Contacts of the strand formed by residues 336 - 344 (chain B) in PDB entry 1LW0
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 GLN 336 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B LYS* 4.7 0.3 - - - +
332B GLN* 2.8 32.5 + - + +
333B GLY 2.5 25.0 + - - +
334B GLN* 3.8 20.4 - - - +
335B GLY* 1.3 73.2 - - - +
337B TRP* 1.3 67.5 + - - +
353B LYS* 5.9 3.1 - - + -
354B TYR 3.4 2.9 - - - +
355B ALA* 3.7 22.6 - - + +
428B GLN* 3.4 30.8 + - - +
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Residues in contact with TRP 337 (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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408A ALA* 3.8 27.1 - - + -
329B ILE* 4.0 18.2 - - + -
330B GLN 3.3 10.3 - - - +
331B LYS* 3.4 45.3 - - + -
332B GLN* 4.1 1.1 - - - -
335B GLY* 3.8 4.6 - - - -
336B GLN* 1.3 84.0 - - - +
338B THR* 1.3 70.7 + - - +
339B TYR* 5.6 0.9 - - + -
353B LYS* 3.4 6.3 - - - +
354B TYR* 2.6 63.2 + + + +
364B ASP* 3.6 29.8 - - + -
367B GLN* 2.9 32.3 + - + +
368B LEU* 4.1 20.2 - - + -
371B ALA* 5.5 3.1 - - + -
392B PRO* 4.3 7.4 - - + -
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Residues in contact with THR 338 (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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242B GLN* 6.0 1.1 - - + -
329B ILE* 3.3 2.8 - - - -
330B GLN* 2.6 65.4 + - - +
332B GLN* 3.0 39.0 + - + +
337B TRP* 1.3 81.6 - - - +
339B TYR* 1.3 59.1 + - - +
340B GLN* 4.1 4.5 - - - -
352B GLY 3.8 6.5 - - - +
353B LYS* 3.7 20.9 - - + -
427B TYR* 3.9 11.1 - - + +
428B GLN* 3.9 9.9 - - + +
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Residues in contact with TYR 339 (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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327B ALA* 6.0 1.1 - - + -
328B GLU 3.1 13.5 - - - +
329B ILE* 4.2 5.2 - - + -
337B TRP* 6.2 0.4 - - + -
338B THR* 1.3 75.6 - - - +
340B GLN* 1.3 77.4 + - - +
341B ILE* 4.4 13.7 - - + -
350B LYS* 3.6 20.7 - - + -
351B THR* 3.5 4.8 - - - -
352B GLY* 3.1 47.2 + - - +
353B LYS 3.7 14.8 - - - -
354B TYR* 4.8 7.2 - - + -
371B ALA* 5.9 0.4 - - + -
374B LYS* 3.3 31.5 + - + -
375B ILE* 3.5 43.1 - - + -
378B GLU* 3.1 23.3 + - - -
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Residues in contact with GLN 340 (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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327B ALA* 3.6 1.8 - - - -
328B GLU* 3.1 36.0 + - - +
330B GLN* 2.3 48.9 + - - -
338B THR* 3.7 3.4 + - - -
339B TYR* 1.3 88.7 + - - +
341B ILE* 1.3 62.0 + - - +
342B TYR* 3.7 11.9 - - + -
348B ASN* 3.4 30.5 - - - +
350B LYS 3.4 5.8 - - - -
351B THR* 3.7 7.9 - - + -
423B VAL* 5.4 0.3 - - - +
427B TYR* 3.6 35.7 + - + +
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Residues in contact with ILE 341 (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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325B LEU* 4.1 20.0 - - + -
326B ILE 3.2 10.8 - - - +
327B ALA* 4.4 7.0 - - + -
339B TYR* 4.4 9.6 - - + -
340B GLN* 1.3 73.7 - - - +
342B TYR* 1.3 57.6 + - - +
348B ASN* 3.6 1.1 - - - -
349B LEU* 2.7 34.0 + - + -
350B LYS* 2.7 35.0 + - + +
375B ILE* 3.8 32.3 - - + +
378B GLU* 4.9 2.9 - - + +
379B SER* 3.8 15.3 - - - +
383B TRP* 4.0 30.5 - - + -
387B PRO* 5.2 0.9 - - + -
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Residues in contact with TYR 342 (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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325B LEU* 3.8 1.9 - - - +
326B ILE* 2.8 73.8 + - + +
328B GLU* 3.2 38.6 + - + +
340B GLN* 3.7 19.1 - - + -
341B ILE* 1.3 77.2 - - - +
343B GLN* 1.3 65.9 + - - +
344B GLU 3.4 17.5 - - - -
345B PRO* 3.6 26.5 - - + +
346B PHE 5.8 0.2 - - - -
347B LYS 3.3 21.3 - - - +
348B ASN* 3.8 16.6 - - - +
349B LEU* 4.1 6.5 - - - +
390B LYS* 4.1 7.6 - - - -
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Residues in contact with GLN 343 (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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318B TYR 3.8 6.9 - - - +
319B TYR* 3.3 22.3 - - - -
320B ASP* 2.5 57.2 + - - +
323B LYS* 3.6 26.3 + - + +
324B ASP 3.5 17.5 - - - +
325B LEU* 3.8 5.2 - - + +
326B ILE* 4.3 11.2 - - - +
342B TYR* 1.3 83.0 - - - +
344B GLU* 1.3 63.2 + - + +
345B PRO* 4.4 1.9 - - - +
347B LYS 4.2 2.8 + - - -
349B LEU* 3.8 14.7 - - + +
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Residues in contact with GLU 344 (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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342B TYR* 3.4 6.6 - - - -
343B GLN* 1.3 81.2 - - + +
345B PRO* 1.3 83.2 - - + +
346B PHE 3.4 0.2 + - - -
347B LYS* 2.9 60.7 + - + +
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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