Contacts of the strand formed by residues 348 - 355 (chain B) in PDB entry 3LX9
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 ALA 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B LEU* 2.8 44.3 + - + +
345B SER 3.5 15.5 + - - +
346B GLY 3.0 1.7 + - - +
347B LEU* 1.3 79.5 - - - +
349B TRP* 1.3 65.0 + - - +
416B GLN* 4.7 2.9 - - - +
417B LEU 3.2 13.2 - - - +
418B GLU* 3.7 24.2 - - - +
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Residues in contact with TRP 349 (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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329B TYR* 3.7 23.6 - - - -
341B GLU* 3.8 13.7 - - + -
342B ARG 3.4 10.1 - - - -
343B PRO* 3.5 46.9 - - + -
344B LEU* 3.8 4.7 - - - -
347B LEU* 3.7 16.1 + - - +
348B ALA* 1.3 87.2 + - - +
350B ALA* 1.3 61.9 + - - +
351B VAL* 4.8 3.1 - - + -
373B GLY* 3.5 36.3 + - - +
374B LYS* 4.4 14.8 - - + -
376B VAL* 4.8 8.2 - - + +
377B ALA* 3.5 29.1 - - + +
415B LEU 4.0 0.2 - - - +
416B GLN* 3.3 5.2 - - - +
417B LEU* 2.7 53.0 + - + +
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Residues in contact with ALA 350 (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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289B ILE* 3.6 13.6 - - + +
319B ILE* 3.7 43.5 - - + -
341B GLU* 3.1 5.0 - - - +
342B ARG* 2.8 37.6 + - + +
344B LEU* 3.8 6.4 - - + +
349B TRP* 1.3 74.2 - - - +
351B VAL* 1.3 63.0 + - - +
414B LEU* 4.6 1.6 - - + -
415B LEU 3.3 5.6 - - - +
416B GLN* 4.5 0.7 - - - +
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Residues in contact with VAL 351 (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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339B VAL* 4.1 18.2 - - + -
340B TRP 3.4 10.1 - - - +
341B GLU* 4.2 13.0 - - + +
349B TRP* 4.8 4.0 - - + -
350B ALA* 1.3 80.3 - - - +
352B ALA* 1.3 62.8 - - - +
353B MET* 4.4 11.2 - - + -
367B ILE* 6.1 1.1 - - + -
372B LEU* 4.1 26.7 - - + -
413B VAL 3.6 1.7 - - - +
414B LEU* 3.4 4.6 - - - +
415B LEU* 2.7 57.6 + - + +
417B LEU* 4.0 22.0 - - + -
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.9 28.0 - - + -
289B ILE* 3.9 19.8 - - + +
338B GLU 3.8 0.7 - - - +
339B VAL* 3.3 3.6 - - - +
340B TRP* 2.8 43.7 + - + +
351B VAL* 1.3 73.9 - - - +
353B MET* 1.3 62.3 + - - +
354B ILE* 4.1 1.1 - - + -
412B THR* 3.9 7.6 - - + -
413B VAL 3.3 4.5 - - - -
414B LEU* 4.0 7.0 - - + -
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Residues in contact with MET 353 (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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338B GLU 3.3 6.3 - - - +
339B VAL* 4.1 16.4 - - + -
351B VAL* 4.4 9.9 - - + -
352B ALA* 1.3 77.0 - - - +
354B ILE* 1.3 59.1 + - - +
365B TYR* 3.8 25.6 - - + +
367B ILE* 4.4 15.9 - - - -
403B LEU* 4.7 1.8 - - + +
405B SER* 3.4 34.8 - - - +
407B ILE* 3.6 20.0 - - + +
412B THR* 3.3 3.9 - - - +
413B VAL* 2.9 46.1 + - + +
415B LEU* 3.5 27.4 - - + -
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Residues in contact with ILE 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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236B TRP* 4.8 4.5 - - + -
243B LEU* 4.2 14.6 - - + -
282B THR* 4.2 10.1 - - + +
286B LEU* 3.7 33.7 - - + -
337B PHE* 3.3 9.5 - - - -
338B GLU* 2.8 51.0 + - + +
340B TRP* 4.0 21.8 - - + +
352B ALA 5.0 0.2 - - - -
353B MET* 1.3 76.3 - - - +
355B ASN* 1.3 70.6 + - - +
356B ARG* 3.7 15.1 + - + -
407B ILE* 4.3 0.7 - - - -
411B GLY 3.5 7.2 - - - +
412B THR* 3.5 19.7 - - + +
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Residues in contact with ASN 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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336B ASN 3.8 2.5 - - - -
337B PHE* 4.1 7.2 - - + -
354B ILE* 1.3 71.2 - - - +
356B ARG* 1.3 57.4 + - - +
357B GLN* 3.0 18.3 + - - +
361B GLY 4.4 1.2 + - - -
363B ARG* 3.1 40.5 + - - +
407B ILE* 2.9 36.5 + - + +
408B ASN 3.3 13.5 - - - +
409B PRO* 3.7 17.1 - - - +
410B THR* 2.8 36.0 + - - -
411B GLY 3.1 7.7 + - - -
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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