Contacts of the strand formed by residues 284 - 297 (chain X) in PDB entry 2AE0
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6X THR 4.0 10.5 - - - -
7X ASP 3.6 16.0 + - - +
8X ARG* 3.9 10.5 - - - -
9X GLY* 3.5 21.5 - - - -
276X PRO* 3.9 13.2 - - + -
277X LEU 3.4 14.1 - - - -
278X LEU* 4.1 2.7 - - - -
283X LYS* 1.3 89.8 - - - +
285X ASN* 1.3 60.3 + - - +
286X GLY* 3.3 27.8 + - - -
287X GLN 3.5 21.1 - - - -
288X TYR* 3.3 37.0 - + - -
326X HIS* 3.9 12.3 + - + -
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Residues in contact with ASN 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277X LEU* 3.0 42.7 + - - +
278X LEU 4.0 12.3 + - - -
279X ASP* 4.1 22.2 - - + +
283X LYS 3.1 1.2 + - - +
284X PHE* 1.3 72.1 - - - +
286X GLY* 1.3 56.8 + - - +
287X GLN* 2.9 33.1 + - - +
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Residues in contact with GLY 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284X PHE* 3.3 34.1 + - - -
285X ASN* 1.3 77.5 - - - +
287X GLN* 1.3 61.6 - - - +
288X TYR* 4.1 8.0 - - - -
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Residues in contact with GLN 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277X LEU* 2.9 43.6 + - + +
284X PHE* 3.5 8.1 - - - -
285X ASN* 2.9 25.0 + - - +
286X GLY* 1.3 82.8 - - - +
288X TYR* 1.3 65.4 + - - +
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Residues in contact with TYR 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X GLY 2.5 32.7 + - - -
10X GLN 4.4 0.3 + - - -
11X GLN* 3.4 27.9 + - - +
274X GLU* 3.6 24.5 - - + +
275X VAL 3.1 9.6 - - - +
276X PRO* 3.6 18.8 - - + -
277X LEU* 4.4 3.6 - - - +
284X PHE* 3.3 28.9 - + - -
286X GLY 4.1 7.9 - - - -
287X GLN* 1.3 77.9 - - - +
289X GLU* 1.3 66.0 + - - +
290X LEU 4.4 0.2 + - - -
327X TYR 3.7 12.3 - - - -
328X GLY* 4.5 0.2 - - - -
329X ARG* 3.4 29.8 - - - -
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Residues in contact with GLU 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X ILE* 3.6 28.8 - - + +
255X ARG* 4.5 6.8 + - - -
273X ALA 3.1 4.0 - - - +
274X GLU* 3.5 3.3 - - - -
275X VAL* 2.8 36.1 + - + +
277X LEU* 3.5 38.0 - - + +
288X TYR* 1.3 77.0 - - - +
290X LEU* 1.3 61.4 + - - +
291X ARG* 3.1 31.2 + - + +
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Residues in contact with LEU 290 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ALA* 4.0 11.9 - - + -
30X VAL 4.1 10.5 - - - +
31X GLY 3.9 7.2 - - - +
32X ALA 3.7 27.1 - - - +
33X PRO* 3.9 4.5 - - + -
34X ILE* 2.9 37.9 + - + +
74X THR* 3.9 23.6 - - + -
272X LEU* 3.7 27.4 - - + -
273X ALA 3.3 13.0 - - - +
274X GLU* 3.8 28.1 + - + +
289X GLU* 1.3 70.9 - - - +
291X ARG* 1.3 59.3 + - - +
331X TRP* 4.8 0.7 - - + -
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Residues in contact with ARG 291 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X PRO* 4.4 1.8 - - - -
34X ILE* 3.8 15.4 + - + +
35X ASN* 3.4 34.5 - - - +
38X ASP* 4.3 7.9 + - - -
255X ARG* 3.2 69.4 - - - +
271X LEU 3.8 0.3 - - - +
272X LEU* 3.6 4.7 - - - +
273X ALA* 2.8 37.3 + - - +
275X VAL* 4.9 15.2 - - + +
289X GLU* 3.1 39.1 + - - +
290X LEU* 1.3 79.6 - - - +
292X LEU* 1.3 65.3 + - - +
293X MET* 4.6 4.8 - - + +
309X ILE* 6.5 0.2 - - - -
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Residues in contact with LEU 292 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X PRO* 3.9 16.6 - - + +
35X ASN* 2.9 30.2 + - - +
36X ALA* 5.6 1.1 - - - -
39X PHE* 3.6 22.4 - - + -
64X VAL* 3.8 12.8 - - + -
67X TRP* 4.2 3.8 - - + -
68X LEU* 3.6 41.5 - - + -
256X ALA* 3.7 5.4 - - - +
270X THR* 4.3 11.0 - - + -
271X LEU 3.3 13.0 - - - +
272X LEU* 4.1 10.1 - - + -
291X ARG* 1.3 73.0 - - - +
293X MET* 1.3 63.6 + - - +
333X LEU* 3.8 26.9 - - + -
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Residues in contact with MET 293 (chain X).
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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39X PHE* 4.5 1.3 - - - -
98X PHE* 4.4 12.1 - - + -
255X ARG 3.4 17.3 - - - +
256X ALA* 3.3 13.9 - - - -
257X SER 4.0 1.3 - - - +
258X VAL* 3.5 31.6 - - + -
270X THR* 3.7 2.3 - - - +
271X LEU* 2.8 48.9 + - + +
273X ALA* 3.7 28.9 - - + -
275X VAL* 4.6 11.2 - - + -
291X ARG* 4.6 5.6 - - + -
292X LEU* 1.3 79.6 - - - +
294X VAL* 1.3 67.1 + - - +
307X PHE* 5.9 0.2 - - + -
309X ILE* 4.0 21.3 - - - -
330X VAL* 5.7 0.2 - - + -
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Residues in contact with VAL 294 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X PHE* 3.8 25.6 - - + -
42X GLN* 4.4 4.9 - - + -
43X ILE* 3.9 15.7 - - + -
46X ILE* 3.9 4.7 - - + -
61X TYR* 3.8 11.2 - - + +
256X ALA 3.0 10.8 + - - +
257X SER* 3.2 6.6 - - - -
258X VAL* 3.0 22.1 + - - -
268X GLY* 3.7 25.8 - - - +
269X THR 3.3 12.1 - - - +
270X THR* 4.7 1.6 - - - +
293X MET* 1.3 79.9 - - - +
295X ALA* 1.3 66.4 + - - +
296X LEU* 3.2 24.3 + - + +
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Residues in contact with ALA 295 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X VAL* 3.5 16.9 - - + +
260X SER* 3.4 24.9 - - - +
265X ILE* 3.9 13.9 - - + +
266X PRO 3.8 18.4 - - - +
267X PRO* 3.3 6.4 - - + +
268X GLY 2.7 28.6 + - - -
269X THR 3.1 11.2 + - - +
271X LEU* 4.8 1.9 - - + +
294X VAL* 1.3 67.7 - - - +
296X LEU* 1.3 61.1 + - - +
297X ASP 3.8 1.6 - - - +
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Residues in contact with LEU 296 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X GLN* 3.3 46.2 - - + +
46X ILE* 3.9 25.4 - - + -
53X LEU* 4.0 18.2 - - + -
246X GLY* 3.5 8.1 - - - -
248X SER* 2.6 46.5 + - - +
250X VAL* 4.0 11.2 - - + -
252X LEU* 3.8 14.6 - - + -
257X SER* 4.3 2.2 - - - -
258X VAL 3.0 5.8 + - - -
267X PRO* 5.2 2.5 - - - -
294X VAL* 3.2 16.9 + - + +
295X ALA* 1.3 82.4 - - - +
297X ASP* 1.3 62.3 + - - +
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Residues in contact with ASP 297 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X TYR* 2.9 38.0 + - - +
245X LYS 4.9 0.5 - - - +
246X GLY* 3.4 16.7 - - - -
247X ALA* 2.8 23.9 + - - +
252X LEU* 4.0 5.7 - - + +
258X VAL 3.3 2.5 + - - +
259X ALA* 3.5 9.0 - - - -
260X SER* 3.0 22.3 + - - +
295X ALA* 3.8 0.9 - - - +
296X LEU* 1.3 78.8 + - - +
298X VAL* 1.3 86.4 + - - +
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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