Contacts of the strand formed by residues 353 - 359 (chain B) in PDB entry 5LSO
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 VAL 353 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LEU 3.8 9.4 - - - +
310B ARG* 4.0 11.3 - - - +
311B ASN 4.2 4.9 + - - -
312B MET* 5.1 3.0 + - + +
313B VAL* 3.8 27.7 + - + +
314B GLY 3.6 25.8 - - - +
318B VAL* 3.7 32.8 - - + -
322B LEU* 4.7 0.4 - - + -
341B ILE* 4.0 15.7 - - + -
342B PHE 3.7 3.6 - - - +
343B GLU* 3.9 15.3 - - + +
349B ASP 5.2 0.2 + - - -
351B GLU 4.3 2.4 - - - +
352B ALA* 1.3 78.2 - - - +
354B ARG* 1.3 63.7 + - - +
355B ILE* 4.1 11.0 + - + +
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Residues in contact with ARG 354 (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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308B LEU* 3.6 34.3 - - + +
309B LEU 3.8 3.1 - - - -
310B ARG* 4.3 12.2 - - + +
340B VAL 3.5 1.7 - - - +
341B ILE* 3.5 2.4 - - - +
342B PHE* 2.8 45.7 + - + +
344B ILE* 3.8 24.9 - - + +
351B GLU* 4.1 22.1 + - - +
352B ALA 4.8 0.2 - - - +
353B VAL* 1.3 77.5 - - - +
355B ILE* 1.3 63.2 + - - +
356B PHE* 3.7 11.8 - - + -
387B TYR* 3.7 11.1 - - - -
397B LEU 2.8 36.0 + - - -
398B ALA 3.4 2.5 + - - -
399B GLU 2.8 37.9 + - - +
400B GLN* 4.3 9.9 - - - +
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Residues in contact with ILE 355 (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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307B VAL 3.7 0.9 - - - +
308B LEU* 3.5 2.6 - - - +
309B LEU* 2.8 51.9 + - + +
312B MET* 3.9 26.2 - - + -
322B LEU* 3.8 25.6 - - + -
326B THR* 3.8 38.1 - - + +
339B CYS* 3.9 19.1 - - - -
340B VAL 3.4 4.9 - - - +
341B ILE* 4.4 11.2 - - + -
353B VAL* 4.5 11.2 - - + -
354B ARG* 1.3 74.8 - - - +
356B PHE* 1.3 65.7 + - - +
357B LEU* 4.9 0.9 - - + -
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Residues in contact with PHE 356 (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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306B VAL* 4.3 7.6 - - + -
307B VAL 3.3 5.8 - - - +
308B LEU* 4.2 9.4 - - + -
338B LYS 3.8 0.6 - - - +
339B CYS* 3.3 7.3 - - - -
340B VAL* 2.8 42.5 + - + +
342B PHE* 4.2 2.5 - - + -
354B ARG* 3.7 30.5 - - + -
355B ILE* 1.3 76.7 - - - +
357B LEU* 1.3 63.5 + - - +
358B GLU 4.2 0.2 - - - -
387B TYR* 3.7 42.2 - + + -
392B PHE* 3.4 34.8 - + + -
397B LEU* 3.3 53.8 - - + -
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Residues in contact with LEU 357 (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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305B LYS 3.5 1.2 - - - +
306B VAL* 3.3 6.4 - - - -
307B VAL* 2.8 45.3 + - + +
309B LEU* 4.0 22.9 - - + -
326B THR* 4.2 9.9 - - + -
327B LYS* 4.4 9.2 - - - -
330B CYS* 3.5 33.7 - - + -
336B VAL* 3.8 22.9 - - + -
338B LYS 3.3 1.3 - - - -
339B CYS* 3.8 26.0 - - + -
355B ILE* 4.9 1.3 - - + -
356B PHE* 1.3 75.4 - - - +
358B GLU* 1.3 60.7 + - - +
359B PHE* 3.6 19.8 + - + -
372B LEU* 5.3 0.2 - - + -
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Residues in contact with GLU 358 (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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305B LYS* 3.7 21.7 + - + +
306B VAL* 4.2 9.0 - - + +
336B VAL* 3.6 3.2 - - - +
337B GLY* 2.7 35.2 + - - -
338B LYS* 2.9 49.5 + - + +
356B PHE 4.2 0.4 - - - -
357B LEU* 1.3 71.2 - - - +
359B PHE* 1.3 63.9 + - - +
389B LEU* 4.3 4.5 - - - -
392B PHE* 3.3 21.5 - - + -
393B ARG* 2.7 37.7 + - - -
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Residues in contact with PHE 359 (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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305B LYS* 2.8 39.2 + - - +
307B VAL* 3.7 23.6 - - + -
330B CYS* 3.5 38.1 - - + -
333B TYR* 4.1 3.4 - - + -
334B GLY 3.7 4.9 - - - -
335B LYS 3.4 16.2 - - - +
336B VAL* 3.7 13.2 - - + -
337B GLY* 4.5 0.7 - - - -
357B LEU* 4.0 15.7 - - + -
358B GLU* 1.3 83.0 - - - +
360B GLU* 1.3 64.3 + - - +
361B ARG 3.3 17.7 - - - +
364B SER* 3.5 20.9 - - - -
365B ALA* 3.9 10.8 - - - +
368B ALA* 3.9 20.9 - - + -
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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