Contacts of the strand formed by residues 280 - 291 (chain B) in PDB entry 5O67
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 ALA 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B PHE* 3.1 35.8 + - - +
278B ASP* 3.8 0.2 - - - +
279B PRO* 1.3 78.0 - - + +
281B VAL* 1.3 63.3 + - - +
282B LEU* 3.8 3.8 + - + +
323B VAL* 4.1 9.0 - - + -
324B ALA 3.5 4.5 - - - -
325B PHE* 3.8 11.0 - - + -
327C LEU* 3.8 31.0 - - + -
331C MET* 4.5 11.4 - - - -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 6.3 0.7 - - + -
95B LEU* 4.2 31.0 - - + -
96B TYR* 4.3 15.9 - - + +
274B VAL* 3.9 21.3 - - + -
275B LYS 3.7 7.6 - - - +
276B THR* 3.8 21.3 - - + +
279B PRO 4.6 5.2 - - - +
280B ALA* 1.3 76.3 - - - +
282B LEU* 1.3 70.0 + - - +
283B PHE* 3.7 5.0 - - + -
323B VAL* 3.5 4.2 - - - -
324B ALA 2.9 36.5 + - - +
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Residues in contact with LEU 282 (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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274B VAL* 3.7 0.7 - - - -
275B LYS* 3.2 31.8 + - + +
277B PHE* 4.0 27.4 - - + -
280B ALA* 3.8 2.4 + - + +
281B VAL* 1.3 77.5 - - - +
283B PHE* 1.3 64.5 + - - +
322B GLY 3.5 9.2 - - - +
323B VAL* 4.0 14.8 - - + -
331C MET* 4.5 15.5 - - + -
371C MET* 4.0 29.6 - - + -
373C ILE* 5.1 10.5 - - + -
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 5.3 0.2 - - + -
99B ALA* 3.7 41.3 - - + +
273B MET 3.4 13.2 - - - +
274B VAL* 4.3 6.3 - - + -
281B VAL* 3.7 14.1 - - + -
282B LEU* 1.3 77.2 - - - +
284B GLY* 1.3 63.4 + - - +
285B SER* 6.0 0.7 - - - -
320B GLY 6.0 0.4 - - - -
321B VAL* 3.2 8.2 - - - +
322B GLY* 2.9 59.2 + - - +
323B VAL 3.8 17.0 - - - -
324B ALA* 4.0 11.0 - - + -
334B SER* 4.7 8.5 - - - -
335B PHE 4.2 0.4 - - - -
336B SER* 4.0 17.7 - - - -
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Residues in contact with GLY 284 (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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99B ALA 5.6 1.9 - - - +
272B SER* 3.5 3.5 - - - -
273B MET* 3.2 31.9 + - - +
283B PHE* 1.3 82.9 - - - +
285B SER* 1.3 66.1 + - - -
320B GLY 3.1 12.8 - - - -
321B VAL* 4.1 6.5 - - - -
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU 3.2 13.0 - - - -
272B SER* 4.5 3.6 - - - -
283B PHE* 6.0 1.0 - - - -
284B GLY* 1.3 77.8 - - - -
286B VAL* 1.3 63.6 + - - +
319B PHE* 3.3 5.7 - - - +
320B GLY 3.0 30.2 + - - -
501B LDA 3.5 46.7 - - - +
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Residues in contact with VAL 286 (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 GLY* 3.2 2.3 - - - -
271B LEU* 2.8 55.9 + - + +
285B SER* 1.3 76.5 - - - +
287B SER* 1.3 70.2 + - - +
288B TYR* 6.3 0.7 - - + -
317B PHE* 5.9 4.3 - - + -
318B GLN 3.7 11.9 - - - +
319B PHE* 4.4 7.4 - - + +
501B LDA 4.5 4.0 - - - -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 4.1 9.4 - - - +
269B PRO 3.2 17.9 - - - -
270B GLY* 3.6 7.0 - - - -
286B VAL* 1.3 84.0 - - - +
288B TYR* 1.3 66.8 + - - +
317B PHE* 3.4 3.6 - - - +
318B GLN* 2.7 50.1 + - - +
501B LDA 3.6 25.6 - - - +
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Residues in contact with TYR 288 (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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268B THR* 3.2 23.3 - - - -
269B PRO* 3.2 42.3 + - + +
286B VAL* 6.3 0.9 - - + -
287B SER* 1.3 79.5 - - - +
289B THR* 1.3 66.7 + - - +
290B HIS* 4.8 13.2 - - + -
315B ASP* 6.1 1.8 - - + -
316B SER 3.1 16.6 - - - +
317B PHE* 3.8 10.5 - - + -
318B GLN* 3.9 2.5 - - - -
343B ARG* 6.1 0.7 - - - +
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Residues in contact with THR 289 (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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266B SER* 3.9 12.1 - - - +
267B ILE 3.5 4.3 - - - -
268B THR* 2.9 24.6 + - - +
288B TYR* 1.3 75.5 - - - +
290B HIS* 1.3 58.9 + - - +
291B ASN* 3.7 28.0 - - - +
315B ASP* 3.3 9.4 - - - +
316B SER* 2.8 41.7 + - - +
318B GLN* 3.7 11.8 + - - -
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Residues in contact with HIS 290 (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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266B SER* 3.4 2.4 - - - -
267B ILE* 2.9 41.1 + - + +
288B TYR* 4.2 15.9 + - + -
289B THR* 1.3 72.1 - - - +
291B ASN* 1.3 72.7 + - - +
292B LEU* 3.7 24.0 + - + +
315B ASP* 3.2 24.6 + - - -
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Residues in contact with ASN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ASN* 4.2 8.3 + - - -
264B VAL* 3.9 13.5 - - + +
265B TRP 3.6 5.6 - - - +
266B SER* 3.3 18.7 + - - -
289B THR* 3.7 17.2 - - - +
290B HIS* 1.3 91.7 - - - +
292B LEU* 1.3 65.0 + - - +
293B GLU 4.1 0.5 + - - -
312B ARG* 5.5 5.4 - - - +
313B LEU* 4.0 31.5 + - + +
314B GLY 3.1 28.7 + - - -
315B ASP* 3.1 11.3 + - - +
316B SER* 5.4 0.4 + - - -
342B GLN* 5.2 1.8 - - - +
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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