Contacts of the strand formed by residues 238 - 250 (chain A) in PDB entry 6PAU
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ILE 3.5 0.5 - - - +
234A ARG* 3.2 1.1 - - - -
235A ILE* 2.9 45.0 + - - +
237A ASP* 1.3 80.6 + - - +
239A VAL* 1.3 60.9 + - - +
240A LYS* 3.7 7.8 + - - -
481A TRP* 3.9 30.7 - - - -
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Residues in contact with VAL 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 ASN* 4.4 19.3 - - + +
233A ILE 3.6 5.8 - - - +
234A ARG* 3.9 24.9 - - + +
237A ASP 3.6 5.2 + - - +
238A SER* 1.3 72.3 - - - +
240A LYS* 1.3 67.5 + - - +
365A VAL* 4.1 24.9 - - + -
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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
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141A ASP* 5.3 6.9 + - - -
232A ASN* 3.6 4.6 - - - -
233A ILE 2.9 32.0 + - - +
235A ILE* 4.7 1.1 - - + -
238A SER* 4.4 12.1 - - - +
239A VAL* 1.3 80.6 - - - +
241A LYS* 1.3 64.8 + - - +
242A MET* 3.4 30.0 + - + +
278A GLN* 3.4 25.7 + - - +
481A TRP* 4.0 33.4 - - + -
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Residues in contact with LYS 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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230A PRO* 4.6 0.4 - - + -
231A ALA 3.6 15.0 - - - +
232A ASN* 3.1 32.5 + - - +
240A LYS* 1.3 76.3 - - - +
242A MET* 1.3 67.3 + - - +
276A ILE* 3.6 35.7 - - + +
277A PHE 5.0 0.2 + - - -
278A GLN* 4.7 6.6 - - - +
509A GOL 3.8 19.1 + - - +
510A GOL 3.3 31.1 + - - +
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Residues in contact with MET 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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230A PRO* 3.5 5.2 - - - +
231A ALA 2.9 32.6 + - - +
233A ILE* 3.7 37.0 - - + +
235A ILE* 4.0 20.2 - - + -
240A LYS* 3.7 27.1 - - + +
241A LYS* 1.3 81.7 - - - +
243A VAL* 1.3 70.7 + - - +
276A ILE* 3.8 4.3 - - - +
278A GLN* 3.5 30.5 - - + +
279A ALA 4.0 21.8 - - - +
280A VAL* 4.3 1.1 - - - -
478A LEU* 4.3 15.0 - - + -
481A TRP* 5.4 3.1 - - + -
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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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210A TRP* 3.7 31.4 - - + -
228A ALA* 3.8 9.0 - - + -
229A ILE 3.2 8.1 - - - +
242A MET* 1.3 83.4 - - - +
244A GLU* 1.3 63.0 + - - +
245A ILE* 3.9 16.6 - - + -
271A VAL* 3.6 38.4 - - + -
276A ILE* 4.2 2.7 - - + -
278A GLN 3.4 2.7 + - - +
279A ALA* 3.3 22.6 - - + +
280A VAL* 2.9 25.3 + - - +
1000C MYR 3.9 3.8 - - + -
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Residues in contact with GLU 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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227A SER* 3.7 0.9 + - - +
228A ALA* 3.3 4.0 - - - -
229A ILE* 2.9 48.8 + - + +
231A ALA* 3.4 28.5 - - + +
233A ILE* 3.7 11.6 - - - +
243A VAL* 1.3 72.7 - - - +
245A ILE* 1.3 63.0 + - - +
246A ASN* 4.0 3.4 + - + +
280A VAL* 3.3 23.8 - - + +
364A PRO* 5.4 1.2 - - - +
493A LEU* 4.0 2.8 - - - +
495A LEU* 3.6 21.1 - - + +
506A GOL 2.6 42.4 + - - -
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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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226A ILE* 3.8 23.6 - - + -
227A SER 3.2 4.7 - - - +
228A ALA* 3.5 29.2 - - + -
243A VAL* 3.9 5.2 - - + -
244A GLU* 1.3 70.0 - - - +
246A ASN* 1.3 69.7 + - - +
267A ILE* 4.1 9.6 - - + -
271A VAL* 5.0 0.2 - - + -
279A ALA* 4.3 9.6 - - + -
280A VAL 3.2 5.8 + - - +
281A TYR* 3.6 26.2 - - + +
282A THR 4.8 0.5 + - - -
495A LEU* 4.8 5.2 - - - +
3C LYS* 4.5 0.5 + - - -
1000C MYR 3.6 70.3 - - + +
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Residues in contact with ASN 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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180A TYR* 3.3 13.2 + - - -
192A TYR* 5.5 0.3 + - - -
200A ALA* 6.0 0.2 - - - +
201A LEU* 5.8 0.2 - - + -
226A ILE* 3.9 1.7 - - - +
227A SER* 2.9 36.4 + - - +
229A ILE* 6.4 1.3 - - + -
244A GLU* 5.0 3.8 - - + +
245A ILE* 1.3 78.8 - - - +
247A PHE* 1.3 104.3 + - + +
248A LEU 3.2 4.0 + - - -
282A THR* 6.0 0.7 - - - -
495A LEU* 4.7 8.9 - - + +
496A GLN* 2.8 38.1 + - - +
3C LYS* 3.4 12.1 + - - +
1000C MYR 3.2 5.8 - - - -
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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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176A LEU* 3.9 20.8 - - + +
180A TYR* 3.4 23.1 + + - -
192A TYR* 3.8 37.7 - + - -
196A PHE* 5.0 0.2 - + - -
197A LEU* 3.8 23.3 - - + -
200A ALA* 4.1 21.1 - - + -
201A LEU* 3.8 21.8 - - + -
225A PHE* 3.2 34.1 - + + +
226A ILE* 4.4 0.2 - - - -
227A SER* 3.7 15.0 - - - -
246A ASN* 1.3 104.2 + - + +
248A LEU* 1.3 64.6 + - - +
249A CYS* 3.1 8.5 + - - +
496A GLN* 4.9 1.3 - - - -
1000C MYR 3.2 2.4 + - - -
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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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180A TYR* 3.6 2.5 - - - -
225A PHE 3.3 12.8 - - - +
226A ILE* 4.1 17.3 - - + -
246A ASN 3.2 1.8 + - - -
247A PHE* 1.3 75.2 - - - +
249A CYS* 1.3 62.6 + - - +
260A ALA* 4.4 9.6 - - + +
263A LEU* 4.0 21.1 - - + -
264A ILE* 4.1 24.2 - - + -
511A 4PS 3.0 63.0 + - + +
1000C MYR 3.0 38.7 + - + +
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Residues in contact with CYS 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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175A LEU* 4.2 16.3 - - + +
176A LEU* 3.8 26.0 - - + -
179A ASN* 3.5 43.5 - - - -
180A TYR* 3.8 11.4 - - + -
224A GLY* 3.3 3.1 - - - -
225A PHE* 2.9 33.5 + - + +
247A PHE 3.1 1.8 + - - +
248A LEU* 1.3 77.1 - - - +
250A VAL* 1.3 69.3 + - - +
511A 4PS 3.5 6.3 - - - -
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Residues in contact with VAL 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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179A ASN* 4.1 1.4 - - - +
223A VAL* 3.3 10.1 - - + +
224A GLY* 4.7 0.4 - - - -
248A LEU* 4.8 0.4 - - + -
249A CYS* 1.3 84.3 - - - +
251A HIS* 1.3 68.6 + - - +
254A LEU* 3.6 26.5 - - + +
255A ARG* 2.8 34.9 + - + -
259A VAL* 4.3 10.1 - - + -
260A ALA* 4.2 6.1 - - + +
263A LEU* 4.1 20.6 - - + -
501A MG 4.4 0.7 - - - -
511A 4PS 2.9 47.4 + - + +
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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