Contacts of the strand formed by residues 412 - 419 (chain B) in PDB entry 3LXA
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 THR 412 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ASN 4.5 1.8 + - - -
281B VAL* 3.6 19.1 - - - +
282B THR* 2.6 44.2 + - - +
285B ALA* 3.8 14.4 - - + -
286B LEU* 3.7 20.4 - - + -
352B ALA* 3.9 3.1 - - + -
353B MET 3.2 20.4 - - - +
354B ILE* 3.6 7.7 - - + +
388B LEU* 3.9 1.7 - - - +
389B PRO* 3.9 11.5 - - - +
407B ILE* 4.0 2.0 - - - +
411B GLY* 1.3 72.4 + - - -
413B VAL* 1.3 75.6 + - - +
414B LEU 3.9 0.9 + - - -
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Residues in contact with VAL 413 (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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351B VAL 3.5 2.4 - - - +
352B ALA* 3.3 2.4 - - - -
353B MET* 2.8 53.6 + - + +
386B GLN* 3.7 14.6 - - - +
388B LEU 3.3 10.8 - - - +
389B PRO* 4.3 11.4 - - + -
394B LEU* 6.2 0.2 - - + -
405B SER* 4.3 9.0 - - - +
406B HIS 3.9 13.7 - - - +
407B ILE* 3.7 27.1 - - + +
412B THR* 1.3 75.5 - - - +
414B LEU* 1.3 61.0 + - - +
415B LEU* 3.6 24.9 - - + -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ALA* 4.1 20.0 - - + +
288B ALA* 5.0 2.7 - - + -
289B ILE* 4.1 16.2 - - + -
316B VAL* 4.2 18.4 - - + -
319B ILE* 4.4 16.6 - - + -
350B ALA* 4.6 4.3 - - + -
351B VAL 3.4 20.6 - - - +
352B ALA* 4.0 12.6 - - + +
386B GLN* 3.5 0.2 - - - -
387B LEU* 2.7 36.6 + - + -
388B LEU* 3.0 43.5 + - + +
412B THR 3.9 1.4 - - - -
413B VAL* 1.3 72.8 - - - +
415B LEU* 1.3 70.4 + - - +
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Residues in contact with LEU 415 (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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319B ILE* 4.8 1.0 - - - +
350B ALA* 3.2 8.5 - - - +
351B VAL* 2.6 48.2 + - + +
353B MET* 3.6 27.6 - - + -
372B LEU* 5.7 3.6 - - + -
384B ILE* 4.1 10.1 - - + -
385B THR 3.3 3.6 - - - +
386B GLN* 3.6 21.5 - - + +
387B LEU* 4.9 2.5 - - - -
394B LEU* 4.3 6.5 - - + -
403B LEU* 3.9 24.5 - - + -
405B SER* 5.5 0.4 - - - +
413B VAL* 3.6 15.7 - - + -
414B LEU* 1.3 90.1 - - - +
416B GLN* 1.3 59.8 + - - +
417B LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 416 (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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315B ASP* 5.0 1.2 - - - +
319B ILE* 3.6 23.5 - - + +
344B LEU* 3.6 23.3 - - - +
348B ALA* 4.0 12.1 - - - +
349B TRP 3.3 4.3 - - - +
350B ALA* 4.7 0.4 - - - +
383B PHE 3.5 1.6 - - - +
384B ILE* 3.4 4.5 - - - -
385B THR* 2.7 48.8 + - - +
387B LEU* 4.1 14.8 - - + +
415B LEU* 1.3 73.9 - - - +
417B LEU* 1.3 69.4 + - - +
418B GLU* 4.2 17.1 + - + +
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Residues in contact with LEU 417 (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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348B ALA* 3.3 10.9 - - - +
349B TRP* 2.7 42.5 + - + +
351B VAL* 4.0 18.4 - - + -
372B LEU* 3.7 25.4 - - + -
377B ALA* 3.9 18.2 - - + +
378B CYS* 3.7 24.0 - - - -
382B CYS* 4.4 8.1 - - + -
383B PHE 3.6 3.4 - - - -
384B ILE* 3.8 22.0 - - + -
415B LEU* 3.9 22.9 - - + -
416B GLN* 1.3 82.3 - - - +
418B GLU* 1.3 59.9 + - - +
419B ASN 4.1 0.4 + - - -
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Residues in contact with GLU 418 (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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346B GLY 5.3 1.7 - - - +
348B ALA* 3.6 20.8 - - - +
382B CYS* 2.9 7.1 - - - -
383B PHE* 2.8 49.0 + - + +
385B THR* 5.5 3.1 - - - +
416B GLN* 4.2 18.8 + - + +
417B LEU* 1.3 73.1 - - - +
419B ASN* 1.3 61.1 + - - +
420B THR 3.4 0.2 + - - -
422B GLN* 6.1 0.9 - - + -
423B MET* 3.6 30.2 - - + +
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Residues in contact with ASN 419 (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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346B GLY 5.6 0.2 + - - -
347B LEU* 4.0 29.3 + - + +
376B VAL 2.9 27.6 + - - +
377B ALA* 3.0 18.5 + - - +
379B ASN 3.5 19.5 + - - +
380B PRO* 4.4 0.2 - - - +
381B ALA 3.6 4.9 + - - -
417B LEU 4.1 1.2 - - - -
418B GLU* 1.3 71.5 - - - +
420B THR* 1.3 60.8 + - - +
421B MET* 3.1 38.3 + - - +
422B GLN* 2.9 33.5 + - + +
423B MET* 3.6 5.4 + - - +
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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