Contacts of the helix formed by residues 352 - 363 (chain B) in PDB entry 5L26
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 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B PRO* 4.5 8.0 - - - +
350B GLN 3.8 1.2 + - - -
351B LEU* 1.3 78.5 - - - +
353B ASP* 1.3 64.9 + - - +
354B THR* 3.7 12.0 - - - +
355B THR* 2.5 34.8 + - - -
356B LYS* 3.2 21.5 + - - +
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Residues in contact with ASP 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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201B TYR* 4.9 2.8 + - - -
351B LEU 4.0 0.6 + - - -
352B SER* 1.3 73.7 - - - +
354B THR* 1.3 61.9 + - - +
355B THR 3.3 0.2 + - - -
356B LYS* 3.4 7.7 + - - +
357B ALA* 3.3 21.7 + - - +
416B THR* 5.1 3.2 - - - +
420B GLY* 6.0 3.1 - - - -
421B ALA 5.6 5.8 - - - +
422B SER* 5.0 19.8 - - - +
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Residues in contact with THR 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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311B GLY 4.9 4.8 + - - +
313B PRO* 5.2 9.2 - - + -
352B SER* 3.7 14.8 - - - +
353B ASP* 1.3 80.1 - - - +
355B THR* 1.3 65.4 + - - +
357B ALA* 3.6 2.6 + - - +
358B ILE* 3.2 28.9 + - - +
413B GLY* 3.2 24.5 + - - -
416B THR* 3.4 19.8 + - - -
417B GLY* 4.8 7.5 - - - -
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Residues in contact with THR 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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312B VAL* 3.8 22.2 - - + -
313B PRO* 3.5 20.3 - - - +
316B GLU* 4.1 14.8 - - + +
351B LEU* 4.8 8.7 - - + -
352B SER* 2.5 32.6 + - - -
353B ASP 3.2 0.6 - - - -
354B THR* 1.3 76.7 - - - +
356B LYS* 1.3 65.1 + - - +
358B ILE* 3.1 10.5 + - - +
359B ILE* 3.0 46.6 + - + +
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Residues in contact with LYS 356 (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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201B TYR* 4.6 4.7 - - + -
339B PHE* 3.8 15.2 - - + -
343B LEU* 4.5 21.5 - - + -
351B LEU* 5.2 7.8 - - + +
352B SER 3.2 10.0 + - - +
353B ASP* 3.8 9.6 - - - +
355B THR* 1.3 78.8 - - - +
357B ALA* 1.3 54.4 + - - +
359B ILE* 4.9 0.4 - - - -
360B SER* 2.6 38.1 + - - +
422B SER* 5.7 5.2 - - - -
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Residues in contact with ALA 357 (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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201B TYR* 3.7 28.2 - - + +
353B ASP 3.3 7.7 + - - +
354B THR 3.8 7.9 - - - +
355B THR 3.1 0.6 - - - -
356B LYS* 1.3 77.8 - - - +
358B ILE* 1.3 64.3 + - - +
360B SER* 3.4 0.7 + - - -
361B PHE* 3.1 30.9 + - - -
412B ALA* 4.6 7.2 - - + +
416B THR* 3.6 32.3 - - + +
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Residues in contact with ILE 358 (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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310B ILE* 3.5 39.0 - - + +
311B GLY* 3.5 35.9 - - - +
312B VAL* 3.7 14.1 - - + +
354B THR* 3.2 20.2 + - - +
355B THR* 3.1 7.9 + - - +
357B ALA* 1.3 77.5 - - - +
359B ILE* 1.3 59.9 + - + +
361B PHE 3.3 1.7 + - - -
362B ALA* 2.8 29.7 + - + +
409B ALA* 3.3 23.3 - - + +
413B GLY* 3.5 22.9 - - - +
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Residues in contact with ILE 359 (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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316B GLU 5.6 0.2 - - - +
319B ILE* 5.2 1.3 - - + -
320B ALA* 3.9 25.6 - - + +
323B LEU* 3.7 27.4 - - + -
324B ILE* 6.1 1.8 - - + -
339B PHE* 3.6 34.8 - - + -
351B LEU* 4.5 8.3 - - + -
355B THR* 3.0 35.3 + - + +
356B LYS 4.1 0.2 - - - +
358B ILE* 1.3 78.9 - - + +
360B SER* 1.3 57.4 + - - +
362B ALA* 4.2 5.4 - - - -
363B LEU* 2.9 49.2 + - + +
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Residues in contact with SER 360 (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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197B VAL* 5.2 4.5 - - - -
198B PRO* 4.2 10.6 - - - +
201B TYR* 3.5 34.8 - - - +
202B LEU* 4.4 4.4 - - - +
205B ALA* 5.2 0.5 - - - +
336B TYR* 2.9 31.6 + - - -
339B PHE* 3.6 17.3 - - - -
356B LYS* 2.6 23.8 + - - +
357B ALA 3.8 1.1 - - - -
358B ILE 3.3 0.2 - - - -
359B ILE* 1.3 76.9 - - - +
361B PHE* 1.3 61.0 + - - +
364B CYS* 3.6 6.4 - - - +
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Residues in contact with PHE 361 (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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47B LEU* 4.1 13.9 - - + -
201B TYR* 3.4 47.3 - + + -
204B ALA* 3.6 17.7 - - + -
205B ALA* 3.5 40.0 - - + +
208B MET* 3.7 12.3 - - + -
357B ALA* 3.1 28.1 + - + +
360B SER* 1.3 76.7 - - - +
362B ALA* 1.3 63.2 + - - +
363B LEU 3.2 2.4 + - - -
364B CYS* 3.4 13.7 + - - +
405B ASN* 3.7 13.6 - - - +
408B SER* 4.0 19.2 - - - +
409B ALA* 3.8 18.6 - - - +
412B ALA* 3.4 16.2 - - + -
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Residues in contact with ALA 362 (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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310B ILE* 4.8 1.8 - - + -
324B ILE* 4.5 11.4 - - + +
327B LYS* 3.3 19.9 - - - +
358B ILE* 2.8 20.7 + - + +
359B ILE* 3.8 5.8 - - - +
361B PHE* 1.3 77.3 - - - +
363B LEU* 1.3 66.1 + - + +
405B ASN* 3.4 21.8 - - - +
406B LEU* 4.2 18.6 - - + +
409B ALA* 3.6 12.3 - - + +
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Residues in contact with LEU 363 (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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323B LEU* 3.9 17.3 - - + +
324B ILE* 3.9 25.4 - - + -
327B LYS* 3.5 14.9 - - + -
332B GLU* 3.6 9.0 - - - +
335B ALA* 3.7 39.7 - - + +
336B TYR* 3.2 35.2 - - + +
339B PHE* 4.4 2.9 - - + -
359B ILE* 2.9 41.5 + - + +
362B ALA* 1.3 82.5 - - + +
364B CYS* 1.3 60.1 + - - +
365B GLY 2.9 9.3 + - - -
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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