Contacts of the strand formed by residues 222 - 235 (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 LEU 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.9 31.4 - - + -
171A GLU* 3.8 39.0 + - + +
172A LEU* 3.8 16.4 - - + +
175A LEU* 3.9 28.2 - - + +
213A GLY* 4.3 1.3 - - - -
214A VAL 3.5 21.8 - - - +
215A ARG* 3.9 23.6 - - + +
220A LYS 3.4 3.0 + - - -
221A LYS* 1.3 80.6 - - - +
223A VAL* 1.3 63.6 + - - +
224A GLY 3.5 12.8 - - - +
251A HIS* 4.8 1.6 - - - -
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Residues in contact with VAL 223 (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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156A PHE* 4.0 19.1 - - + -
175A LEU* 4.1 5.8 - - - -
214A VAL* 2.8 19.8 + - + +
215A ARG 4.0 1.1 - - - -
216A VAL* 3.6 36.1 - - + +
221A LYS* 3.8 14.8 - - + +
222A LEU* 1.3 79.1 - - - +
224A GLY* 1.3 59.5 + - - +
250A VAL* 3.3 6.8 - - + +
251A HIS* 2.8 42.6 + - + -
254A LEU* 3.5 28.5 - - + -
259A VAL* 6.0 1.3 - - + -
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Residues in contact with GLY 224 (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* 4.1 3.3 - - - +
213A GLY* 3.3 4.0 - - - -
214A VAL* 2.9 38.9 + - - -
222A LEU* 3.5 8.2 - - - +
223A VAL* 1.3 81.7 - - - +
225A PHE* 1.3 64.0 + - - +
249A CYS 3.3 9.0 - - - -
250A VAL* 4.4 2.7 - - - -
259A VAL* 5.2 1.6 - - - -
263A LEU* 4.3 8.5 - - - -
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Residues in contact with PHE 225 (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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161A LEU* 3.7 30.7 - - + -
172A LEU* 3.6 31.6 - - + -
175A LEU* 3.9 17.5 - - + -
176A LEU* 5.3 0.9 - - + -
201A LEU* 4.3 9.4 - - + -
211A HIS* 3.7 33.7 - + + -
212A CYS 3.3 15.0 - - - -
213A GLY* 4.1 0.4 - - - -
224A GLY* 1.3 74.9 - - - +
226A ILE* 1.3 75.7 + - - +
227A SER* 3.8 24.9 - - - -
247A PHE* 3.2 25.9 - - + +
248A LEU* 3.3 5.0 - - - +
249A CYS* 2.9 31.6 + - + +
263A LEU* 3.9 6.3 - - - +
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Residues in contact with ILE 226 (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 0.5 - - - +
212A CYS* 2.9 40.0 + - + +
225A PHE* 1.3 84.6 - - - +
227A SER* 1.3 66.7 + - - +
245A ILE* 3.8 28.5 - - + -
246A ASN 3.9 7.9 - - - +
247A PHE 4.0 0.9 - - - -
248A LEU* 4.1 24.7 - - + -
263A LEU* 3.7 26.2 - - + +
264A ILE* 4.3 17.0 - - + -
267A ILE* 3.8 36.3 - - + -
1000C MYR 5.0 0.7 - - + -
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Residues in contact with SER 227 (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 LEU* 3.1 35.2 - - - +
210A TRP 3.2 9.0 - - - -
211A HIS* 4.2 3.1 - - - -
225A PHE* 3.8 11.4 - - - -
226A ILE* 1.3 78.4 - - - +
228A ALA* 1.3 60.8 + - - +
229A ILE* 5.4 0.7 - - - +
244A GLU 3.7 0.6 + - - +
245A ILE* 3.2 10.7 - - - +
246A ASN* 2.9 51.6 + - - +
247A PHE* 3.7 2.8 - - - -
267A ILE* 4.6 3.1 - - - -
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Residues in contact with ALA 228 (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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206A TRP* 5.8 0.3 - - - -
207A LEU 5.2 1.2 + - - +
210A TRP* 3.1 33.1 + - + +
211A HIS* 4.5 4.5 + - - -
227A SER* 1.3 73.4 - - - +
229A ILE* 1.3 68.4 + - - +
243A VAL* 3.8 15.5 - - + -
244A GLU 3.3 4.9 - - - -
245A ILE* 3.5 20.2 - - + -
267A ILE* 4.0 9.4 - - + +
271A VAL* 3.9 16.8 - - + -
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Residues in contact with ILE 229 (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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200A ALA 3.7 19.5 - - - +
201A LEU* 3.6 35.0 - - + +
203A PRO* 3.8 14.6 - - + -
206A TRP* 5.2 1.3 - - + -
210A TRP* 4.2 2.0 - - - -
211A HIS* 4.8 0.4 - - - +
227A SER* 5.4 0.4 - - - +
228A ALA* 1.3 79.7 - - - +
230A PRO* 1.3 72.8 - - + +
243A VAL* 3.2 3.5 - - - -
244A GLU* 2.9 64.2 + - + +
246A ASN* 6.4 1.6 - - + -
374A TRP* 4.1 21.3 - - + -
496A GLN* 5.5 0.7 - - - +
506A GOL 4.2 2.7 - - - +
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Residues in contact with PRO 230 (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 PRO* 4.7 8.7 - - + +
204A PRO 3.7 11.3 - - - +
205A GLY* 3.3 31.2 - - - +
206A TRP* 4.0 10.5 - - - +
210A TRP* 3.7 23.5 - - + -
229A ILE* 1.3 94.9 - - + +
231A ALA* 1.3 63.7 + - - +
241A LYS* 4.6 2.5 - - + -
242A MET 3.5 7.9 - - - +
276A ILE* 5.1 0.2 - - + -
370A GLU* 4.7 2.1 - - - +
374A TRP* 6.1 0.2 - - - -
509A GOL 3.8 17.6 + - - -
510A GOL 3.9 15.7 - - - +
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Residues in contact with ALA 231 (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* 1.3 77.9 - - - +
232A ASN* 1.3 63.6 + - - +
233A ILE* 3.6 14.7 + - + -
241A LYS* 3.6 3.8 - - - +
242A MET* 2.9 34.8 + - - +
244A GLU* 3.4 34.1 - - + +
364A PRO* 5.9 2.2 - - + -
370A GLU* 4.7 3.4 - - - +
509A GOL 3.6 8.0 + - - -
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Residues in contact with ASN 232 (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 ALA* 1.3 71.5 - - - +
233A ILE* 1.3 60.8 + - - +
234A ARG 4.2 0.2 - - - -
239A VAL* 4.4 12.0 - - + +
240A LYS 3.6 2.8 - - - -
241A LYS* 3.1 29.4 + - - +
364A PRO* 3.5 5.7 - - - +
365A VAL* 2.9 56.2 + - + +
367A ASP* 5.5 1.6 + - - +
370A GLU* 4.4 5.3 + - - -
509A GOL 3.4 27.9 + - - -
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Residues in contact with ILE 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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231A ALA* 3.9 16.2 - - + +
232A ASN* 1.3 78.9 - - - +
234A ARG* 1.3 62.6 + - - +
235A ILE 3.8 0.7 + - - -
238A SER 3.5 2.3 - - - +
239A VAL* 4.4 1.8 - - - -
240A LYS* 2.9 34.0 + - - +
242A MET* 3.7 36.5 - - + +
244A GLU* 3.7 22.2 - - + +
280A VAL* 4.2 15.5 - - + -
362A LEU* 3.6 30.1 - - + -
363A ALA 3.7 2.9 - - - +
364A PRO* 4.2 8.1 - - + -
493A LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 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 ASN 4.2 1.0 + - - -
233A ILE* 1.3 72.1 - - - +
235A ILE* 1.3 59.7 + - - +
236A TYR 2.9 34.7 + - - +
237A ASP* 4.8 4.3 - - - +
238A SER 3.2 11.4 - - - +
239A VAL* 3.9 24.0 - - + +
357A LEU 2.7 31.7 + - - -
358A LYS* 3.6 15.0 + - - +
360A PHE 2.8 25.6 + - - -
361A HIS* 3.5 6.8 + - - +
362A LEU* 3.3 7.4 - - - +
363A ALA* 2.8 53.8 + - - +
365A VAL* 4.0 11.4 - - + +
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Residues in contact with ILE 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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234A ARG* 1.3 71.8 - - - +
236A TYR* 1.4 88.2 + - + +
237A ASP 3.0 0.9 + - - -
238A SER* 2.9 30.6 + - - +
240A LYS* 4.7 2.2 - - + -
242A MET* 4.0 21.8 - - + -
291A ILE* 3.5 31.9 - - + -
361A HIS 3.4 5.8 - - - +
362A LEU* 4.6 7.4 - - + -
478A LEU* 3.6 13.0 - - + -
481A TRP* 3.5 37.3 + - + +
483A CYS* 3.5 12.3 - - - -
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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