ILE* 3.7 17.2 + - - +
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Residues in contact with ALA 239 (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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224A TRP* 3.8 26.7 - - + +
228A LEU* 4.2 16.8 - - + -
235A GLU 3.1 10.0 + - - +
236A ALA 3.6 7.9 - - - +
237A HIS 3.3 0.2 - - - -
238A LYS* 1.3 82.0 - - - +
240A LEU* 1.3 63.2 + - - +
242A ILE* 2.9 36.0 + - + +
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Residues in contact with LEU 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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141A LEU* 4.9 1.3 - - + -
224A TRP* 4.7 4.5 - - + -
225A LEU* 3.9 26.9 - - + -
228A LEU* 4.1 10.3 - - + -
236A ALA 3.1 17.5 + - - +
237A HIS 3.9 0.2 - - - +
239A ALA* 1.3 77.5 - - - +
241A CYS* 1.3 58.5 + - - +
242A ILE 2.9 5.7 + - - -
243A LEU* 3.0 28.2 + - + +
246A VAL* 3.4 17.7 - - + +
251A ALA* 3.7 31.9 - - + +
254A ILE* 3.6 39.7 - - + -
255A CYS* 4.0 3.8 - - - -
259A LEU* 3.8 13.9 - - + -
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Residues in contact with CYS 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 HIS* 3.3 40.9 + - - +
238A LYS* 3.6 15.0 - - + +
239A ALA 3.2 1.2 - - - -
240A LEU* 1.3 76.8 - - - +
242A ILE* 1.3 61.4 + - - +
243A LEU 3.3 2.5 - - - +
246A VAL 3.4 17.9 - - - +
247A GLY* 3.8 23.1 - - - -
248A THR* 4.3 2.2 - - - -
251A ALA* 3.8 2.5 - - - -
26E C 5.1 4.3 + - - -
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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