Contacts of the strand formed by residues 291 - 301 (chain B) in PDB entry 4P22
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 ILE 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B SER* 3.4 27.6 - - - +
219B ALA 3.4 11.7 - - - +
220B MET* 3.5 19.7 - - + -
221B VAL* 4.3 0.2 - - - +
249B SER 3.6 0.5 - - - +
250B PHE* 3.2 10.4 - - - -
251B SER* 2.8 39.4 + - - +
252B GLU* 3.2 37.0 - - + +
253B VAL* 4.5 1.2 - - - +
290B GLY* 1.3 79.7 - - - +
292B VAL* 1.3 61.8 + - - +
293B SER* 3.8 7.8 + - - +
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Residues in contact with VAL 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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218B SER* 3.5 2.3 - - - -
219B ALA* 2.9 55.5 + - + +
221B VAL* 3.9 13.0 - - + +
234B CYS* 4.7 7.4 - - - -
242B PHE* 3.7 11.1 - - + -
248B VAL* 3.4 42.0 - - + -
249B SER 3.5 2.9 - - - -
250B PHE* 3.5 20.6 - - + -
275B PHE* 4.1 17.9 - - + -
291B ILE* 1.3 72.8 - - - +
293B SER* 1.3 58.9 + - - +
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PRO* 5.5 6.1 - - - -
217B LEU 3.5 5.8 - - - -
218B SER* 3.0 19.2 + - - -
242B PHE* 4.2 3.6 - - - -
248B VAL* 3.3 6.9 - - - +
249B SER* 2.8 43.7 + - - -
251B SER* 5.7 0.5 + - - -
291B ILE* 3.8 7.8 + - - +
292B VAL* 1.3 74.1 - - - +
294B GLN* 1.3 62.6 + - - +
295B VAL* 3.6 2.2 + - - -
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Residues in contact with GLN 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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216B PRO* 3.8 20.1 - - - +
217B LEU* 3.0 44.1 + - + +
241B GLY 3.6 16.4 + - - -
242B PHE* 4.0 17.5 - - + +
246B ASP* 2.2 38.6 + - + +
247B PHE 3.8 4.5 - - - +
248B VAL* 4.3 0.4 - - - -
293B SER* 1.3 72.4 - - - +
295B VAL* 1.3 63.1 + - - +
296B LYS 4.3 4.0 - - - +
297B VAL* 3.4 26.7 - - + +
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Residues in contact with VAL 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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55B TYR* 5.1 4.0 - - + -
211B SER* 3.9 18.2 + - - +
247B PHE 2.8 13.2 + - - +
249B SER* 3.6 34.8 - - - +
264B PRO* 4.1 26.5 - - + -
293B SER* 3.6 2.4 + - - +
294B GLN* 1.3 76.9 - - - +
296B LYS* 1.3 80.5 + - + +
297B VAL* 5.5 0.3 - - - +
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Residues in contact with LYS 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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430A GLU 3.8 20.6 + - - -
55B TYR* 2.9 35.6 + - + +
209B THR* 3.6 33.7 + - + -
210B ASP* 3.6 8.7 - - - +
211B SER* 3.5 31.4 - - - +
246B ASP* 3.5 2.4 - - - +
247B PHE* 2.8 48.2 + - + +
294B GLN* 4.3 0.7 - - - +
295B VAL* 1.3 99.3 - - + +
297B VAL* 1.3 65.7 + - - +
298B PRO* 4.6 0.4 - - - -
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Residues in contact with VAL 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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209B THR* 3.5 2.5 - - - -
210B ASP* 2.8 48.7 + - - +
211B SER 5.2 6.3 - - - +
246B ASP* 4.0 5.6 - - - +
294B GLN* 3.4 39.7 - - + +
295B VAL 5.5 0.4 - - - +
296B LYS* 1.3 78.9 - - - +
298B PRO* 1.3 73.4 - - + +
299B LYS* 3.6 29.2 - - + +
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Residues in contact with PRO 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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207B ILE* 4.8 7.4 - - + -
208B LEU 3.6 6.7 - - - +
209B THR* 3.9 11.9 - - + -
244B SER 4.6 3.6 - - - +
245B GLY* 3.1 36.3 - - - +
246B ASP* 3.7 14.6 - - - +
297B VAL* 1.3 91.4 - - + +
299B LYS* 1.3 70.2 + - - +
300B LYS* 4.0 18.4 + - - +
416B LYS* 5.3 3.4 - - - -
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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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206B MET 3.9 0.3 - - - +
207B ILE* 3.1 5.2 - - - +
208B LEU* 2.8 35.4 + - + +
210B ASP* 3.7 23.1 - - - +
297B VAL* 3.6 25.2 - - + +
298B PRO* 1.3 82.0 + - - +
300B LYS* 1.3 70.9 + - - +
301B ILE* 3.9 2.4 + - + +
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Residues in contact with LYS 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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204B GLU 5.4 4.5 - - - +
205B GLU* 5.3 4.9 - - - +
206B MET 3.4 9.0 - - - +
207B ILE* 3.0 45.5 - - + +
298B PRO* 4.0 16.2 + - - +
299B LYS* 1.3 80.9 + - - +
301B ILE* 1.3 62.4 + - - +
302B SER* 4.2 0.7 + - - -
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Residues in contact with ILE 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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203B GLY 3.8 2.9 - - - +
204B GLU 3.6 3.2 - - - +
206B MET 2.7 37.0 + - - +
208B LEU* 3.5 39.3 - - + -
299B LYS* 3.9 2.4 - - + -
300B LYS* 1.3 74.7 - - - +
302B SER* 1.3 81.5 + - - +
303B PHE* 3.6 19.1 - - + -
418B MET* 5.5 3.4 - - - -
421B MET* 4.3 21.5 - - + -
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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
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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