Contacts of the helix formed by residues 325 - 342 (chain A) in PDB entry 2YPT
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 LYS 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A CYS* 1.4 73.0 - - - +
326A ASN* 1.3 61.0 + - - +
327A GLU* 3.2 7.9 - - + +
328A GLU* 2.9 41.1 + - + +
329A VAL* 2.9 12.0 + - - +
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Residues in contact with ASN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LYS* 4.3 13.0 - - + +
234A LEU* 3.4 39.7 - - + +
284A LEU* 5.2 9.2 - - - +
324A CYS 4.0 0.2 + - - -
325A LYS* 1.3 71.8 - - - +
327A GLU* 1.4 59.5 + - - +
329A VAL* 3.5 11.5 + - - +
330A LEU* 3.2 35.2 + - + +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 3.2 6.6 - - + +
326A ASN* 1.4 77.4 - - - +
328A GLU* 1.3 61.3 + - + +
330A LEU* 3.8 10.6 + - - +
331A ALA* 3.5 13.9 + - - +
427A LYS* 5.4 2.3 - - - +
430A ASP* 3.5 20.2 - - + +
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Residues in contact with GLU 328 (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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324A CYS* 4.0 11.6 - - + -
325A LYS* 2.9 34.6 + - + +
327A GLU* 1.3 76.1 - - + +
329A VAL* 1.4 58.8 + - - +
331A ALA* 3.3 4.5 + - - +
332A VAL* 3.1 33.0 + - - +
430A ASP* 3.5 24.0 - - + +
433A SER* 3.1 39.8 + - - +
434A ALA* 3.4 13.5 + - + +
437A LYS* 3.8 13.0 - - - +
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 5.9 3.8 - - + -
283A LEU* 3.8 29.6 - - + +
284A LEU* 4.0 28.3 - - + -
324A CYS* 3.6 18.6 - - + +
325A LYS 2.9 19.1 + - - +
326A ASN* 3.7 12.8 - - - +
327A GLU 3.4 0.2 - - - -
328A GLU* 1.4 75.9 - - - +
330A LEU* 1.3 55.5 + - + +
332A VAL* 3.1 9.7 + - - +
333A LEU* 2.9 41.9 + - + +
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Residues in contact with LEU 330 (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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234A LEU* 4.7 5.4 - - + +
237A GLU* 3.7 47.8 - - + +
238A ILE* 3.8 11.9 - - + +
241A MET* 4.7 9.6 - - + -
326A ASN* 3.2 28.3 + - + +
327A GLU* 3.9 10.1 - - - +
328A GLU 3.4 0.2 - - - -
329A VAL* 1.3 74.6 - - + +
331A ALA* 1.3 57.0 + - - +
333A LEU* 3.3 17.9 + - + +
334A GLY* 2.9 24.3 + - - -
427A LYS* 5.0 9.2 - - + +
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Residues in contact with ALA 331 (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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327A GLU 3.5 2.2 + - - -
328A GLU 3.3 10.7 + - - +
329A VAL 3.3 0.2 - - - -
330A LEU* 1.3 75.1 - - - +
332A VAL* 1.4 63.1 + - - +
334A GLY* 3.4 3.7 + - - +
335A HIS* 3.2 20.6 + - - +
422A ALA* 4.2 7.6 - - - +
427A LYS* 3.6 24.6 - - + +
430A ASP* 3.7 13.9 - - + -
431A LEU* 3.5 35.3 - - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 4.2 24.5 - - + -
283A LEU* 4.5 16.4 - - + -
324A CYS* 5.4 1.8 - - - -
328A GLU 3.1 18.5 + - - +
329A VAL* 3.4 10.5 - - - +
331A ALA* 1.4 72.8 - - - +
333A LEU* 1.4 64.7 + - + +
335A HIS* 3.4 13.4 + - + +
336A ALA* 3.2 20.1 + - + +
431A LEU* 5.8 1.1 - - + -
434A ALA* 3.8 20.2 - - + -
435A LEU* 5.6 5.6 - - + -
438A LEU* 4.1 19.1 - - + -
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Residues in contact with LEU 333 (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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238A ILE* 4.5 15.5 - - + -
241A MET* 6.5 1.3 - - + -
252A VAL* 5.7 3.6 - - + -
266A ALA* 5.9 6.5 - - + -
277A ILE* 3.6 42.0 - - + -
279A LEU* 5.5 6.7 - - + -
329A VAL* 2.9 31.2 + - + +
330A LEU* 3.4 29.4 - - + +
331A ALA 3.3 0.2 - - - -
332A VAL* 1.4 75.2 - - + +
334A GLY* 1.3 55.0 + - - +
336A ALA* 3.1 10.2 + - + +
337A LEU* 2.7 50.2 + - + +
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Residues in contact with GLY 334 (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 LEU 2.9 13.9 + - - -
331A ALA* 3.4 6.8 + - - -
333A LEU* 1.3 75.7 - - - +
335A HIS* 1.3 57.6 + - - +
337A LEU* 4.0 9.3 - - - +
338A GLY 3.3 13.5 + - - -
421A PHE* 3.4 18.5 - - - -
422A ALA* 4.3 5.7 - - - -
425A LEU* 3.7 21.4 - - - +
427A LYS* 6.3 1.3 - - - -
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Residues in contact with HIS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA 3.2 11.1 + - - +
332A VAL* 3.4 15.0 - - + +
333A LEU 3.2 0.4 - - - -
334A GLY* 1.3 73.5 - - - +
336A ALA* 1.4 63.6 + - + +
338A GLY* 3.0 21.0 + - - -
339A HIS* 3.6 7.7 + + - -
415A GLU* 3.0 41.0 + - - -
418A ALA* 3.4 48.4 - - + +
419A ASP* 2.8 28.5 + - - +
422A ALA* 4.1 6.9 - - + +
431A LEU* 6.2 1.6 - - + -
435A LEU* 6.3 1.3 - - + -
465A ARG* 3.7 9.2 + - - -
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Residues in contact with ALA 336 (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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266A ALA* 5.7 7.9 - - + +
267A TYR* 5.4 8.7 - - - +
268A PHE* 3.4 40.5 - - + -
332A VAL 3.2 8.6 + - - +
333A LEU* 3.1 14.7 + - + +
335A HIS* 1.4 78.3 - - + +
337A LEU* 1.4 60.8 + - + +
338A GLY 3.1 5.0 + - - -
339A HIS* 3.3 20.8 + - + +
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Residues in contact with LEU 337 (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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241A MET* 5.2 20.2 - - + +
242A ALA* 5.6 3.6 - - + +
245A ILE* 5.2 11.4 - - + -
247A PHE* 3.9 27.4 - - + -
268A PHE* 5.9 0.7 - - - -
277A ILE* 4.7 22.0 - - + -
333A LEU* 2.7 38.1 + - + +
334A GLY* 4.0 10.8 - - - +
336A ALA* 1.4 70.8 - - + +
338A GLY* 1.3 56.3 + - - +
339A HIS 3.4 0.2 - - - -
340A TRP* 3.3 19.2 + - + +
341A LYS* 3.1 27.5 + - - +
421A PHE* 4.4 8.5 - - + -
425A LEU* 5.7 2.7 - - + -
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Residues in contact with GLY 338 (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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334A GLY 3.3 5.1 + - - -
335A HIS 3.0 13.3 + - - -
337A LEU* 1.3 76.6 - - - +
339A HIS* 1.4 53.7 + - - +
341A LYS 4.5 0.4 - - - -
342A LEU* 2.8 45.6 + - - +
344A HIS* 4.5 0.4 - - - -
418A ALA* 4.7 2.5 - - - -
421A PHE* 3.5 31.2 - - - -
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Residues in contact with HIS 339 (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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268A PHE* 3.5 23.8 - + + -
335A HIS* 3.6 17.9 + + - -
336A ALA* 3.3 13.3 + - - +
338A GLY* 1.4 74.9 - - - +
340A TRP* 1.3 59.9 + - - +
343A GLY* 3.4 0.3 + - - -
344A HIS* 2.8 60.1 + - + +
345A THR* 3.4 8.6 + - - +
414A PHE* 3.4 26.0 - - + +
415A GLU* 2.8 29.3 + - + -
418A ALA* 3.6 11.7 - - + +
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Residues in contact with TRP 340 (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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245A ILE* 3.5 22.7 - - + -
246A ASP* 3.6 20.6 - - + -
247A PHE* 3.8 15.0 - - + -
248A PRO* 3.7 23.2 - - + +
268A PHE* 3.8 24.6 - + + -
275A LYS* 4.2 26.6 - - + +
337A LEU* 3.3 22.3 + - + +
339A HIS* 1.3 78.0 - - - +
341A LYS* 1.4 85.1 + - + +
343A GLY* 3.3 12.6 + - - -
345A THR* 4.3 4.9 - - - -
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Residues in contact with LYS 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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245A ILE* 6.3 0.7 - - + -
337A LEU 3.1 16.6 + - - +
338A GLY 4.0 1.1 - - - +
340A TRP* 1.4 89.4 - - + +
342A LEU* 1.4 59.9 + - - +
343A GLY 3.2 5.4 + - - -
421A PHE* 3.7 31.4 - - + -
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Residues in contact with LEU 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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338A GLY 2.8 26.0 + - - +
341A LYS* 1.4 72.1 - - - +
343A GLY* 1.3 61.6 + - - +
344A HIS* 3.3 34.2 + - + +
417A GLN* 3.4 33.7 - - + +
421A PHE* 4.0 23.3 - - + -
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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
------------------------------------------------------------
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