Contacts of the strand formed by residues 297 - 313 (chain B) in PDB entry 1PRE
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 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.6 4.7 - - - +
197B VAL* 2.9 26.6 + - + -
198B LYS* 2.8 32.5 + - + +
200B VAL* 4.4 8.5 - - + -
219B LEU* 5.6 2.0 - - + -
221B TYR* 6.2 0.2 - - + -
295B ILE* 4.6 10.5 - - + +
296B GLU* 1.3 73.2 - - - +
298B TYR* 1.3 59.3 + - - +
410B PHE 3.7 1.1 - - - -
411B ALA* 3.4 28.0 - - + -
452B LEU* 3.3 34.8 - - + -
455B LEU* 5.2 0.4 - - + -
457B PHE* 3.5 37.5 - - + -
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Residues in contact with TYR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 3.8 37.0 + - + -
195B GLN 3.4 6.7 - - - +
196B LEU* 3.7 33.0 - - + -
197B VAL* 4.3 4.9 - - - +
296B GLU* 2.4 50.2 + - + +
297B LEU* 1.3 71.0 - - - +
299B LYS* 1.3 62.3 + - - +
409B GLN* 3.0 9.2 - - - +
410B PHE* 2.7 76.5 + + + +
412B GLY* 4.2 10.3 - - - -
457B PHE* 4.0 1.1 - - - -
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 2.9 5.1 - - - +
195B GLN* 2.7 41.4 + - + +
197B VAL* 3.7 27.5 - - + +
298B TYR* 1.3 74.3 - - - +
300B ALA* 1.3 66.1 + - - +
407B GLU* 5.3 9.4 - - + +
408B SER 3.3 4.0 - - - +
409B GLN* 3.6 22.4 - - + +
454B GLY 5.0 2.0 + - - -
455B LEU* 3.3 35.8 + - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 3.2 13.9 - - - +
194B ARG* 3.8 12.1 - - + -
253B THR* 3.9 26.2 - - - +
255B LEU* 6.5 0.2 - - - -
299B LYS* 1.3 78.4 - - - +
301B ASP* 1.3 66.0 - - - +
302B ILE* 5.4 0.2 - - - -
407B GLU* 3.4 4.3 - - - +
408B SER* 2.7 34.9 + - - +
410B PHE* 4.0 13.0 - - + -
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLN* 4.4 8.8 - - + +
192B SER* 3.3 22.0 + - - -
193B ASP* 3.0 37.1 + - - +
195B GLN* 4.2 4.7 - - - +
253B THR* 5.1 2.7 - - - +
300B ALA* 1.3 78.3 - - - +
302B ILE* 1.3 67.5 - - - +
406B ALA 3.3 16.2 - - - +
407B GLU* 4.1 14.5 - - + +
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 4.4 13.9 - - + -
191B GLN* 3.6 6.3 - - - +
192B SER* 4.7 4.3 - - - +
250B VAL* 3.9 23.8 - - + +
251B GLY* 5.3 1.1 - - - -
253B THR* 3.7 27.8 - - + +
255B LEU* 4.2 9.9 - - + -
301B ASP* 1.3 81.5 - - - +
303B SER* 1.3 64.4 + - - +
304B TYR* 4.2 17.0 - - + -
404B PHE* 3.8 23.6 - - + -
405B SER* 3.1 5.2 - - - -
406B ALA* 3.1 39.2 + - + +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.2 5.0 - - - +
190B THR* 2.7 32.5 + - - -
191B GLN* 3.1 51.1 + - - +
302B ILE* 1.3 75.9 + - - +
304B TYR* 1.3 60.6 + - - +
404B PHE 3.2 7.9 - - - -
405B SER* 4.0 11.0 - - - -
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Residues in contact with TYR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.7 23.4 - + - -
186B HIS* 3.5 17.9 - - + -
187B GLY 4.1 3.4 - - - +
188B ASP 4.1 1.6 - - - +
189B VAL* 3.8 28.9 - - + -
190B THR* 4.3 2.6 + - - -
247B TRP* 3.2 24.8 + - - -
248B PRO 4.1 1.4 + - - -
250B VAL* 3.4 36.6 - - + +
302B ILE* 4.2 13.5 - - + -
303B SER* 1.3 78.9 - - - +
305B PRO* 1.3 73.3 - - + +
306B TYR* 4.3 2.9 - - + -
403B ASP* 4.7 2.9 - - - -
404B PHE* 2.8 62.0 + + + +
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Residues in contact with PRO 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B HIS* 3.3 6.8 - - - +
187B GLY* 2.9 40.1 + - - -
188B ASP 3.5 16.6 - - - +
190B THR* 4.5 4.7 - - - +
304B TYR* 1.3 87.9 - - + +
306B TYR* 1.3 61.7 + - - +
402B GLY 3.6 11.0 - - - +
403B ASP* 4.0 14.6 - - - +
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Residues in contact with TYR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 4.0 20.2 - - + -
185B LYS 3.7 5.6 - - - -
186B HIS* 4.5 0.9 - - - +
229B LYS* 4.1 11.5 - - + +
230B THR 2.9 19.2 + - - -
231B ASN* 3.4 2.9 + - - -
247B TRP* 4.2 7.0 - + + -
265B TRP* 3.1 30.5 + + - -
304B TYR* 3.7 8.5 + - + -
305B PRO* 1.3 76.0 - - - +
307B GLU* 1.3 69.1 + - - +
308B PHE* 3.5 26.7 - + - -
400B ILE 4.0 3.4 - - - -
401B THR* 3.2 40.3 + - - +
402B GLY 3.2 28.5 + - - +
403B ASP 3.6 15.7 - - - -
404B PHE* 4.0 7.0 - - + -
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LYS* 2.6 36.2 + - - -
183B SER 3.9 1.9 - - - +
184B PHE* 4.0 1.4 - - - -
185B LYS* 3.3 46.9 + - + +
186B HIS* 5.8 0.2 - - - -
306B TYR* 1.3 81.7 - - - +
308B PHE* 1.3 68.0 + - - +
309B LYS* 4.2 21.5 + - - +
399B GLY* 5.1 3.6 - - - -
400B ILE 3.1 10.8 - - - -
401B THR* 3.7 14.3 - - + +
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.8 31.0 - - + -
180B ASP 4.3 0.4 - - - -
181B PRO* 4.0 14.4 - - + -
183B SER* 3.6 7.4 - - - +
184B PHE* 3.7 40.2 - + + -
245B PHE* 4.1 20.0 - + - -
247B TRP* 3.3 40.4 - + - -
248B PRO* 4.7 2.7 - - + -
265B TRP* 3.3 22.2 - + - -
306B TYR* 3.5 19.1 - + - -
307B GLU* 1.3 77.6 - - - +
309B LYS* 1.3 64.0 + - - +
399B GLY* 3.8 3.6 - - - -
400B ILE* 2.7 29.9 + - + +
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Residues in contact with LYS 309 (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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185A LYS* 5.8 2.1 - - - +
92B ASP* 3.1 37.3 + - - +
93B ILE 5.6 0.8 + - - -
179B LEU* 3.6 4.1 - - - +
180B ASP* 2.8 34.3 + - + +
183B SER* 2.7 25.5 + - - +
307B GLU* 4.2 22.8 + - + -
308B PHE* 1.3 78.6 - - - +
310B ALA* 1.3 54.1 + - - +
311B ASP* 4.2 0.4 - - - +
397B ARG* 4.0 36.3 - - + +
398B ALA 3.5 12.1 - - - +
399B GLY* 4.2 11.8 - - - +
400B ILE* 4.9 0.4 - - - -
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Residues in contact with ALA 310 (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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177B TYR* 4.2 21.1 - - + -
178B ASN 3.4 14.6 - - - +
179B LEU* 3.9 4.0 - - - +
235B LEU* 5.5 0.4 - - + -
239B VAL* 4.7 3.4 - - + -
308B PHE 4.3 0.2 + - - -
309B LYS* 1.3 71.6 - - - +
311B ASP* 1.3 63.0 + - - +
312B VAL* 4.0 0.2 - - - +
397B ARG* 4.4 1.1 - - - -
398B ALA* 2.7 42.9 + - + +
400B ILE* 3.9 23.6 - - + -
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Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA 3.8 0.7 - - - +
177B TYR* 3.4 5.2 - - - -
178B ASN* 3.0 37.9 + - + +
180B ASP* 4.3 15.2 - - - +
309B LYS* 4.2 1.1 - - - -
310B ALA* 1.3 74.2 - - - +
312B VAL* 1.3 61.1 + - - +
395B PRO* 5.5 4.0 - - - +
396B VAL 3.6 6.9 + - - +
397B ARG* 3.1 26.6 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 5.7 0.9 - - + -
101B VAL* 5.3 6.3 - - + -
105B LEU* 4.7 2.7 - - + -
175B PHE* 3.5 35.0 - - + -
176B ALA 3.6 2.5 - - - -
177B TYR* 3.9 24.0 - - + -
310B ALA 4.0 8.3 - - - +
311B ASP* 1.3 78.1 - - - +
313B SER* 1.3 62.6 + - - +
314B TYR* 4.2 10.2 - - + -
345B ILE* 4.6 1.0 - - - +
396B VAL* 2.7 47.2 + - + +
397B ARG 4.3 0.4 - - - -
398B ALA* 4.1 12.3 - - + +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASN 4.6 0.7 - - - -
175B PHE* 3.4 3.5 - - - -
176B ALA* 3.0 39.6 + - - +
311B ASP 5.3 0.2 + - - -
312B VAL* 1.3 73.6 - - - +
314B TYR* 1.3 70.3 + - - +
344B VAL* 5.8 2.5 - - - -
345B ILE 3.0 19.1 - - - -
346B GLY* 3.7 14.1 - - - -
347B PRO* 3.8 14.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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