Contacts of the strand formed by residues 341 - 351 (chain H) in PDB entry 1LWU
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 SER 341 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334H MET 3.3 11.9 - - - -
335H SER* 2.7 22.0 + - - +
339H GLY 4.3 1.9 + - - -
340H SER* 1.3 82.1 + - - +
342H VAL* 1.3 67.7 + - - +
343H TYR* 4.5 17.8 + - - -
368H ASN* 4.3 6.6 + - - -
460H TRP* 4.3 2.6 - - - -
468H ARG* 5.3 0.5 + - - -
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Residues in contact with VAL 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332H PHE 3.9 0.2 - - - +
333H ASP* 3.8 0.3 - - - -
334H MET* 3.0 50.3 + - + +
341H SER* 1.3 76.9 - - - +
343H TYR* 1.3 69.8 + - - +
368H ASN* 2.9 36.1 - - + +
369H ALA* 3.4 17.5 - - + -
460H TRP* 3.4 44.6 - - + +
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Residues in contact with TYR 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266H HIS* 3.1 43.5 - + + +
331H LEU* 4.2 5.2 - - + -
332H PHE 3.2 9.6 - - - +
333H ASP* 3.9 15.7 - - + -
341H SER* 4.5 17.7 + - - -
342H VAL* 1.3 83.0 - - - +
344H ALA* 1.3 61.0 + - - +
345H GLN* 5.1 3.1 - - - +
367H GLY* 4.9 6.7 - - - -
368H ASN* 2.6 31.6 + - - +
369H ALA* 2.7 33.0 + - - +
502H NDG 4.7 19.3 + - + -
505H MAN 3.9 16.8 + - - -
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Residues in contact with ALA 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332H PHE* 2.8 41.3 + - + -
343H TYR* 1.3 83.2 - - - +
345H GLN* 1.3 59.4 + - - +
346H TYR* 4.2 5.3 - - + -
365H TYR* 3.8 17.5 - - + -
366H SER 3.5 10.7 + - - -
369H ALA* 3.8 13.0 - - + -
457H TRP* 3.8 20.6 - - + -
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Residues in contact with GLN 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266H HIS* 3.8 24.7 + - - +
270H TRP* 4.0 16.5 - - - -
329H GLN* 4.2 10.0 - - - +
330H VAL 3.0 17.5 - - - +
331H LEU* 3.6 28.2 - - + +
343H TYR* 5.1 2.6 - - - +
344H ALA* 1.3 74.8 - - - +
346H TYR* 1.3 65.2 + - - +
364H ASP 3.3 10.4 - - - +
365H TYR* 3.6 2.1 - - - -
366H SER* 3.1 39.2 + - - +
475H ARG* 4.8 3.1 + - - -
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Residues in contact with TYR 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H GLN* 3.4 3.3 - - - +
330H VAL* 2.9 43.0 + - + +
332H PHE* 4.6 3.8 - + - -
344H ALA* 4.2 13.7 - - + -
345H GLN* 1.3 80.3 - - - +
347H ALA* 1.3 64.3 + - - +
348H SER 3.1 2.6 + - - +
362H VAL* 3.5 20.4 - - + -
363H GLU 3.4 15.5 - - - +
364H ASP 3.2 4.0 - - - -
365H TYR* 3.5 32.2 - + + -
370H GLY 4.3 0.3 + - - -
371H ASN* 3.3 18.6 - - - -
372H ALA 3.5 1.4 + - - -
373H LEU* 3.2 49.6 + - + +
374H LEU* 3.7 30.5 - - + -
457H TRP* 4.8 1.9 - + - -
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Residues in contact with ALA 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329H GLN* 3.3 23.1 - - - +
345H GLN 4.2 0.2 - - - -
346H TYR* 1.3 71.4 - - - +
348H SER* 1.3 57.4 + - - +
363H GLU 2.7 6.5 + - - -
364H ASP* 3.2 33.6 + - + +
477H LYS* 3.6 17.7 + - - -
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Residues in contact with SER 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327H THR* 3.3 22.4 - - - +
328H GLN 3.3 2.9 - - - -
346H TYR* 3.1 4.4 - - - +
347H ALA* 1.3 82.1 - - - +
349H PHE* 1.3 60.3 + - - +
350H ARG* 5.3 0.9 - - - +
361H TRP 4.1 3.3 + - - -
362H VAL* 3.0 9.1 - - - +
363H GLU* 2.9 49.1 + - - -
364H ASP* 5.4 0.7 - - - -
477H LYS* 5.7 0.9 - - - -
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Residues in contact with PHE 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319H VAL* 3.8 24.0 - - + -
323H THR* 3.6 19.8 - - + +
327H THR* 3.4 1.7 - - - +
328H GLN* 2.4 36.2 + - + +
330H VAL* 3.4 37.0 - - + +
332H PHE* 5.4 2.5 - + - -
348H SER* 1.3 76.0 + - - +
350H ARG* 1.3 66.1 + - - +
351H PRO* 4.4 9.0 - - + -
360H LEU* 3.6 24.0 - - + -
361H TRP 3.7 1.8 - - - -
362H VAL* 3.8 11.0 - - + -
373H LEU* 5.7 0.2 - - + -
423H TRP* 4.5 13.7 - + - -
472H MET* 3.6 30.3 - - + -
474H LEU* 3.6 22.9 - - + -
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Residues in contact with ARG 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323H THR* 3.3 27.4 + - - -
324H LYS* 4.2 18.4 + - - +
326H HIS* 5.1 0.4 - - - +
327H THR* 3.0 33.1 + - + +
348H SER* 5.3 0.4 - - - +
349H PHE* 1.3 82.2 - - - +
351H PRO* 1.3 78.7 + - + +
352H GLU* 5.0 1.8 + - - +
359H ARG 3.8 0.2 - - - +
360H LEU* 5.3 0.9 - - - -
361H TRP* 2.9 54.7 + - + +
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Residues in contact with PRO 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316H THR* 5.4 1.8 - - + +
319H VAL* 4.7 4.5 - - + +
320H HIS* 2.9 42.1 + - + +
323H THR* 2.8 35.5 + - + +
324H LYS* 5.9 0.2 - - - +
349H PHE* 4.4 10.5 - - + -
350H ARG* 1.3 92.4 + - - +
352H GLU* 1.3 62.2 + - - +
358H TYR* 3.6 18.8 - - + +
359H ARG 2.9 12.6 - - - +
360H LEU* 4.4 5.4 - - + -
423H TRP* 4.9 10.1 - - + -
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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