Contacts of the helix formed by residues 233 - 253 (chain A) in PDB entry 5L04
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 ASN 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ARG* 1.3 80.6 - - - +
234A LEU* 1.3 61.8 + - - +
235A LEU* 3.1 13.1 + - - +
236A THR* 2.8 41.4 + - - -
237A ARG* 3.1 17.5 + - - +
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Residues in contact with LEU 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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233A ASN* 1.3 69.8 - - - +
235A LEU* 1.3 67.4 + - + +
237A ARG* 3.1 31.4 + - + +
238A MET* 3.0 56.0 + - + +
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Residues in contact with LEU 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* 3.1 9.8 + - - +
234A LEU* 1.3 84.4 - - + +
236A THR* 1.3 60.4 + - - +
238A MET* 3.5 25.3 - - + +
239A ARG* 3.0 28.8 + - - +
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Residues in contact with THR 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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232A ARG* 3.7 34.9 - - + +
233A ASN* 2.8 35.4 + - - -
235A LEU* 1.3 71.7 - - - +
237A ARG* 1.3 65.1 + - - +
239A ARG* 3.1 13.0 + - - +
240A ILE* 3.1 34.4 + - + +
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Residues in contact with ARG 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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217A TYR* 5.0 2.5 + - - +
229A ILE* 3.2 41.5 - - + +
230A ARG* 3.8 22.5 + - - +
232A ARG* 2.4 34.6 + - + +
233A ASN* 3.1 18.4 + - - +
234A LEU* 3.1 34.9 + - + +
236A THR* 1.3 73.7 - - - +
238A MET* 1.3 56.9 + - + +
240A ILE* 3.5 3.4 + - - +
241A ASN* 3.2 26.5 + - - +
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Residues in contact with MET 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 LEU* 3.0 42.5 + - + +
235A LEU* 3.5 35.0 - - + +
236A THR 3.2 0.2 - - - -
237A ARG* 1.3 74.9 - - + +
239A ARG* 1.3 68.2 + - - +
241A ASN* 3.7 5.1 + - - +
242A ASN* 3.1 35.6 + - - +
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Residues in contact with ARG 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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183A HIS* 6.3 0.6 - - - -
187A ASN* 4.8 12.7 + - - +
190A LEU* 6.2 0.8 - - - +
235A LEU 3.0 15.4 + - - +
236A THR* 3.3 13.2 - - - +
238A MET* 1.3 77.6 - - - +
240A ILE* 1.3 79.5 - - - +
242A ASN* 3.2 7.8 + - - +
243A VAL* 2.9 60.4 + - + +
261B ALA* 4.3 13.5 - - - +
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Residues in contact with ILE 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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186A GLU* 5.0 3.8 - - - +
190A LEU* 4.1 20.0 - - + +
217A TYR* 3.5 32.3 - - + +
229A ILE* 3.4 36.1 - - + -
232A ARG* 4.1 5.6 - - - +
236A THR* 3.1 37.0 + - + +
237A ARG* 3.9 3.6 - - - +
239A ARG* 1.3 91.3 - - - +
241A ASN* 1.3 69.3 - - - +
243A VAL* 3.0 7.3 + - - +
244A PHE* 3.0 21.8 + - - +
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Residues in contact with ASN 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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216A SER* 4.3 11.1 - - - -
217A TYR* 3.7 28.5 - - + -
218A LYS* 5.1 6.0 - - - +
237A ARG 3.2 14.4 + - - +
238A MET* 3.9 7.0 - - - +
240A ILE* 1.3 81.3 - - - +
242A ASN* 1.3 62.0 + - - +
244A PHE* 3.4 4.3 - - - +
245A LYS* 3.0 54.8 + - - +
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Residues in contact with ASN 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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238A MET* 3.1 29.1 + - - +
239A ARG* 3.5 7.2 - - - +
240A ILE 3.1 0.2 - - - -
241A ASN* 1.3 82.9 - - - +
243A VAL* 1.3 59.7 + - + +
245A LYS* 3.2 9.1 + - - +
246A ASP* 2.8 36.8 + - - +
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Residues in contact with VAL 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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187A ASN* 4.2 7.2 - - - +
190A LEU* 4.2 8.1 - - + -
239A ARG* 2.9 48.7 + - + +
240A ILE* 3.6 7.9 - - - +
242A ASN* 1.3 76.3 - - + +
244A PHE* 1.3 56.5 + - - +
246A ASP* 3.2 13.6 + - + +
247A PHE* 2.9 63.3 + - + -
261B ALA* 4.1 16.2 - - + -
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Residues in contact with PHE 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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190A LEU* 4.0 26.6 - - + +
193A ALA* 4.0 10.5 - - + -
194A VAL* 3.9 21.8 - - + -
197A ILE* 4.5 10.8 - - + -
216A SER* 3.9 11.0 - - - -
217A TYR* 3.3 59.2 - + + -
240A ILE 3.0 11.9 + - - +
241A ASN* 3.4 13.2 - - - +
243A VAL* 1.3 77.6 - - - +
245A LYS* 1.3 72.4 + - + +
247A PHE* 3.4 5.5 + - - +
248A LEU* 3.0 48.9 + - + +
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Residues in contact with LYS 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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210A GLU* 4.0 21.3 + - - +
216A SER* 4.5 12.9 - - - +
241A ASN* 3.0 44.4 + - - +
242A ASN* 3.2 12.8 + - - +
244A PHE* 1.3 90.6 - - + +
246A ASP* 1.3 59.9 + - - +
248A LEU* 3.6 3.1 - - + +
249A LYS* 2.9 62.6 + - + +
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Residues in contact with ASP 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 ASN* 2.8 24.0 + - - +
243A VAL* 3.2 16.8 + - + +
245A LYS* 1.3 71.1 - - - +
247A PHE* 1.3 65.3 + - + +
249A LYS* 3.4 4.6 + - - +
250A GLU* 2.9 32.7 + - - +
261B ALA* 6.2 0.2 - - - +
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Residues in contact with PHE 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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187A ASN* 3.2 28.5 - - - -
190A LEU* 4.2 20.4 - - + -
191A GLY 4.7 2.0 - - - -
194A VAL* 4.0 12.8 - - + -
243A VAL* 2.9 40.1 + - + +
244A PHE* 3.4 4.9 + - - +
246A ASP* 1.3 76.6 - - + +
248A LEU* 1.3 57.8 + - - +
250A GLU* 3.3 3.1 + - - +
251A PHE* 2.9 32.1 + - - +
261B ALA* 4.1 11.0 - - + -
262B LYS 3.1 34.8 - - - -
263B MET* 3.4 21.7 - - - +
264B PRO* 3.7 23.3 - - + -
267B LEU* 4.0 6.3 - - + -
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Residues in contact with LEU 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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194A VAL* 3.8 26.4 - - + +
197A ILE* 4.2 28.3 - - + -
198A SER* 4.3 2.2 - - - +
244A PHE* 3.0 35.9 + - + +
245A LYS* 3.6 5.6 - - + +
247A PHE* 1.3 76.3 - - - +
249A LYS* 1.3 84.2 + - + +
251A PHE 3.4 0.3 + - - -
252A ASN* 2.8 52.9 + - - +
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Residues in contact with LYS 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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208A LEU* 6.1 4.9 - - - -
210A GLU* 5.2 5.5 + - - +
245A LYS* 2.9 58.6 + - + +
246A ASP* 3.9 4.3 - - - +
248A LEU* 1.3 93.2 - - - +
250A GLU* 1.3 67.3 + - - +
252A ASN* 5.2 1.8 - - - -
253A ASN* 3.1 43.1 + - - +
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Residues in contact with GLU 250 (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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246A ASP 2.9 19.0 + - - +
247A PHE 3.3 4.5 + - - +
249A LYS* 1.3 75.5 - - - +
251A PHE* 1.3 60.2 + - - +
253A ASN* 5.2 0.7 - - - -
254A LYS* 3.2 46.6 - - - +
255A THR* 3.3 4.8 + - - +
263B MET* 3.4 32.5 - - + +
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Residues in contact with PHE 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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194A VAL* 3.6 17.9 - - + -
195A LEU* 4.0 6.5 - - + -
198A SER* 3.2 29.4 - - - -
247A PHE 2.9 17.2 + - - +
248A LEU 3.8 4.3 - - - +
249A LYS 3.1 0.4 - - - -
250A GLU* 1.3 77.6 - - - +
252A ASN* 1.3 62.3 + - - +
255A THR* 3.0 46.5 + - + -
256A ILE* 3.0 29.1 + - + +
261A VAL* 4.7 2.7 - - + -
266A LEU* 3.6 32.8 - - + -
263B MET* 4.3 3.4 - - + -
267B LEU* 3.6 25.6 - - + -
269B PHE* 3.5 28.5 - + - -
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Residues in contact with ASN 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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198A SER* 3.2 32.2 + - - +
201A ALA* 5.5 4.3 - - - +
202A MET* 6.0 0.9 - - - +
207A GLN* 4.7 20.7 + - + +
208A LEU 5.8 1.6 + - - -
248A LEU* 2.8 38.7 + - - +
249A LYS* 4.4 1.6 - - - +
251A PHE* 1.3 78.4 - - - +
253A ASN* 1.3 70.9 + - - +
256A ILE* 4.0 25.9 - - + +
257A CYS* 4.4 6.4 - - - -
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Residues in contact with ASN 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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207A GLN* 5.7 2.1 + - - -
208A LEU* 5.8 4.3 - - - +
249A LYS* 3.1 29.8 + - - +
250A GLU* 5.2 0.7 - - - +
252A ASN* 1.3 84.7 - - - +
254A LYS* 1.3 68.3 + - + +
257A CYS* 3.7 16.8 + - - +
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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