Contacts of the strand formed by residues 284 - 297 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 3.8 11.2 - - - -
7A ASP* 3.0 28.9 - - - +
9A GLY* 3.4 24.7 - - - -
276A PRO* 3.6 27.4 - - + -
277A LEU 3.2 17.0 - - - -
278A LEU* 4.5 0.2 - - - -
282A GLY 3.7 3.0 + - - -
283A LYS* 1.3 81.0 - - - +
285A ASN* 1.3 62.1 + - - +
286A GLY* 3.6 30.3 - - - -
287A GLN 3.6 15.5 - - - -
288A TYR* 3.9 12.3 - + - -
326A HIS* 3.8 17.6 + + + +
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Residues in contact with ASN 285 (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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277A LEU* 3.3 23.4 - - - +
278A LEU* 4.1 10.4 - - - +
279A ASP* 4.4 13.7 + - + +
283A LYS* 3.1 7.6 + - - +
284A PHE* 1.3 72.8 - - - +
286A GLY* 1.3 72.6 + - - +
287A GLN* 3.2 40.0 + - + +
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Residues in contact with GLY 286 (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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284A PHE* 3.3 32.4 - - - -
285A ASN* 1.3 81.0 + - - +
287A GLN* 1.3 59.7 + - - +
288A TYR* 3.8 9.9 - - - -
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Residues in contact with GLN 287 (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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277A LEU* 3.0 35.7 + - + +
284A PHE* 3.6 7.3 - - - -
285A ASN* 3.2 30.2 + - - +
286A GLY* 1.3 79.6 - - - +
288A TYR* 1.3 64.4 + - - +
66C GLU* 5.3 7.1 + - - +
69C ARG* 2.9 47.6 - - - +
70C ALA* 4.3 15.3 - - - +
71C GLY 5.5 0.9 - - - +
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Residues in contact with TYR 288 (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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9A GLY* 2.8 26.6 + - - -
11A GLN* 2.8 37.6 + - + -
30A VAL* 5.9 2.8 - - - +
274A GLU* 3.4 48.5 - - + +
275A VAL 3.4 4.9 - - - +
276A PRO* 3.8 15.0 - - + -
277A LEU* 3.4 14.5 - - - +
284A PHE* 3.9 9.4 - + - -
286A GLY 3.8 16.2 - - - -
287A GLN* 1.3 78.1 - - - +
289A GLU* 1.3 64.4 + - - +
327A TYR 4.0 12.3 - - - -
328A GLY* 4.6 4.5 - - - -
329A ARG* 5.1 7.4 - - + -
69C ARG 4.0 8.7 - - - +
71C GLY* 5.4 1.9 + - - -
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Residues in contact with GLU 289 (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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30A VAL* 5.7 0.9 - - - -
34A ILE* 3.2 37.8 - - + +
255A ARG* 4.9 5.9 + - - -
273A ALA 3.1 3.6 - - - +
274A GLU* 3.8 4.3 - - - -
275A VAL* 2.8 49.5 + - + +
277A LEU* 3.7 27.2 - - + +
288A TYR* 1.3 79.6 - - - +
290A LEU* 1.3 61.6 + - - +
291A ARG* 2.9 29.1 + - + +
324A TYR* 5.0 1.7 + - - -
68C LEU* 6.0 1.9 - - - +
69C ARG* 5.5 7.4 + - - -
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Residues in contact with LEU 290 (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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29A ALA* 3.6 16.6 - - + -
30A VAL* 3.8 11.5 - - + +
31A GLY 3.4 38.4 - - - +
32A ALA 4.4 2.9 - - - +
33A PRO* 3.5 26.5 - - + +
34A ILE* 3.3 28.9 + - + +
74A THR* 3.7 14.4 - - + -
272A ILE* 3.7 22.9 - - + -
273A ALA 3.7 10.5 - - - +
274A GLU* 3.4 19.3 + - + +
289A GLU* 1.3 70.8 - - - +
291A ARG* 1.3 64.2 + - - +
331A TRP* 5.1 0.7 - - + -
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Residues in contact with ARG 291 (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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33A PRO* 4.9 1.6 - - - -
34A ILE* 3.3 25.4 - - + +
35A ASN* 3.3 43.2 - - - +
38A ASP* 5.9 0.6 - - - -
254A GLY 4.6 2.2 + - - -
255A ARG* 3.3 67.2 - - - +
271A LEU 3.6 1.4 - - - +
272A ILE* 3.3 4.8 - - - +
273A ALA 2.9 35.3 + - - +
275A VAL* 4.7 11.9 - - + -
289A GLU* 2.9 28.3 + - + +
290A LEU* 1.3 80.3 - - - +
292A LEU* 1.3 63.0 + - - +
293A MSE 4.0 15.5 + - + +
309A ILE* 6.1 0.7 - - - -
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Residues in contact with LEU 292 (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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33A PRO* 4.5 18.1 - - + +
35A ASN* 3.2 25.7 + - - +
36A ALA* 5.4 2.7 - - - -
39A PHE* 3.4 33.5 - - + +
64A VAL* 4.0 20.2 - - + -
67A TRP* 4.1 11.7 - - + -
68A LEU* 4.1 21.8 - - + -
256A ALA* 3.8 3.3 - - - -
270A THR* 4.4 7.2 - - + -
271A LEU 3.6 1.6 - - - +
272A ILE* 3.6 31.6 - - + +
291A ARG* 1.3 72.9 - - - +
293A MSE 1.3 62.1 + - - +
333A LEU* 3.8 19.7 - - + -
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Residues in contact with MSE 293 (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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39A PHE* 4.2 1.6 - - - -
98A PHE* 4.8 7.4 - - + -
255A ARG 3.4 24.9 - - - +
256A ALA 3.3 13.0 - - - -
257A SER* 3.9 3.4 - - - +
258A VAL* 3.5 32.5 - - + -
270A THR* 3.6 1.7 - - - -
271A LEU* 2.7 53.2 + - + +
273A ALA* 3.8 29.8 - - + +
275A VAL* 3.8 19.7 - - + -
291A ARG* 4.4 13.5 - - + +
292A LEU* 1.3 79.7 - - - +
294A VAL* 1.3 62.5 + - - +
309A ILE* 4.0 16.2 - - + -
330A VAL* 5.9 0.2 - - + -
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Residues in contact with VAL 294 (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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39A PHE* 3.4 33.2 - - + -
42A GLN* 4.3 11.7 - - + -
43A ILE* 4.3 9.0 - - + -
46A ILE* 3.9 10.5 - - + -
61A TYR* 4.0 2.5 - - + +
256A ALA 3.1 6.9 + - - +
257A SER* 3.2 7.3 - - - -
258A VAL* 3.1 22.7 + - - -
268A GLY* 3.7 33.4 - - - +
269A THR 3.4 4.9 - - - +
270A THR* 4.7 3.8 - - - -
293A MSE 1.3 75.5 - - - +
295A ALA* 1.3 64.9 + - - +
296A LEU* 3.2 23.7 + - + +
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Residues in contact with ALA 295 (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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258A VAL* 3.5 11.3 - - + +
260A SER* 3.4 28.5 - - - +
265A ILE* 4.3 9.2 - - + -
266A PRO 3.9 16.8 - - - +
267A PRO* 3.2 7.5 - - + +
268A GLY 2.8 28.8 + - - -
269A THR 3.2 14.6 + - - +
271A LEU* 4.6 5.6 - - + +
294A VAL* 1.3 69.4 - - - +
296A LEU* 1.3 60.3 + - - +
297A ASP 3.8 1.6 - - - -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLN* 3.3 43.1 - - + +
46A ILE* 4.1 15.3 - - + -
53A LEU* 4.0 25.6 - - + -
246A GLY* 4.1 2.4 + - - -
247A ALA 3.8 1.7 + - - -
248A SER* 3.4 37.3 + - - +
250A VAL* 3.9 17.6 - - + +
252A LEU* 3.9 19.4 - - + +
257A SER* 4.6 2.0 - - - -
258A VAL 3.2 4.2 + - - -
268A GLY 4.2 0.2 - - - +
294A VAL* 3.2 23.1 + - + +
295A ALA* 1.3 81.8 - - - +
297A ASP* 1.3 64.2 + - - +
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Residues in contact with ASP 297 (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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101A TYR* 2.9 32.6 + - - +
246A GLY* 3.7 12.1 - - - -
247A ALA* 2.8 22.1 + - - +
248A SER* 4.2 0.4 + - - -
252A LEU* 4.3 4.8 - - + +
258A VAL 3.7 2.5 + - - +
259A ALA* 3.2 7.1 - - + -
260A SER* 2.9 25.3 + - - +
267A PRO* 5.7 0.8 - - - +
295A ALA 3.8 0.8 - - - -
296A LEU* 1.3 79.8 - - - +
298A VAL* 1.3 80.6 + - - +
3E NAG 3.6 3.5 - - - -
4E NAG 3.0 33.4 + - - +
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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