Contacts of the helix formed by residues 238 - 258 (chain A) in PDB entry 4LXZ
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 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLY 4.3 3.6 - - - +
237A ILE* 1.3 76.1 - - - +
239A ASP* 1.3 64.5 + - - +
240A GLU* 3.6 8.6 + - - +
241A SER* 3.0 30.4 + - - -
242A TYR* 3.0 18.9 + - - +
280A ASN* 3.8 20.6 - - + +
281A LEU* 3.4 11.5 - - - +
352A PRO* 5.8 2.2 - - + -
357A ASN* 3.4 19.1 + - - +
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASP* 1.3 75.0 - - - +
240A GLU* 1.3 57.3 + - - +
242A TYR* 3.4 1.7 + - - +
243A GLY* 2.9 28.9 + - - -
280A ASN 4.4 1.3 + - - -
281A LEU* 3.4 9.7 - - - +
282A THR* 2.6 56.0 + - - +
284A LYS* 4.9 1.4 - - - +
285A GLY* 3.3 24.8 + - - -
288A LYS* 5.0 3.6 + - - +
352A PRO* 6.3 0.2 - - - -
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Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASP* 3.3 10.6 + - - +
239A ASP* 1.3 78.9 - - - +
241A SER* 1.3 56.3 + - - +
243A GLY* 3.5 1.2 + - - -
244A GLN* 3.0 27.5 + - - +
288A LYS* 6.2 0.4 - - - +
222C GLY* 5.2 8.3 + - - -
225C LYS* 4.1 27.9 + - - +
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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
----------------------------------------------------------
237A ILE* 3.7 21.8 - - - -
238A ASP* 3.0 20.2 + - - -
240A GLU* 1.3 73.2 - - - +
242A TYR* 1.4 65.7 + - - +
244A GLN* 3.1 33.6 + - - +
245A ILE* 3.6 9.5 + - - +
357A ASN* 3.1 15.6 + - - -
359A ASN 4.3 3.6 + - - -
361A PRO* 5.7 3.8 - - - +
364A MET* 3.8 13.6 - - - +
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Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 3.5 26.2 + - + +
203A PHE* 3.2 26.9 + + + +
233A MET* 3.8 20.6 - - + -
237A ILE* 3.9 21.6 - - + +
238A ASP 3.0 16.5 + - - +
239A ASP* 3.9 2.7 - - - +
241A SER* 1.4 74.5 - - - +
243A GLY* 1.3 59.1 + - - +
245A ILE* 3.1 9.9 + - + +
246A PHE* 2.9 46.6 + + + +
279A PHE* 4.4 9.5 - + - -
281A LEU* 3.7 38.1 - - + -
285A GLY 5.2 4.7 - - - +
289A CYS* 3.6 31.6 - - - -
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Residues in contact with GLY 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP 2.9 16.0 + - - -
240A GLU 3.8 1.8 - - - -
242A TYR* 1.3 77.2 - - - +
244A GLN* 1.4 59.4 + - - +
245A ILE 3.4 0.3 + - - -
246A PHE* 4.1 9.3 + - - -
247A LYS* 4.3 7.1 + - - +
248A PRO* 4.3 7.6 - - - +
288A LYS* 3.6 34.6 + - - -
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Residues in contact with GLN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU 3.0 13.0 + - - +
241A SER* 3.1 27.0 + - - +
243A GLY* 1.4 74.1 - - - +
245A ILE* 1.3 62.8 + - + +
248A PRO* 3.3 18.4 - - - +
361A PRO* 3.2 41.4 + - - +
364A MET* 3.8 16.4 - - - +
365A GLU* 4.1 13.1 + - - +
368A LYS* 4.4 4.9 - - - -
194C THR* 4.2 5.9 - - - +
221C ALA* 4.1 25.4 - - + +
222C GLY 5.3 1.0 + - - -
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Residues in contact with ILE 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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203A PHE* 3.5 35.2 - - + -
231A PHE* 3.8 19.7 - - + -
233A MET* 3.9 11.0 - - + -
241A SER 3.8 0.7 - - - +
242A TYR* 3.5 11.4 - - + +
244A GLN* 1.3 87.8 - - + +
246A PHE* 1.3 69.1 + - + +
247A LYS 3.6 1.3 - - - -
248A PRO* 3.6 5.4 - - - +
249A ILE* 3.1 27.8 + - + +
364A MET* 3.4 56.5 - - + +
368A LYS* 4.1 15.3 - - + -
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Residues in contact with PHE 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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178A ILE* 3.8 12.1 - - + -
180A ILE* 3.6 16.2 - - + -
203A PHE* 3.5 35.4 - + - -
242A TYR* 2.9 34.0 + + + +
243A GLY* 4.1 3.6 + - - -
244A GLN 3.9 0.2 - - - -
245A ILE* 1.3 81.1 - - + +
247A LYS* 1.3 59.9 + - - +
249A ILE* 3.8 0.5 - - - +
250A ILE* 2.9 49.2 + - + +
264A LEU* 5.0 0.7 - - + -
289A CYS* 3.5 51.1 - - + -
292A VAL* 3.9 19.5 - - + -
293A VAL* 4.1 7.2 - - + -
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY* 4.3 8.6 + - - +
246A PHE* 1.3 78.5 - - - +
248A PRO* 1.4 65.3 - - + +
250A ILE* 4.2 0.2 - - - +
251A SER* 2.8 48.7 + - - +
288A LYS* 6.0 5.2 - - - -
292A VAL* 4.0 36.3 - - + +
295A THR* 5.9 4.9 - - - -
296A PHE* 5.8 2.2 - - + -
217C ARG* 4.7 21.1 - - - +
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Residues in contact with PRO 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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243A GLY 4.3 2.5 - - - +
244A GLN 3.3 22.9 - - - +
245A ILE* 3.6 12.1 - - - +
247A LYS* 1.4 93.2 - - + +
249A ILE* 1.4 55.9 + - - +
251A SER* 3.6 5.0 + - - -
252A LYS* 3.1 28.9 + - - +
368A LYS* 3.9 22.2 - - + +
372A PHE* 3.7 12.8 - - + -
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Residues in contact with ILE 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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201A VAL* 4.4 8.7 - - + -
203A PHE* 3.9 23.1 - - + -
229A VAL* 4.9 7.4 - - + -
231A PHE* 4.5 13.0 - - + -
245A ILE 3.1 23.4 + - - +
246A PHE 3.9 1.8 - - - +
248A PRO* 1.4 71.3 - - - +
250A ILE* 1.3 63.2 + - + +
252A LYS* 3.2 3.6 + - - +
253A VAL* 2.9 39.7 + - + +
368A LYS* 3.8 28.5 - - + -
371A LEU* 3.8 33.4 - - + -
372A PHE* 3.9 14.4 - - + -
375A LEU* 4.5 3.8 - - + +
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 4.9 1.6 - - + -
178A ILE* 3.8 39.0 - - + -
201A VAL* 4.2 19.7 - - + -
203A PHE* 4.2 6.3 - - + -
246A PHE* 2.9 42.9 + - + +
247A LYS 4.2 1.1 - - - +
249A ILE* 1.3 76.0 - - + +
251A SER* 1.3 57.8 + - - +
253A VAL* 3.2 8.7 + - + +
254A MET* 2.8 46.1 + - + +
292A VAL* 4.5 7.2 - - + -
293A VAL* 4.6 6.7 - - + -
296A PHE* 4.0 20.0 - - + -
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Residues in contact with SER 251 (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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247A LYS* 2.8 45.2 + - - +
248A PRO* 3.8 5.8 - - - -
250A ILE* 1.3 72.8 - - - +
252A LYS* 1.4 55.2 + - - +
254A MET* 3.3 2.9 + - - +
255A GLU* 3.0 30.1 + - - +
296A PHE* 3.7 24.1 - - - -
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Residues in contact with LYS 252 (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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248A PRO 3.1 17.6 + - - +
249A ILE 3.7 3.4 - - - +
251A SER* 1.4 72.2 - - - +
253A VAL* 1.3 60.6 + - - +
255A GLU* 3.0 30.9 + - - +
256A MET* 2.9 50.5 + - + +
372A PHE* 3.8 29.6 - - + +
375A LEU* 3.7 27.8 - - + -
376A ARG* 6.3 4.7 - - + -
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Residues in contact with VAL 253 (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 LEU* 3.6 32.1 - - + -
199A MET* 3.6 24.2 - - - -
201A VAL* 4.3 12.1 - - + -
229A VAL* 5.1 2.5 - - + -
249A ILE* 2.9 29.5 + - + +
250A ILE* 3.5 8.7 - - + +
252A LYS* 1.3 75.8 - - - +
254A MET* 1.3 54.2 + - - +
257A TYR* 2.7 42.0 + - + +
375A LEU* 3.8 30.3 - - + -
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Residues in contact with MET 254 (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 LEU* 3.8 20.4 - - + -
250A ILE* 2.8 33.1 + - + +
251A SER 3.6 4.7 - - - +
252A LYS 3.3 0.2 - - - -
253A VAL* 1.3 71.4 - - - +
255A GLU* 1.3 59.4 + - - +
258A GLN* 2.9 31.5 + - - +
259A PRO* 3.7 26.9 - - - +
262A VAL* 3.9 18.2 - - + -
293A VAL* 4.7 8.5 - - + -
296A PHE* 3.7 56.3 - - + -
298A LEU* 3.9 9.4 - - + -
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Residues in contact with GLU 255 (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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251A SER 3.0 16.8 + - - +
252A LYS* 3.0 38.9 + - - +
254A MET* 1.3 78.1 - - - +
256A MET* 1.3 68.1 + - - +
258A GLN* 3.1 26.4 + - - +
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Residues in contact with MET 256 (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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252A LYS* 2.9 38.5 + - + +
253A VAL* 4.2 2.2 - - - +
255A GLU* 1.3 94.2 - - - +
257A TYR* 1.3 61.6 + - - +
258A GLN* 4.1 8.1 + - - +
375A LEU* 3.4 29.2 - - + +
376A ARG* 4.5 8.1 - - - +
378A LEU* 3.8 42.0 - - + +
379A PRO* 4.4 18.7 - - - +
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Residues in contact with TYR 257 (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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174A ARG* 3.0 49.1 + - + +
175A VAL 3.6 17.7 - - - -
176A LEU* 4.3 4.7 - - + -
196A ASP 2.7 30.2 + - - -
197A ARG 3.0 23.4 + - - -
198A VAL 3.2 2.3 + - - -
199A MET* 3.3 34.1 + - + -
227A TYR* 3.6 29.4 - + - -
253A VAL* 2.7 21.9 + - + +
256A MET* 1.3 73.3 - - - +
258A GLN* 1.3 67.8 + - - +
259A PRO* 3.7 17.7 - - + -
378A LEU* 4.0 9.9 - - + -
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Residues in contact with GLN 258 (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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174A ARG* 2.9 33.4 + - - +
254A MET 2.9 21.1 + - - +
255A GLU* 3.1 24.6 + - - +
256A MET* 4.1 9.0 + - - +
257A TYR* 1.3 69.4 - - - +
259A PRO* 1.4 71.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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