Contacts of the helix formed by residues 235 - 249 (chain A) in PDB entry 3LX9
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ASP* 2.5 30.7 + - - +
234A ASP* 1.3 73.5 - - - +
236A TRP* 1.3 63.7 + - - +
237A LYS* 3.7 10.5 + - - +
238A SER* 3.0 19.1 + - - -
239A ILE* 3.3 23.0 + - - +
274A GLY 4.3 3.4 - - - -
275A LEU* 3.4 10.0 - - - +
236B TRP* 5.8 2.0 - - - -
358B GLU* 3.3 25.6 - - - -
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Residues in contact with TRP 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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235A SER* 1.3 70.6 - - - +
237A LYS* 1.3 65.9 + - - +
239A ILE* 3.2 28.4 + - + -
240A LYS* 2.9 54.9 + - + +
243A LEU* 5.2 3.4 - - + -
274A GLY 4.3 3.4 + - - +
275A LEU* 3.4 6.3 - - - +
279A GLN* 3.6 45.5 - - + +
282A THR* 3.9 25.8 - - + -
354A ILE* 4.9 2.0 - - + -
355A ASN 5.3 0.2 - - - -
356A ARG* 4.2 18.2 - - - -
358A GLU* 2.8 37.0 + - - -
410A THR* 3.5 34.7 - - + +
235B SER* 5.7 2.2 - - - -
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Residues in contact with LYS 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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235A SER* 3.8 10.1 - - - +
236A TRP* 1.3 80.2 - - - +
238A SER* 1.3 58.7 + - - +
240A LYS* 3.7 17.7 - - - +
241A SER* 2.9 30.2 + - - -
237B LYS* 6.5 2.0 - - + -
240B LYS* 5.6 8.2 - - - +
358B GLU* 5.7 0.9 - - - +
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Residues in contact with SER 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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231A ASP 4.1 3.6 + - - -
232A ILE* 3.3 14.6 - - - +
233A ASP* 3.1 48.8 + - - -
235A SER* 3.0 12.2 + - - -
236A TRP 3.2 0.2 - - - -
237A LYS* 1.3 77.6 - - - +
239A ILE* 1.3 57.6 + - - +
241A SER* 3.1 9.1 + - - -
242A ILE* 2.9 33.8 + - - +
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Residues in contact with ILE 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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232A ILE* 3.4 17.5 - - + -
235A SER 3.3 13.4 + - - +
236A TRP* 3.2 29.8 + - + +
238A SER* 1.3 75.5 - - - +
240A LYS* 1.3 58.2 + - - +
242A ILE* 3.3 5.6 + - - +
243A LEU* 3.0 40.7 + - + +
269A VAL* 4.4 4.7 - - + -
275A LEU* 4.2 16.8 - - + -
279A GLN 5.1 0.9 - - - +
282A THR* 4.9 0.7 - - + -
283A GLN* 3.3 49.4 - - + +
287A TRP* 4.1 12.6 - - + -
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 2.9 60.4 + - + +
237A LYS* 3.7 14.2 - - - +
239A ILE* 1.3 72.7 - - - +
241A SER* 1.3 62.7 + - - +
243A LEU* 3.9 6.0 - - - +
244A ASP* 2.9 37.9 + - - +
356A ARG* 3.6 35.2 - - - +
358A GLU* 2.7 27.4 + - - +
237B LYS* 5.6 9.5 - - - +
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Residues in contact with SER 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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229A PHE* 3.4 21.7 - - - -
237A LYS* 2.9 17.3 + - - -
238A SER* 3.3 12.6 - - - -
240A LYS* 1.3 78.5 - - - +
242A ILE* 1.3 56.3 + - - +
244A ASP* 4.0 4.5 - - - +
245A TRP* 3.0 30.1 + - - +
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Residues in contact with ILE 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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229A PHE* 4.0 26.7 - - + -
230A ALA 4.5 5.6 - - - +
232A ILE* 3.5 43.5 - - + -
238A SER* 2.9 21.4 + - - +
239A ILE* 3.3 4.7 + - - +
241A SER* 1.3 74.4 - - - +
243A LEU* 1.3 57.0 + - - +
245A TRP* 3.4 2.3 + - - +
246A THR* 2.7 40.4 + - - +
265A PRO* 3.4 46.7 - - + +
287A TRP* 3.9 11.9 - - + -
290A MET* 5.2 1.3 - - + -
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Residues in contact with LEU 243 (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 TRP* 5.2 4.0 - - + -
239A ILE* 3.0 35.8 + - + +
240A LYS* 3.9 6.3 - - - +
242A ILE* 1.3 77.0 - - - +
244A ASP* 1.3 61.0 + - - +
246A THR* 3.2 4.0 + - - -
247A SER* 2.9 31.6 + - - -
282A THR* 4.2 9.2 - - + -
286A LEU* 3.7 45.5 - - + -
287A TRP* 4.0 14.6 - - + -
290A MET* 4.1 13.5 - - + -
338A GLU* 5.4 1.6 - - - +
340A TRP* 3.8 12.0 - - + -
354A ILE* 4.2 14.8 - - + -
356A ARG* 5.0 7.0 - - - +
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Residues in contact with ASP 244 (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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240A LYS* 2.9 21.5 + - - +
241A SER* 4.0 4.8 - - - +
243A LEU* 1.3 73.2 - - - +
245A TRP* 1.3 61.6 + - - +
247A SER* 3.3 8.1 + - - -
248A PHE* 2.9 31.0 + - - +
338A GLU* 4.0 5.4 - - - +
356A ARG* 2.8 43.0 + - - -
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Residues in contact with TRP 245 (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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209A TRP* 3.3 42.2 - + - -
216A TYR* 4.6 3.6 - - - -
228A ASN* 3.5 43.1 - - + -
229A PHE* 3.1 47.8 - + + -
241A SER 3.0 19.4 + - - +
242A ILE* 3.7 3.6 - - + +
244A ASP* 1.3 77.6 - - - +
246A THR* 1.3 69.2 + - - +
248A PHE* 3.4 2.1 + - - -
249A ASN* 2.7 51.0 + - + +
252A ARG* 3.8 26.2 - - - -
253A ILE* 3.9 22.2 - - + -
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Residues in contact with THR 246 (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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242A ILE* 2.7 27.6 + - - +
243A LEU 3.2 4.2 + - - -
245A TRP* 1.3 89.3 - - - +
247A SER* 1.3 59.8 + - - +
249A ASN 3.1 2.1 + - - -
250A GLN* 2.8 34.3 + - + +
253A ILE* 4.0 18.1 - - + +
254A VAL* 5.8 0.7 - - + -
265A PRO* 4.9 3.1 - - - +
290A MET* 3.8 30.3 - - + -
327A GLN* 4.3 11.7 - - - +
340A TRP* 4.4 9.2 - - + -
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Residues in contact with SER 247 (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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243A LEU 2.9 23.0 + - - -
244A ASP* 3.3 12.1 + - - -
246A THR* 1.3 72.1 - - - +
248A PHE* 1.3 64.5 + - - +
250A GLN* 3.4 28.3 + - - +
251A GLU* 4.2 3.1 - - - +
330A GLN* 3.7 34.9 + - - +
333A GLN* 5.0 3.1 + - - -
340A TRP* 3.7 19.8 - - - -
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Residues in contact with PHE 248 (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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244A ASP 2.9 21.4 + - - +
245A TRP* 3.6 6.3 - - - +
247A SER* 1.3 78.6 + - - +
249A ASN* 1.3 73.3 + - - +
250A GLN 3.5 0.2 - - - -
251A GLU* 3.5 11.1 - - - +
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Residues in contact with ASN 249 (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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209A TRP* 4.1 8.3 + - - +
245A TRP* 2.7 63.4 + - + +
246A THR 3.1 3.1 + - - +
248A PHE* 1.3 97.3 - - - +
250A GLN* 1.3 61.5 + - - +
251A GLU* 3.3 3.6 - - - -
252A ARG* 3.0 51.4 + - - +
253A ILE* 3.3 12.7 + - + +
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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