Contacts of the helix formed by residues 322 - 337 (chain D) in PDB entry 5YL4
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 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C GLU* 5.2 4.0 + - - -
286D VAL* 4.9 0.9 - - - +
321D MET* 1.3 72.3 - - - +
323D MET* 1.3 62.7 + - - +
324D LYS* 3.7 10.7 + - - +
325D GLU* 3.5 34.9 + - - +
326D VAL* 3.2 24.2 + - - +
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Residues in contact with MET 323 (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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221C ARG* 3.7 46.9 - - + +
223C THR* 5.7 8.7 - - + -
321D MET* 3.4 6.5 + - - +
322D SER* 1.3 69.0 + - - +
324D LYS* 1.3 60.4 + - - +
326D VAL* 3.2 7.9 + - + +
327D ASP* 2.9 36.0 + - - +
353D VAL* 4.0 37.0 - - + -
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Residues in contact with LYS 324 (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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214C ARG* 6.6 0.4 - - - +
220C GLU* 3.8 47.1 - - + +
221C ARG* 4.1 15.3 - - + +
322D SER* 3.7 10.3 + - - +
323D MET* 1.3 76.4 - - - +
325D GLU* 1.3 56.4 + - - +
327D ASP* 3.2 5.2 + - - +
328D GLU* 2.9 62.0 + - + +
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Residues in contact with GLU 325 (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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285D THR* 5.8 0.3 - - - -
286D VAL* 3.9 29.6 - - + +
287D PRO* 3.9 17.1 - - + +
322D SER* 3.3 26.5 + - - +
324D LYS* 1.3 78.3 - - - +
326D VAL* 1.3 57.2 + - - +
328D GLU* 3.5 14.0 + - + +
329D GLN* 2.9 42.3 + - + +
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Residues in contact with VAL 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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286D VAL* 3.7 22.7 - - + -
317D PHE* 3.8 21.3 - - + -
321D MET* 3.9 22.4 - - + -
322D SER 3.2 14.5 + - - +
323D MET* 3.2 12.5 + - - +
325D GLU* 1.3 76.2 - - - +
327D ASP* 1.3 60.3 + - - +
329D GLN* 3.4 1.4 + - - +
330D MET* 2.9 29.5 + - - +
351D THR* 3.7 29.6 - - + -
353D VAL* 4.3 11.0 - - + -
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Residues in contact with ASP 327 (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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176C GLN* 5.2 2.7 - - - +
210C TYR* 3.9 5.4 + - - -
221C ARG* 2.9 43.1 + - - +
323D MET* 2.9 26.5 + - - +
324D LYS* 3.2 5.6 + - - +
326D VAL* 1.3 78.6 - - - +
328D GLU* 1.3 66.1 + - + +
330D MET* 4.2 4.0 - - - +
331D LEU* 3.2 34.7 + - + +
351D THR* 5.5 4.5 - - - +
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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
----------------------------------------------------------
324D LYS* 2.9 52.0 + - + +
325D GLU* 3.7 15.9 - - + +
327D ASP* 1.3 77.2 - - + +
329D GLN* 1.3 63.5 + - - +
331D LEU* 3.5 9.8 + - + +
332D ASN* 3.0 27.1 + - - +
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Residues in contact with GLN 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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286D VAL* 4.4 3.8 - - + -
287D PRO* 3.6 50.9 - - + +
290D THR* 3.8 24.0 - - - +
291D GLN* 5.5 4.0 + - - +
325D GLU* 2.9 25.3 + - + +
326D VAL 4.0 2.2 - - - +
328D GLU* 1.3 81.4 - - - +
330D MET* 1.3 63.4 + - - +
332D ASN* 3.3 26.7 + - - +
333D VAL* 3.1 25.6 + - - +
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Residues in contact with MET 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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290D THR* 3.7 20.9 - - - +
293D MET* 4.8 0.2 - - - +
294D PHE* 3.6 25.1 - - + -
315D ALA* 4.3 8.1 - - + -
317D PHE* 3.8 25.8 - - + -
326D VAL* 2.9 23.2 + - + +
327D ASP* 4.3 4.5 - - - +
329D GLN* 1.3 75.3 - - - +
331D LEU* 1.3 61.3 + - + +
333D VAL* 3.3 16.3 - - + +
334D GLN* 3.1 23.8 + - - +
349D VAL* 3.5 31.6 - - + -
351D THR* 3.5 21.3 - - + +
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Residues in contact with LEU 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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176C GLN* 6.5 0.9 - - + -
327D ASP* 3.2 28.7 + - + +
328D GLU* 3.6 8.5 - - + +
330D MET* 1.3 75.1 - - + +
332D ASN* 1.3 61.5 + - - +
334D GLN* 3.3 16.6 + - + +
335D ASN* 2.8 41.9 + - - +
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Residues in contact with ASN 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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291D GLN* 5.6 2.9 + - - +
328D GLU 3.0 15.0 + - - +
329D GLN* 3.3 31.8 - - - +
331D LEU* 1.3 74.9 - - - +
333D VAL* 1.3 62.8 + - - +
335D ASN* 3.3 9.4 + - - +
336D LYS* 2.8 77.7 + - - +
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Residues in contact with VAL 333 (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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290D THR* 4.0 24.7 - - + +
291D GLN* 4.7 16.2 - - + -
294D PHE* 3.9 38.6 - - + -
329D GLN* 3.1 10.8 + - - +
330D MET* 3.3 21.5 - - + +
332D ASN* 1.3 82.7 - - - +
334D GLN* 1.3 59.8 + - + +
336D LYS* 4.6 2.9 - - + -
337D ASN* 2.9 49.8 + - + +
341D PHE* 4.2 1.9 - - - -
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Residues in contact with GLN 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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330D MET* 3.1 31.9 + - - +
331D LEU* 3.3 17.8 + - + +
333D VAL* 1.3 80.4 - - + +
335D ASN* 1.3 60.5 + - - +
337D ASN 3.6 0.2 - - - -
338D SER* 3.2 27.4 + - - -
341D PHE* 4.1 18.5 - - + -
347D ASN* 5.3 3.8 - - - -
348D ASN* 4.6 4.7 + - - +
349D VAL* 3.5 50.9 + - + +
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Residues in contact with ASN 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 LEU* 2.8 36.6 + - - +
332D ASN* 3.5 8.8 - - - +
334D GLN* 1.3 79.2 - - - +
336D LYS* 1.3 64.0 + - + +
337D ASN 3.4 0.5 + - - -
338D SER* 3.6 14.7 + - - -
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Residues in contact with LYS 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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291D GLN* 5.1 10.5 - - - +
332D ASN* 2.8 55.9 + - - +
333D VAL* 5.1 1.6 - - + -
335D ASN* 1.3 77.5 - - + +
337D ASN* 1.3 72.3 + - - +
338D SER 3.6 1.5 + - - -
340D TYR* 5.8 0.7 - - - -
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Residues in contact with ASN 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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294D PHE* 6.2 4.5 - - + +
306D ARG* 3.2 30.4 + - - +
333D VAL* 2.9 40.0 + - + +
334D GLN 3.6 3.6 - - - -
336D LYS* 1.3 90.0 - - - +
338D SER* 1.3 64.8 + - - +
339D SER 3.3 2.7 - - - -
340D TYR* 3.0 36.3 + - + +
341D PHE* 3.2 19.9 - - + -
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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