Contacts of the helix formed by residues 352 - 364 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A PRO* 4.7 4.5 - - - +
316A GLU* 3.1 15.3 + - - -
351A LEU* 1.3 76.7 - - - +
353A ASP* 1.3 65.1 + - - +
354A THR* 3.5 13.7 - - - +
355A THR* 2.6 32.9 + - - -
356A LYS* 3.1 22.2 + - - +
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Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A TYR* 4.7 3.8 + - - -
351A LEU 4.7 3.5 - - - +
352A SER* 1.3 74.6 - - - +
354A THR* 1.3 61.9 + - - +
356A LYS* 3.5 7.3 + - - +
357A ALA* 3.2 21.5 + - - +
416A THR* 5.3 2.8 - - - +
421A ALA* 5.9 6.6 - - + +
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Residues in contact with THR 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLY 5.1 4.0 + - - +
313A PRO* 5.5 6.5 - - + -
352A SER* 3.5 17.0 - - - +
353A ASP* 1.3 79.8 - - - +
355A THR* 1.3 63.6 + - - +
357A ALA* 3.5 3.0 + - - +
358A ILE* 3.1 33.1 + - + +
413A GLY* 3.6 24.3 + - - -
416A THR* 4.1 24.0 + - - -
417A GLY* 5.2 2.4 - - - -
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Residues in contact with THR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A VAL* 3.8 22.4 - - + -
313A PRO* 3.5 16.3 - - - +
316A GLU* 2.6 26.8 + - + +
351A LEU* 4.5 6.3 - - + -
352A SER* 2.6 28.1 + - - -
354A THR* 1.3 77.5 - - - +
356A LYS* 1.3 64.5 + - - +
358A ILE* 3.2 9.1 + - - +
359A ILE* 3.0 48.0 + - + +
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Residues in contact with LYS 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PRO* 6.3 0.2 - - - -
201A TYR* 4.8 3.1 - - + -
339A PHE* 3.4 14.1 - - + -
343A LEU* 4.1 24.9 - - + -
351A LEU* 4.8 8.7 - - + +
352A SER 3.1 15.7 + - - +
353A ASP* 3.8 7.9 - - - +
354A THR 3.4 0.2 - - - -
355A THR* 1.3 77.7 - - - +
357A ALA* 1.3 53.3 + - - +
359A ILE* 4.8 0.9 - - - -
360A SER* 2.6 37.9 + - - +
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A TYR* 3.6 38.8 - - + +
353A ASP 3.2 9.1 + - - +
354A THR 3.6 8.7 - - - +
355A THR 3.1 0.4 - - - -
356A LYS* 1.3 77.8 - - - +
358A ILE* 1.3 64.8 + - - +
360A SER* 3.2 1.6 + - - -
361A PHE* 3.1 30.6 + - + -
412A ALA* 4.5 4.3 - - + -
416A THR* 3.8 22.4 - - + +
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 3.6 39.0 - - + +
311A GLY* 3.6 33.4 - - - +
312A VAL* 3.7 15.5 - - + -
320A ALA* 6.1 0.2 - - + -
324A ILE* 6.2 0.2 - - + -
354A THR* 3.1 25.5 + - - +
355A THR* 3.2 7.6 + - - +
357A ALA* 1.3 77.5 - - - +
359A ILE* 1.3 59.5 + - + +
362A ALA* 3.0 27.1 + - + +
409A ALA* 3.4 20.5 - - + +
412A ALA* 4.6 0.4 - - - +
413A GLY* 3.6 25.6 - - - -
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Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU 5.5 0.7 - - - +
319A ILE* 5.0 1.1 - - + -
320A ALA* 4.0 29.2 - - + +
323A LEU* 3.6 22.7 - - + -
324A ILE* 5.8 2.0 - - + -
339A PHE* 3.5 35.7 - - + -
351A LEU* 4.0 13.2 - - + -
355A THR* 3.0 32.3 + - + +
356A LYS 4.1 0.2 - - - +
358A ILE* 1.3 75.7 - - + +
360A SER* 1.3 66.1 + - - +
362A ALA* 4.3 5.2 - - - -
363A LEU* 2.9 41.4 + - + +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A VAL* 5.0 4.5 - - - -
198A PRO* 4.1 9.7 - - - +
201A TYR* 3.7 31.4 - - - +
202A LEU* 4.8 2.9 - - - +
336A TYR* 2.9 28.7 + - - -
339A PHE* 3.5 20.9 - - - -
356A LYS 2.6 24.2 + - - -
357A ALA 3.2 6.3 + - - -
359A ILE* 1.3 77.1 - - - +
361A PHE* 1.3 60.9 + - - +
364A CYS* 3.4 5.7 + - - +
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.5 11.0 - - + -
201A TYR* 3.4 55.2 - + + -
204A ALA* 3.7 11.4 - - + -
205A ALA* 3.6 20.8 - - + +
208A MET* 3.4 28.3 - - + -
357A ALA* 3.1 27.1 + - + +
358A ILE 4.0 0.2 - - - +
360A SER* 1.3 74.4 - - - +
362A ALA* 1.3 65.3 + - - +
364A CYS* 3.2 21.7 + - - +
405A ASN* 3.7 10.6 - - - +
408A SER* 4.1 14.9 - - - -
409A ALA* 3.7 21.1 - - - +
412A ALA* 3.5 20.4 - - + -
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 4.9 2.0 - - + -
324A ILE* 4.2 29.7 - - + +
327A LYS* 3.3 21.3 + - - +
358A ILE 3.0 19.1 + - - +
359A ILE* 3.3 6.3 + - - +
361A PHE* 1.3 77.9 - - - +
363A LEU* 1.3 59.4 - - + +
405A ASN* 3.6 20.5 - - - +
406A LEU* 4.3 9.5 - - + +
409A ALA* 3.8 10.5 - - + +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A LEU* 4.0 22.7 - - + +
324A ILE* 4.1 13.9 - - + +
327A LYS* 3.6 12.0 - - + -
332A GLU* 3.5 20.4 - - - +
335A ALA* 3.7 43.3 - - + +
336A TYR* 3.3 30.8 - - + -
339A PHE* 4.0 5.6 - - + -
359A ILE* 2.9 43.1 + - + +
362A ALA* 1.3 80.1 - - + +
364A CYS* 1.3 59.2 + - - +
365A GLY 2.9 9.3 + - - -
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Residues in contact with CYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ALA 4.1 4.0 - - - +
183A SER* 5.3 0.2 - - - -
184A VAL* 3.8 26.6 - - - +
192A TYR* 5.6 1.6 - - - -
202A LEU* 3.7 31.9 - - + -
205A ALA* 3.6 30.2 - - + +
206A SER* 4.6 0.9 - - - -
336A TYR* 3.0 14.7 + - - +
360A SER 3.5 9.4 - - - +
361A PHE 3.2 11.8 + - - +
362A ALA 3.3 0.2 - - - -
363A LEU* 1.3 73.0 - - - +
365A GLY* 1.3 57.2 + - - +
405A ASN* 3.0 19.1 - - - +
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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