Contacts of the strand formed by residues 284 - 297 (chain B) in PDB entry 2PI8
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 PHE 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B THR 4.2 12.6 - - - -
7B ASP 4.1 9.6 - - - +
8B ARG 3.5 26.7 - - - +
9B GLY* 3.5 22.0 - - - -
10B GLN 5.6 1.1 - - - -
276B PRO* 3.6 26.9 - - + -
277B LEU 3.3 16.6 - - - -
278B LEU* 4.5 1.3 - - - -
282B GLY 3.8 2.4 + - - -
283B LYS* 1.3 80.9 - - - +
285B ASN* 1.3 62.3 + - - +
286B GLY* 3.7 29.2 - - - -
287B GLN 3.7 15.3 - - - -
288B TYR* 3.8 16.4 - + - -
326B HIS* 3.8 10.7 + + + -
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU* 3.3 28.4 - - - +
278B LEU* 4.1 6.7 - - - +
279B ASP* 4.4 13.9 + - - +
283B LYS* 3.1 7.3 + - - +
284B PHE* 1.3 72.5 - - - +
286B GLY* 1.3 73.5 + - - +
287B GLN* 3.1 38.5 + - + +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B PHE* 3.3 31.1 - - - -
285B ASN* 1.3 80.8 + - - +
287B GLN* 1.3 60.9 + - - +
288B TYR* 3.9 10.4 - - - -
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Residues in contact with GLN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU* 3.0 34.8 + - + +
284B PHE* 3.7 5.7 - - - -
285B ASN* 3.3 29.3 - - - +
286B GLY* 1.3 78.7 - - - +
288B TYR* 1.3 65.2 + - - +
66D GLU* 3.0 31.7 + - - +
69D ARG* 3.2 35.5 - - - +
70D ALA* 5.0 7.5 - - - +
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY 2.7 34.4 + - - -
10B GLN 3.7 9.0 + - - -
11B GLN* 3.7 18.3 - - + +
30B VAL* 5.0 13.3 - - + +
274B GLU* 3.4 38.8 - - + +
275B VAL 3.4 4.7 - - - +
276B PRO* 3.8 13.0 - - + -
277B LEU* 3.4 16.5 - - - +
284B PHE* 3.8 9.3 - + - -
286B GLY 3.9 15.5 - - - -
287B GLN* 1.3 76.5 - - - +
289B GLU* 1.3 62.7 + - - +
327B TYR 3.9 11.2 - - - -
328B GLY* 4.1 6.7 - - - -
329B ARG* 3.5 30.3 - - - -
69D ARG* 3.6 13.4 + - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 5.1 1.8 - - - -
34B ILE* 3.2 33.8 - - + +
255B ARG* 5.0 5.0 + - - -
273B ALA 3.1 3.5 - - - +
274B GLU* 3.7 4.0 - - - -
275B VAL* 2.8 50.5 + - + +
277B LEU* 3.7 19.1 - - + +
288B TYR* 1.3 79.0 - - - +
290B LEU* 1.3 60.8 + - - +
291B ARG* 2.8 30.2 + - + +
324B TYR* 5.5 1.0 + - - -
69D ARG* 3.2 32.3 + - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA* 3.4 30.3 - - + -
30B VAL* 4.4 11.0 - - + +
31B GLY 4.0 3.8 - - - +
32B ALA* 3.8 36.3 - - - +
33B PRO* 3.9 7.7 - - + +
34B ILE* 3.4 28.9 + - + +
74B THR* 5.2 1.8 - - - -
272B ILE* 3.7 37.0 - - + -
273B ALA 3.4 10.8 - - - +
274B GLU* 3.4 23.3 + - + +
289B GLU* 1.3 71.6 - - - +
291B ARG* 1.3 64.6 + - - +
331B TRP* 4.6 3.4 - - + -
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 5.3 1.1 - - - -
34B ILE* 3.5 26.2 - - + +
35B ASN* 3.5 31.4 - - - +
38B ASP* 4.2 8.3 + - - -
255B ARG* 3.4 66.8 + - - +
271B LEU 3.6 1.9 - - - +
272B ILE* 3.3 4.5 - - - -
273B ALA* 2.9 34.6 + - - +
275B VAL* 4.7 12.6 - - + -
289B GLU* 2.8 28.0 + - + +
290B LEU* 1.3 79.6 - - - +
292B LEU* 1.3 63.2 + - - +
293B MSE 4.0 16.3 - - + +
309B ILE* 6.1 0.9 - - - -
37D GLY* 5.6 1.6 - - - -
69D ARG* 5.2 1.6 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 4.0 18.6 - - + -
35B ASN* 2.7 33.0 + - - +
39B PHE* 3.6 34.0 - - + -
64B VAL* 5.2 1.3 - - + -
67B TRP* 4.2 6.1 - - + -
68B LEU* 3.5 42.8 - - + -
256B ALA* 3.8 4.0 - - - -
270B THR* 4.3 8.7 - - + -
271B LEU 3.6 0.4 - - - -
272B ILE* 3.6 30.5 - - + +
291B ARG* 1.3 72.3 - - - +
293B MSE 1.3 61.0 + - - +
333B LEU* 3.6 20.4 - - + -
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Residues in contact with MSE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 4.5 0.2 - - - -
98B PHE* 5.0 4.5 - - + -
255B ARG 3.5 23.6 - - - +
256B ALA 3.2 14.1 - - - +
257B SER 3.9 1.6 - - - +
258B VAL* 3.5 33.2 - - + -
270B THR* 3.6 2.6 - - - +
271B LEU* 2.7 53.1 + - + +
273B ALA* 3.7 29.6 - - + -
275B VAL* 3.8 20.2 - - + -
291B ARG* 4.2 14.6 - - + +
292B LEU* 1.3 78.6 - - - +
294B VAL* 1.3 64.7 + - - +
309B ILE* 4.1 19.3 - - + -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.5 25.1 - - + -
42B GLN* 4.1 22.9 - - + -
43B ILE* 4.2 10.3 - - + -
46B ILE* 3.8 16.2 - - + -
61B TYR* 4.0 1.3 - - + +
256B ALA 3.1 6.1 + - - -
257B SER* 3.2 6.9 - - - -
258B VAL* 3.1 21.3 + - - -
268B GLY* 3.7 27.4 - - - +
269B THR 3.4 11.4 - - - +
270B THR* 4.6 5.2 - - - +
293B MSE 1.3 78.7 - - - +
295B ALA* 1.3 65.5 + - - +
296B LEU* 3.2 9.7 + - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B VAL* 3.5 15.3 - - + +
260B SER* 3.4 29.8 - - - +
265B ILE* 4.3 9.4 - - + -
266B PRO 3.9 16.6 - - - +
267B PRO* 3.2 6.2 - - + +
268B GLY 2.7 29.8 + - - -
269B THR 3.1 13.3 + - - +
271B LEU* 4.6 2.2 - - + +
294B VAL* 1.3 68.8 - - - +
296B LEU* 1.3 60.1 + - - +
297B ASP 3.8 1.1 - - - -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLN* 3.2 41.7 - - + +
46B ILE* 3.9 28.7 - - + -
53B LEU* 4.2 9.6 - - + -
246B GLY* 4.2 2.1 + - - -
247B ALA 3.8 2.1 + - - -
248B SER* 3.2 44.8 + - - +
250B VAL* 4.0 14.2 - - + +
252B LEU* 3.9 19.4 - - + +
257B SER* 4.5 1.6 - - - -
258B VAL 3.2 5.5 + - - -
267B PRO* 4.9 0.2 - - - -
268B GLY 4.2 7.0 - - - +
294B VAL* 3.2 15.3 + - + +
295B ALA* 1.3 82.0 - - - +
297B ASP* 1.3 64.7 + - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR* 2.9 29.1 + - - +
246B GLY* 3.7 9.6 - - - -
247B ALA* 2.8 22.8 + - - +
248B SER* 4.2 0.4 + - - -
252B LEU* 4.2 5.1 - - + +
258B VAL 3.7 2.5 + - - +
259B ALA* 3.8 7.2 - - + -
260B SER* 2.9 26.0 + - - +
267B PRO* 5.7 0.6 - - - +
295B ALA 3.8 0.4 - - - -
296B LEU* 1.3 79.9 - - - +
298B VAL* 1.3 80.8 + - - +
3F NAG 3.1 6.9 - - - -
4F NAG 2.9 37.1 + - - +
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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