Contacts of the strand formed by residues 289 - 302 (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 SER 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B VAL* 4.0 1.7 - - - +
206B ASN 2.7 34.1 + - - +
285B VAL* 3.4 6.6 - - - +
286B PRO* 3.2 39.3 + - - +
287B ALA 3.1 6.8 + - - -
288B ARG* 1.3 78.6 + - - +
290B LYS* 1.3 60.9 + - - +
419B PRO* 4.7 1.2 - - - +
420B VAL 3.5 15.2 + - - -
421B PRO* 4.0 7.3 - - - +
422B LEU* 3.6 6.7 - - - +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 3.4 53.5 - - + +
204B ALA 3.3 6.3 - - - +
205B VAL* 3.5 30.1 - - + -
285B VAL* 4.1 2.5 - - - -
289B SER* 1.3 76.9 - - - +
291B ILE* 1.3 59.7 - - - +
418B ALA 4.0 0.3 - - - +
419B PRO* 3.2 1.5 - - - +
420B VAL* 2.6 57.7 + - - +
421B PRO 5.0 1.4 + - - -
422B LEU* 4.1 11.2 - - + -
423B ALA* 4.3 24.2 - - - +
444B GLU* 5.1 3.1 - - - +
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Residues in contact with ILE 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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203B TRP* 3.3 8.2 - - - -
204B ALA* 3.0 48.8 + - + +
283B PRO* 3.5 33.9 - - + -
284B THR 4.8 5.4 - - - +
285B VAL* 4.5 18.6 - - + +
290B LYS* 1.3 71.0 - - - +
292B PRO* 1.3 68.8 - - + +
293B VAL* 4.2 0.8 - - + +
416B ILE* 3.6 23.6 - - + -
417B GLY 3.9 12.6 - - - +
419B PRO* 3.6 29.6 - - + -
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Residues in contact with PRO 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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134A GLN* 4.1 20.2 - - - +
135A TYR* 3.8 13.9 - - - +
202B GLY 3.4 4.0 - - - +
203B TRP* 3.3 26.9 - - + -
291B ILE* 1.3 90.1 - - + +
293B VAL* 1.3 60.4 + - - +
416B ILE* 3.2 5.4 - - - +
417B GLY* 2.9 53.4 + - - -
418B ALA 3.2 20.9 - - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 4.1 2.6 + - - -
201B VAL* 3.1 5.0 - - - +
202B GLY 2.9 35.3 + - - +
203B TRP 4.5 1.8 - - - -
204B ALA* 4.3 21.3 - - + +
217B VAL* 6.1 8.7 - - + -
281B VAL* 6.1 0.7 - - + -
291B ILE* 4.2 8.5 - - + +
292B PRO* 1.3 79.3 - - - +
294B LYS* 1.3 60.2 + - - +
295B ILE* 4.6 9.9 - - + -
414B ILE* 4.8 9.4 - - + -
415B GLU 3.5 5.6 - - - +
416B ILE* 4.0 17.0 - - + -
443B LEU* 6.3 0.7 - - + -
445B ILE* 4.0 34.3 - - + -
462B LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 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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135A TYR* 3.3 37.0 + - + +
138A GLU* 2.8 31.2 + - - -
199B THR* 4.1 10.8 - - - +
200B VAL 3.2 4.5 - - - -
201B VAL* 3.9 18.6 - - + +
293B VAL* 1.3 72.9 - - - +
295B ILE* 1.3 71.0 - - - +
296B GLU* 3.3 26.8 + - + -
413B ASN 4.2 0.7 - - - +
414B ILE* 3.9 0.7 - - - +
415B GLU* 2.8 50.7 + - + +
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Residues in contact with ILE 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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199B THR* 3.2 2.8 - - - -
200B VAL* 2.6 49.3 + - + +
219B LEU* 4.1 29.2 - - + -
293B VAL* 4.6 7.2 - - + -
294B LYS* 1.3 81.0 - - - +
296B GLU* 1.3 63.7 + - - +
297B LEU* 3.8 7.5 + - + +
411B ALA* 4.2 15.7 - - + -
412B GLY 4.5 7.2 - - - +
413B ASN 4.6 4.0 - - - +
414B ILE* 4.0 29.4 - - + -
445B ILE* 3.8 28.0 - - + -
447B LEU* 6.2 0.4 - - + -
462B LEU* 4.7 10.3 - - + -
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Residues in contact with GLU 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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114A LYS* 5.6 0.9 + - - -
138A GLU* 4.7 1.2 - - - +
196B LEU* 3.4 26.6 - - + +
198B LYS 4.0 0.9 - - - -
199B THR* 3.9 12.8 - - + +
294B LYS* 3.3 33.1 + - - -
295B ILE* 1.3 72.2 - - - +
297B LEU* 1.3 57.6 - - - +
298B TYR* 2.4 42.2 + - + +
411B ALA* 3.6 0.9 - - - +
412B GLY* 2.8 32.7 + - - +
413B ASN 4.8 4.0 + - - -
415B GLU* 4.4 5.7 - - - +
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Residues in contact with LEU 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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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
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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
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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
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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
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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
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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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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