Contacts of the helix formed by residues 325 - 342 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D CYS* 1.3 74.5 - - - +
326D ASN* 1.4 59.4 + - - +
327D GLU* 3.2 7.6 - - + +
328D GLU* 2.9 40.8 + - + +
329D VAL* 2.9 12.2 + - - +
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Residues in contact with ASN 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D LYS* 4.3 12.8 - - + +
234D LEU* 3.4 42.1 - - + +
284D LEU 5.3 5.0 - - - +
324D CYS 4.0 0.4 + - - -
325D LYS* 1.4 71.1 - - - +
327D GLU* 1.4 59.7 + - - +
329D VAL* 3.5 11.6 + - - +
330D LEU* 3.2 24.6 + - - +
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Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D LYS* 3.1 6.5 + - + +
326D ASN* 1.4 77.0 - - - +
328D GLU* 1.3 60.8 + - + +
330D LEU* 3.8 6.1 + - - +
331D ALA 3.5 14.7 + - - -
427D LYS* 4.1 3.2 - - - +
430D ASP* 3.4 33.4 - - - +
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Residues in contact with GLU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D CYS* 4.0 12.7 - - + -
325D LYS* 2.9 33.8 + - + +
327D GLU* 1.3 76.1 - - + +
329D VAL* 1.4 58.5 + - - +
331D ALA* 3.3 4.1 + - - +
332D VAL* 3.1 32.6 + - - +
430D ASP* 3.5 24.9 - - + +
433D SER* 3.1 38.7 + - - +
434D ALA* 3.4 13.5 + - + +
437D LYS* 3.8 12.4 - - - +
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Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D LEU* 5.9 7.0 - - + -
279D LEU* 5.7 6.7 - - + -
283D LEU* 3.8 30.7 - - + +
284D LEU* 4.5 10.3 - - + -
324D CYS* 3.6 17.9 - - + +
325D LYS 2.9 18.9 + - - +
326D ASN* 3.7 15.0 - - - +
328D GLU* 1.4 75.3 - - - +
330D LEU* 1.4 57.2 + - - +
332D VAL* 3.1 10.5 + - - +
333D LEU* 2.9 42.4 + - + +
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D GLU* 5.8 9.9 - - + +
238D ILE* 6.3 1.3 - - - -
241D MET* 3.5 29.0 - - + +
326D ASN 3.2 17.6 + - - +
327D GLU* 3.9 7.6 - - - +
328D GLU 3.4 0.2 - - - -
329D VAL* 1.4 75.8 - - - +
331D ALA* 1.4 57.0 + - - +
333D LEU* 3.3 17.2 + - + +
334D GLY* 2.9 22.7 + - - -
427D LYS* 3.9 7.2 - - + -
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLU 3.5 2.0 + - - +
328D GLU 3.3 10.0 + - - +
329D VAL 3.3 0.4 - - - -
330D LEU* 1.4 75.0 - - - +
332D VAL* 1.4 62.7 + - - +
334D GLY* 3.3 2.8 + - - -
335D HIS 3.2 16.5 + - - -
422D ALA* 4.2 5.0 - - - +
427D LYS* 3.6 24.6 - - + +
430D ASP* 3.6 13.9 - - + -
431D LEU* 3.4 42.6 - - - +
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Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D ALA* 4.2 24.7 - - + -
283D LEU* 4.4 17.3 - - + -
324D CYS* 5.4 1.6 - - - -
328D GLU 3.1 18.2 + - - +
329D VAL* 3.1 11.6 + - - +
331D ALA* 1.4 73.7 - - - +
333D LEU* 1.4 64.5 + - + +
335D HIS* 3.4 9.1 + - + +
336D ALA* 3.2 20.1 + - - +
431D LEU* 4.0 10.3 - - + -
434D ALA* 3.8 20.6 - - + -
435D LEU* 5.6 0.9 - - + -
438D LEU* 4.0 18.8 - - + -
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Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 4.5 23.1 - - + -
241D MET* 4.6 4.3 - - - -
266D ALA* 5.9 6.5 - - + -
277D ILE* 4.6 20.6 - - + -
278D VAL 6.0 1.3 - - - +
279D LEU* 5.4 11.4 - - + -
329D VAL* 2.9 31.9 + - + +
330D LEU* 3.4 17.7 - - + +
332D VAL* 1.4 74.4 - - + +
334D GLY* 1.3 53.7 + - - +
336D ALA* 3.1 9.7 + - + +
337D LEU* 2.7 51.6 + - + +
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D MET* 4.6 2.7 - - - -
330D LEU 2.9 14.9 + - - -
331D ALA* 3.3 6.4 + - - -
333D LEU* 1.3 73.9 - - - +
335D HIS* 1.3 59.9 + - - +
337D LEU* 3.8 9.7 + - - +
338D GLY 3.3 13.2 + - - -
421D PHE* 3.5 18.9 - - - -
422D ALA* 4.3 6.0 - - - -
425D LEU* 3.7 22.5 - - - +
427D LYS* 6.3 1.3 - - - -
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Residues in contact with HIS 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ALA 3.2 10.9 + - - +
332D VAL* 3.4 13.5 - - + +
333D LEU 3.2 0.6 - - - -
334D GLY* 1.3 73.1 - - - +
336D ALA* 1.4 63.9 + - + +
338D GLY* 3.0 16.1 + - - -
339D HIS* 3.6 8.2 + + - -
415D GLU* 3.0 49.2 + - - -
418D ALA* 3.3 45.6 - - + +
419D ASP* 2.8 27.0 + - - -
422D ALA* 4.1 3.8 - - + +
431D LEU* 4.2 12.8 - - + -
465D ARG* 3.6 8.5 + - - -
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Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D ALA* 5.7 7.6 - - + +
267D TYR* 5.4 10.3 - - - +
268D PHE* 5.2 19.5 - - + +
332D VAL 3.2 9.0 + - - +
333D LEU* 3.1 14.7 + - + +
335D HIS* 1.4 77.2 - - + +
337D LEU* 1.4 61.8 + - + +
338D GLY 3.1 5.4 + - - -
339D HIS* 3.3 28.3 + - - +
340D TRP* 3.9 4.3 + - - +
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Residues in contact with LEU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D MET* 4.2 27.1 - - + +
242D ALA* 5.6 3.4 - - + +
245D ILE* 5.2 11.0 - - + -
247D PHE* 4.0 27.4 - - + -
333D LEU* 2.7 37.8 + - + +
334D GLY* 4.0 11.9 - - - +
335D HIS 3.3 0.2 - - - -
336D ALA* 1.4 70.5 - - + +
338D GLY* 1.3 57.3 + - - +
340D TRP* 3.3 18.2 + - + +
341D LYS* 3.1 27.7 + - - +
421D PHE* 4.4 8.3 - - + -
425D LEU* 5.7 1.6 - - + -
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Residues in contact with GLY 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D GLY 3.3 4.9 + - - -
335D HIS 3.0 12.2 + - - -
337D LEU* 1.3 75.3 - - - +
339D HIS* 1.4 54.9 + - - +
341D LYS* 4.5 0.4 - - - -
342D LEU* 2.8 46.1 + - - +
344D HIS* 4.5 0.2 - - - -
418D ALA* 4.6 2.2 - - - -
421D PHE* 3.5 31.2 - - - -
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Residues in contact with HIS 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D HIS* 3.6 18.3 + + - -
336D ALA* 3.3 18.9 + - + +
338D GLY* 1.4 75.7 - - - +
340D TRP* 1.3 59.3 + - - +
343D GLY* 3.4 0.9 + - - -
344D HIS* 2.8 59.7 + - + +
345D THR* 3.4 15.9 + - - +
414D PHE* 3.4 26.2 - - + +
415D GLU* 2.8 29.1 + - + -
418D ALA* 3.6 11.3 - - + +
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Residues in contact with TRP 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ILE* 3.5 23.3 - - + -
246D ASP* 3.6 19.7 - - + -
247D PHE* 3.8 15.5 - - + -
248D PRO* 3.7 26.7 - - + +
275D LYS* 5.8 5.9 - - + +
336D ALA 3.9 2.6 + - - +
337D LEU* 3.3 23.6 + - + +
338D GLY 3.2 0.2 - - - -
339D HIS* 1.3 78.5 - - - +
341D LYS* 1.4 85.3 + - + +
343D GLY* 3.3 12.5 + - - -
345D THR* 4.2 9.8 + - - +
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Residues in contact with LYS 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ILE* 6.4 0.4 - - + -
337D LEU 3.1 16.2 + - - +
338D GLY 4.0 1.1 - - - +
340D TRP* 1.4 90.6 - - + +
342D LEU* 1.4 58.5 + - - +
343D GLY 3.2 6.2 + - - -
421D PHE* 3.7 31.4 - - + -
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Residues in contact with LEU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D GLY 2.8 26.2 + - - +
341D LYS* 1.4 71.1 - - - +
343D GLY* 1.3 61.1 + - - +
344D HIS* 3.3 32.0 + - + +
417D GLN* 3.4 41.4 - - + +
421D PHE* 4.0 24.2 - - + -
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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