Contacts of the strand formed by residues 341 - 351 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334E MET 3.3 12.1 - - - -
335E SER* 2.6 22.7 + - - -
339E GLY 4.9 1.7 + - - -
340E SER* 1.3 81.2 + - - +
342E VAL* 1.3 68.0 + - - +
343E TYR* 4.6 17.0 + - - -
368E ASN* 4.3 6.6 + - - -
460E TRP* 4.3 2.2 - - - -
468E ARG* 5.3 0.5 + - - -
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Residues in contact with VAL 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ASP* 3.7 0.3 - - - -
334E MET* 3.0 49.9 + - + +
341E SER* 1.3 78.9 - - - +
343E TYR* 1.3 69.3 + - - +
368E ASN* 2.8 36.1 - - + +
369E ALA* 3.4 17.9 - - + -
460E TRP* 3.5 42.8 - - + +
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Residues in contact with TYR 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E HIS* 3.1 42.8 - + + +
331E LEU* 4.2 5.2 - - + -
332E PHE 3.1 9.9 - - - +
333E ASP* 3.9 15.5 - - + -
341E SER* 4.6 18.5 + - - -
342E VAL* 1.3 81.6 - - - +
344E ALA* 1.3 59.7 + - - +
345E GLN* 5.1 3.4 - - - +
367E GLY* 4.4 7.2 - - - -
368E ASN* 2.7 32.3 + - - +
369E ALA* 2.7 32.9 + - - +
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Residues in contact with ALA 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E LEU* 4.4 0.2 - - - +
332E PHE* 2.8 39.5 + - + -
343E TYR* 1.3 83.2 - - - +
345E GLN* 1.3 59.2 + - - +
346E TYR* 4.2 6.4 - - + -
365E TYR* 3.8 17.0 - - + -
366E SER 3.5 10.5 + - - -
369E ALA* 3.8 12.8 - - + -
457E TRP* 3.8 21.5 - - + -
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Residues in contact with GLN 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E HIS* 3.8 24.3 + - - +
270E TRP* 4.0 17.9 - - - -
329E GLN* 4.2 9.1 - - - +
330E VAL 3.0 18.2 - - - +
331E LEU* 3.6 26.5 - - + +
343E TYR* 5.1 2.8 - - + +
344E ALA* 1.3 75.0 - - - +
346E TYR* 1.3 64.0 + - - +
347E ALA 4.2 0.2 - - - -
364E ASP 3.3 9.4 - - - +
365E TYR* 3.6 1.9 - - - -
366E SER* 3.1 40.4 + - - +
367E GLY* 5.9 0.4 - - - -
475E ARG* 4.8 3.3 + - - -
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Residues in contact with TYR 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E GLN* 3.4 3.3 - - - +
330E VAL* 2.9 42.8 + - + +
332E PHE* 4.6 4.0 - + - -
344E ALA* 4.2 13.2 - - + -
345E GLN* 1.3 81.2 - - - +
347E ALA* 1.3 65.2 + - - +
348E SER* 3.0 10.8 + - - +
362E VAL* 3.5 19.1 - - + -
363E GLU 3.4 7.0 - - - +
364E ASP 3.2 3.8 - - - -
365E TYR* 3.6 31.2 - + + -
370E GLY 4.3 0.5 + - - -
371E ASN* 3.3 18.4 - - - -
372E ALA 3.5 1.2 + - - -
373E LEU* 3.1 51.4 + - + +
374E LEU* 3.7 29.6 - - + -
457E TRP* 4.9 1.5 - + - -
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Residues in contact with ALA 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E GLN* 3.3 22.6 - - - +
345E GLN 4.2 0.2 - - - -
346E TYR* 1.3 71.6 - - - +
348E SER* 1.3 57.4 + - - +
363E GLU 2.7 7.3 + - - -
364E ASP* 3.2 31.8 + - + +
477E LYS* 3.6 17.5 + - - -
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Residues in contact with SER 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E THR* 3.3 22.0 - - - +
328E GLN 3.2 3.4 - - - -
346E TYR* 3.0 4.4 - - - +
347E ALA* 1.3 81.5 - - - +
349E PHE* 1.3 60.0 + - - +
350E ARG* 5.3 0.9 - - - +
361E TRP 4.1 2.8 + - - -
362E VAL* 3.0 10.5 - - - +
363E GLU* 2.9 47.0 + - - +
364E ASP* 5.4 0.9 - - - -
477E LYS* 5.6 1.1 - - - -
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Residues in contact with PHE 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E VAL* 3.8 23.1 - - + -
323E THR* 3.6 19.3 - - + +
327E THR* 3.4 1.2 - - - +
328E GLN 2.4 47.3 + - - +
329E GLN 4.1 0.2 - - - -
330E VAL* 3.4 36.3 - - + +
332E PHE* 5.4 2.5 - + - -
348E SER* 1.3 70.7 + - - +
350E ARG* 1.3 66.5 + - - +
351E PRO* 4.5 8.1 - - + -
360E LEU* 3.5 24.5 - - + -
361E TRP 3.7 1.8 - - - -
362E VAL* 3.8 11.2 - - + -
423E TRP* 4.5 15.0 - + - -
472E MET* 3.6 28.7 - - + -
474E LEU* 3.6 23.1 - - + -
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Residues in contact with ARG 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E THR* 3.3 28.0 + - - -
324E LYS* 4.2 19.8 + - - +
326E HIS* 5.1 0.8 - - - +
327E THR* 3.0 32.7 + - + +
348E SER* 5.3 0.7 - - - +
349E PHE* 1.3 83.3 - - - +
351E PRO* 1.3 78.8 + - + +
352E GLU* 5.7 1.6 + - + +
360E LEU* 4.9 1.1 - - - -
361E TRP* 2.9 54.9 + - + +
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Residues in contact with PRO 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E THR* 5.4 2.0 - - + +
319E VAL* 4.7 4.0 - - + -
320E HIS* 3.0 42.2 + - + +
323E THR* 2.8 36.4 + - + +
324E LYS* 5.9 0.2 - - - +
349E PHE* 4.5 10.3 - - + -
350E ARG* 1.3 92.5 + - - +
352E GLU* 1.3 61.2 + - - +
358E TYR* 3.5 18.6 - - + +
359E ARG 2.9 11.7 - - - +
360E LEU* 4.4 5.4 - - + -
423E TRP* 4.9 10.3 - - + -
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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