Contacts of the strand formed by residues 265 - 271 (chain B) in PDB entry 5IJ0
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 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B ILE* 4.5 15.7 - - + -
192B LEU* 5.5 2.5 - - + -
193B VAL* 3.8 32.3 - - + -
199B THR* 3.4 31.2 - - + -
201B CYS* 4.1 12.6 - - - -
262B ARG 3.9 11.2 - - - -
263B LEU 3.6 1.8 - - - -
264B HIS* 1.3 90.9 - + - +
266B PHE* 1.3 65.8 + - - +
267B MET* 5.7 0.6 - - - +
370B ASN* 3.3 21.1 - - - +
371B SER 4.9 0.7 + - - +
374B ILE* 4.1 16.6 - - + +
378B PHE* 3.7 27.6 - + - -
418B LEU* 3.9 13.5 - - + -
422B TYR* 3.3 23.5 + + - +
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Residues in contact with PHE 266 (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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198B GLU* 3.3 30.7 - - + -
199B THR 3.2 16.3 + - - +
200B TYR* 3.8 21.9 - + + -
201B CYS* 3.1 31.5 + - - +
253B LEU* 6.4 0.4 - - + -
257B MET* 3.4 41.7 - - + -
258B VAL* 3.7 15.7 - - + -
264B HIS 3.0 22.4 - - - -
265B PHE* 1.3 79.1 - - - +
267B MET* 1.3 63.6 + - - +
268B PRO* 3.7 2.1 - - - +
368B ILE* 3.6 19.3 - - + -
369B GLY 3.3 11.9 - - - -
370B ASN* 3.5 19.5 - - - -
374B ILE* 5.8 0.2 - - - -
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Residues in contact with MET 267 (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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265B PHE 5.7 0.7 - - - +
266B PHE* 1.3 77.6 - - - +
268B PRO* 1.3 67.4 - - - +
299B MET* 3.5 30.1 - - + +
301B ALA* 3.6 19.5 - - + -
303B CYS* 3.4 32.3 - - - -
305B PRO* 5.0 5.4 - - + -
310B TYR* 4.9 4.5 - - + -
367B PHE* 3.7 1.2 - - - +
368B ILE* 4.6 1.1 - - - -
369B GLY 3.1 31.0 + - - +
370B ASN 4.8 1.6 - - - -
371B SER* 3.6 38.8 - - - +
373B ALA* 4.3 9.0 - - + -
374B ILE* 4.6 18.8 - - + -
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Residues in contact with PRO 268 (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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167B PHE* 6.3 0.4 - - + -
200B TYR* 4.6 18.6 - - + -
201B CYS 3.3 20.6 - - - +
202B ILE* 3.5 29.6 - - + -
232B THR* 4.2 14.6 - - + -
266B PHE 3.7 6.7 - - - +
267B MET* 1.3 87.8 - - + +
269B GLY* 1.3 59.0 + - - +
299B MET* 4.3 3.6 - - - +
300B MET* 3.4 40.5 + - + +
301B ALA 5.0 1.8 - - - +
367B PHE* 3.2 8.1 - - - +
368B ILE* 4.6 6.3 - - + -
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Residues in contact with GLY 269 (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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232B THR* 4.6 0.3 - - - +
268B PRO* 1.3 75.5 - - - +
270B PHE* 1.3 61.8 + - - +
293B MET* 5.6 2.0 - - - -
298B ASN 4.2 11.9 - - - -
299B MET* 5.3 1.8 - - - -
300B MET* 3.8 7.9 - - - +
366B THR* 3.1 10.6 + - - -
367B PHE* 2.5 47.8 + - - -
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Residues in contact with PHE 270 (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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228B LEU* 4.0 16.6 - - + -
231B ALA* 4.6 24.9 - - + -
232B THR* 4.0 26.9 - - - +
235B GLY* 5.9 2.2 - - - -
269B GLY* 1.3 75.1 - - - +
271B ALA* 1.3 63.7 + - - +
272B PRO* 3.8 17.7 - - + -
273B LEU* 3.3 44.5 - - + +
292B GLN* 5.0 1.7 - - - +
293B MET* 4.6 5.4 - - - +
298B ASN* 4.6 11.2 + - - +
300B MET* 4.4 6.5 - - + +
318B ARG* 6.2 3.8 - - - -
358B PRO* 5.4 5.4 - - + -
361B LEU* 5.4 7.0 - - + -
364B SER* 3.4 24.7 - - - -
365B SER 3.5 13.5 - - - -
366B THR* 4.5 5.2 - - - +
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Residues in contact with ALA 271 (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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270B PHE* 1.3 80.7 - - - +
272B PRO* 1.3 68.7 - - + +
289B LEU* 3.8 24.5 - - + +
292B GLN* 3.8 14.1 - - + -
293B MET* 3.8 6.0 - - + +
364B SER* 2.5 26.0 + - - -
365B SER* 2.9 29.8 + - - +
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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