Contacts of the strand formed by residues 294 - 299 (chain B) in PDB entry 4O9U
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 LYS 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B GLY* 1.3 76.7 - - - +
295B VAL* 1.3 62.1 + - - +
296B VAL* 5.2 1.1 - - + -
325B GLU* 3.2 31.8 + - - +
327B LYS* 5.7 0.7 - - - -
364B GLU* 3.1 47.8 + - - +
367B THR* 3.3 43.0 + - - +
368B VAL* 3.2 20.7 - - + +
369B ASP* 2.9 29.7 + - - +
370B VAL 3.6 3.6 + - - -
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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
----------------------------------------------------------
289B LEU* 4.2 27.1 - - + +
292B ALA* 3.9 24.9 - - + -
294B LYS* 1.3 75.8 - - - +
296B VAL* 1.3 72.3 + - - +
297B PHE* 4.3 16.2 - - + -
319B LEU* 5.0 7.6 - - + -
324B VAL* 3.9 17.0 - - + -
325B GLU* 3.1 14.2 + - - +
326B VAL* 3.6 4.8 - - - +
327B LYS* 3.2 22.3 + - - +
370B VAL* 3.5 15.0 - - + +
372B VAL* 4.5 10.8 - - + -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS* 5.2 4.0 - - + -
295B VAL* 1.3 84.2 - - - +
297B PHE* 1.3 65.1 + - - +
298B VAL* 3.7 5.9 + - + +
325B GLU* 5.9 0.2 - - - +
327B LYS* 3.2 25.6 - - + +
328B PHE 4.5 0.2 - - - -
329B ALA* 3.7 31.0 - - + +
361B ILE* 4.7 11.0 - - + -
365B PHE* 4.3 17.7 - - + -
368B VAL* 3.8 30.7 - - + -
370B VAL 3.5 5.1 + - - -
371B ALA* 3.8 4.2 - - - -
372B VAL 3.3 20.6 + - - -
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 5.6 3.1 - - + -
295B VAL* 4.8 7.2 - - + -
296B VAL* 1.3 71.5 - - - +
298B VAL* 1.3 61.2 + - - +
299B PRO* 3.3 7.4 - - + +
312B LEU* 3.7 31.2 - - + -
315B LEU* 4.6 18.8 - - + -
316B ALA* 4.0 11.9 - - + -
319B LEU* 3.7 26.5 - - + -
326B VAL* 3.7 27.1 - - + -
327B LYS 3.2 7.2 + - - -
328B PHE* 3.8 32.7 - + + -
329B ALA 3.2 24.1 + - - -
372B VAL* 3.4 37.0 - - + +
374B ILE* 5.2 1.8 - - + -
440B LEU* 5.2 0.9 - - + -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 4.0 12.8 - - + +
297B PHE* 1.3 77.7 - - - +
299B PRO* 1.3 61.9 - - - +
329B ALA* 4.0 15.7 - - + +
331B HIS* 5.9 0.9 - - + +
365B PHE* 5.0 3.1 - - + -
371B ALA* 5.4 0.2 - - + -
372B VAL 2.8 11.3 + - - +
373B VAL* 3.4 23.0 - - + +
374B ILE* 2.8 30.3 + - - +
376B ALA* 4.0 3.0 - - + +
379B VAL* 5.2 2.5 - - + -
380B VAL* 3.6 26.2 - - + -
397B LEU* 3.9 20.6 - - + -
399B VAL* 4.2 16.6 - - + -
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Residues in contact with PRO 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PHE* 3.3 13.0 - - + +
298B VAL* 1.3 88.0 - - - +
300B GLY* 1.3 57.9 + - - +
303B MET* 4.2 14.1 - - - -
312B LEU* 4.9 5.2 - - + -
328B PHE* 5.2 4.7 - - + -
329B ALA 3.5 15.1 - - - +
330B ILE* 3.7 24.0 - - + -
331B HIS* 5.7 0.3 - - - +
334B ALA* 3.7 18.7 - - - +
341B MET* 3.6 20.2 - - + -
345B LEU* 4.6 7.4 - - + -
374B ILE* 3.5 16.6 - - + +
376B ALA* 4.1 4.6 - - - +
379B VAL* 5.0 0.5 - - - +
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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