Contacts of the helix formed by residues 340 - 357 (chain A) in PDB entry 2YD0
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A PHE* 4.5 1.9 - - - -
339A SER* 1.3 77.5 - - - +
341A ALA* 1.3 65.5 + - - +
342A SER* 3.6 8.5 + - - -
343A SER* 3.0 25.1 + - - -
344A LYS* 3.2 21.3 + - - +
725A ARG* 4.6 1.6 - - - +
765A VAL* 3.5 18.6 - - - -
766A ASP* 5.6 0.7 - - - -
796A THR* 3.5 18.8 + - - +
800A GLN* 5.0 2.7 - - - -
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Residues in contact with ALA 341 (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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340A SER* 1.3 74.3 - - - +
342A SER* 1.3 62.8 + - - +
344A LYS* 3.2 9.5 + - - +
345A LEU* 3.0 22.7 + - - +
722A VAL* 4.1 29.7 - - + +
725A ARG* 3.9 51.8 - - + +
726A MET* 4.5 3.1 - - + -
766A ASP* 5.0 1.4 + - - +
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Residues in contact with SER 342 (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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340A SER* 3.3 8.0 + - - -
341A ALA* 1.3 77.2 - - - +
343A SER* 1.3 58.2 + - - +
345A LEU* 3.4 5.6 + - - +
346A GLY* 2.8 25.3 + - - -
726A MET* 3.8 30.8 - - - +
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Residues in contact with SER 343 (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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330A SER 4.9 8.5 + - - +
333A LEU 4.9 1.7 + - - -
334A PHE* 4.7 0.2 - - - -
339A SER* 3.9 13.0 + - - -
340A SER* 3.0 22.5 + - - -
341A ALA 3.3 0.2 - - - -
342A SER* 1.3 80.0 + - - +
344A LYS* 1.3 57.4 + - - +
346A GLY* 3.2 2.4 + - - +
347A ILE* 2.9 42.2 + - - +
796A THR* 3.6 17.8 + - - -
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Residues in contact with LYS 344 (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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281A TYR* 3.4 45.2 + - + +
334A PHE* 4.0 32.8 - - + -
340A SER 3.2 12.7 + - - +
341A ALA* 3.2 11.0 + - - +
343A SER* 1.3 73.7 + - - +
345A LEU* 1.3 66.9 + - - +
347A ILE* 3.5 6.2 + - - +
348A THR* 3.0 27.6 + - - -
393A GLU* 4.3 16.0 + - - +
394A LEU* 4.1 21.9 - - + +
722A VAL* 5.4 8.1 - - + +
725A ARG* 6.3 0.7 - - - +
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Residues in contact with LEU 345 (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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341A ALA 3.0 13.6 + - - +
342A SER* 3.6 9.0 - - - +
344A LYS* 1.3 78.8 - - - +
346A GLY* 1.3 63.5 + - - +
348A THR* 3.3 2.1 + - - -
349A MET* 3.1 40.4 + - + +
394A LEU* 4.2 20.3 - - + +
396A VAL* 4.0 21.5 - - + -
399A TYR* 3.6 30.5 - - + -
722A VAL* 4.5 10.1 - - + -
726A MET* 4.0 18.2 - - + -
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Residues in contact with GLY 346 (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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331A ALA* 5.0 2.7 - - - -
342A SER 2.8 15.0 + - - -
343A SER* 3.6 4.0 - - - -
344A LYS 3.2 0.2 - - - -
345A LEU* 1.3 75.3 - - - +
347A ILE* 1.3 61.0 + - - +
349A MET* 4.0 5.4 - - - +
350A THR* 2.7 35.2 + - - -
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Residues in contact with ILE 347 (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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281A TYR* 4.0 19.7 - - + -
282A ALA* 4.1 12.8 - - + -
285A ALA* 5.6 0.4 - - + -
330A SER 4.3 4.5 + - - +
331A ALA* 3.4 31.6 - - - +
332A LEU 3.6 18.6 - - - +
333A LEU 3.6 27.1 - - - +
334A PHE* 3.9 17.7 - - + -
343A SER* 2.9 31.2 + - - +
344A LYS* 3.9 5.4 - - - +
345A LEU 3.4 0.2 - - - -
346A GLY* 1.3 71.8 - - - +
348A THR* 1.3 65.5 + - - +
350A THR* 3.4 0.7 + - - -
351A VAL* 3.0 34.6 + - + +
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Residues in contact with THR 348 (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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281A TYR* 2.6 29.2 + - - -
285A ALA* 5.0 3.6 - - + -
289A LEU* 3.9 5.4 - - + +
344A LYS 3.0 10.2 + - - -
345A LEU 3.3 7.2 + - - -
347A ILE* 1.3 79.3 - - - +
349A MET* 1.3 57.9 + - - +
351A VAL* 3.8 4.0 - - - +
352A ALA* 2.9 29.5 + - - +
387A VAL* 3.7 30.1 - - + -
391A HIS* 3.7 29.2 - - + +
394A LEU* 3.8 8.9 - - + +
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Residues in contact with MET 349 (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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345A LEU* 3.1 29.0 + - + +
346A GLY* 4.0 5.4 - - - +
348A THR* 1.3 73.0 - - - +
350A THR* 1.3 55.3 + - - +
352A ALA* 3.3 3.6 - - - +
353A HIS* 2.8 29.1 + - - +
383A GLU* 3.2 41.5 - - + +
384A PHE* 3.6 43.1 - - + -
387A VAL* 3.7 24.2 - - - -
396A VAL* 3.8 23.6 - - + -
399A TYR* 6.1 1.3 - - + -
1950A BES 5.7 1.6 - - + -
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Residues in contact with THR 350 (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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317A GLY* 4.7 1.6 - - - +
318A ALA* 3.6 29.8 - - + -
327A TYR* 3.9 10.8 - - + -
331A ALA* 4.2 21.4 - - + +
346A GLY 2.7 24.2 + - - -
347A ILE 3.9 2.2 - - - -
349A MET* 1.3 75.7 - - - +
351A VAL* 1.3 58.8 + - - +
353A HIS* 3.0 7.1 + - - +
354A GLU* 2.9 30.1 + - + +
1950A BES 4.3 22.7 - - + +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA* 4.7 6.5 - - + +
285A ALA* 4.6 2.2 - - + -
286A ALA* 3.9 17.7 - - - +
289A LEU* 4.1 7.0 - - + -
308A LEU* 4.1 13.7 - - + -
327A TYR* 4.3 9.0 - - + -
331A ALA 5.0 0.7 - - - +
332A LEU* 4.1 25.8 - - + -
347A ILE* 3.0 31.8 + - + +
348A THR* 3.8 4.5 - - - +
350A THR* 1.3 71.6 - - - +
352A ALA* 1.3 67.0 + - - +
354A GLU* 3.3 1.2 + - - +
355A LEU* 2.9 49.0 + - + +
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Residues in contact with ALA 352 (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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289A LEU* 3.7 13.6 - - + +
293A TYR* 2.8 22.9 + - - -
348A THR 2.9 18.1 + - - +
349A MET 3.3 6.3 - - - +
351A VAL* 1.3 76.1 - - - +
353A HIS* 1.3 57.9 + - - +
356A ALA* 2.9 17.8 + - - +
383A GLU* 4.0 8.7 - - - -
386A SER* 3.7 12.1 - - - +
387A VAL* 3.5 26.2 - - + -
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Residues in contact with HIS 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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349A MET 2.8 20.2 + - - +
350A THR* 3.0 10.0 + - - +
352A ALA* 1.3 75.9 - - - +
354A GLU* 1.3 78.3 + - - +
356A ALA* 3.2 5.5 + - - +
357A HIS* 3.1 22.0 + + - -
376A GLU* 3.8 4.5 - - - -
379A ALA* 3.6 17.4 + - + +
380A LYS* 3.7 16.9 - - + -
383A GLU* 2.8 29.1 + - - +
438A TYR* 3.9 4.3 - + - -
1946A ZN 2.1 36.6 - - - -
1950A BES 3.0 27.1 + - + +
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Residues in contact with GLU 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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318A ALA* 3.6 10.5 - - + +
319A MET* 3.6 12.5 - - - +
320A GLU* 2.9 31.4 + - - +
325A THR* 4.4 7.9 - - + -
327A TYR* 3.6 35.0 - - + +
350A THR 2.9 17.5 + - - +
351A VAL 4.0 0.7 - - - +
353A HIS* 1.3 86.4 - - - +
355A LEU* 1.3 61.8 + - - +
357A HIS* 3.2 12.5 + - - +
358A GLN* 2.9 23.7 + - - -
1950A BES 3.1 35.1 + - - +
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Residues in contact with LEU 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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286A ALA* 3.5 30.1 - - + +
289A LEU* 3.9 6.5 - - + -
290A LEU* 3.9 34.1 - - + +
293A TYR* 3.9 16.4 - - + -
306A GLN* 4.0 27.4 - - + +
308A LEU* 5.2 4.0 - - + -
325A THR* 4.8 6.1 - - + +
327A TYR* 5.0 4.7 - - - +
351A VAL* 2.9 38.7 + - + +
354A GLU* 1.3 73.9 - - - +
356A ALA* 1.3 66.4 + - - +
357A HIS 3.1 0.2 - - - -
358A GLN* 3.0 14.1 + - + +
359A TRP* 3.2 19.6 - - - -
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Residues in contact with ALA 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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293A TYR* 3.4 23.7 - - + +
297A PHE* 4.8 1.7 - - + -
352A ALA 2.9 20.2 + - - +
353A HIS 3.3 6.3 - - - +
355A LEU* 1.3 77.4 - - - +
357A HIS* 1.3 62.4 + - - +
358A GLN 3.0 1.7 + - - -
359A TRP* 3.1 15.7 + - - +
360A PHE* 3.1 14.6 + - + +
379A ALA* 4.1 13.9 - - - +
382A MET* 3.8 21.3 - - + -
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Residues in contact with HIS 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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320A GLU* 3.3 42.2 + - + -
353A HIS* 3.1 26.6 + + - -
354A GLU* 3.4 2.9 - - - +
355A LEU 3.1 0.6 - - - -
356A ALA* 1.3 75.3 - - - +
358A GLN* 1.3 63.8 + - - +
359A TRP 3.0 1.3 + - - -
360A PHE* 2.8 26.3 + - - -
361A GLY* 4.5 1.0 - - - -
362A ASN* 3.0 22.5 + - - +
375A ASN* 3.3 28.3 + - + +
376A GLU* 3.3 13.0 - - - -
379A ALA* 3.3 4.8 - - + +
1946A ZN 2.1 31.3 - - - -
1950A BES 2.4 16.0 + - - -
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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