Contacts of the helix formed by residues 315 - 330 (chain B) in PDB entry 4YC3
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 ASP 315 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309B SER* 5.5 1.7 + - - -
313B GLU* 3.0 13.3 + - + +
314B VAL* 1.3 75.4 - - - +
316B VAL* 1.3 65.0 + - - +
317B GLU* 3.4 12.6 + - - +
318B GLN* 3.3 31.8 + - + +
319B HIS* 3.1 21.9 + - - +
357B ASN* 3.4 26.4 + - - -
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B VAL* 4.4 18.4 - - + -
315B ASP* 1.3 71.8 + - - +
317B GLU* 1.3 60.5 + - - +
319B HIS* 3.2 8.6 + - + +
320B THR* 2.9 42.8 + - - +
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ASP* 3.4 11.5 + - - +
316B VAL* 1.3 78.9 - - - +
318B GLN* 1.3 52.2 + - - +
320B THR* 3.3 6.4 + - - -
321B LEU* 2.9 34.5 + - - +
355B LEU* 3.8 30.7 - - + +
357B ASN* 5.2 2.8 + - - +
409B ALA* 5.9 4.5 - - + -
411B ILE* 3.8 20.1 - - + +
414B LEU* 4.3 13.3 - - - +
416B GLN* 5.6 0.2 - - - +
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B SER* 5.4 0.9 - - - +
315B ASP* 3.3 31.4 + - + +
317B GLU* 1.3 78.7 - - - +
319B HIS* 1.3 63.0 + - - +
321B LEU* 3.4 2.1 + - - +
322B ALA* 3.1 22.2 + - - +
348B PHE* 3.2 49.1 - - + +
351B ALA* 3.4 13.1 + - - +
352B LEU* 3.4 33.9 + - + +
355B LEU* 3.7 8.0 - - - +
357B ASN* 2.9 24.0 + - + +
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Residues in contact with HIS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B LEU* 5.7 1.5 - - + +
305B LEU* 3.8 27.2 - - + +
306B ARG* 4.0 30.3 + - + +
309B SER* 2.9 33.6 + - - +
315B ASP 3.1 9.4 + - - +
316B VAL* 3.6 11.4 - - + +
318B GLN* 1.3 79.1 - - - +
320B THR* 1.3 60.5 + - - +
322B ALA* 3.3 7.0 + - - +
323B LYS* 2.9 55.9 + - - +
348B PHE* 5.7 0.2 - - - -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B VAL* 2.9 27.5 + - - +
317B GLU* 3.6 7.4 - - - -
319B HIS* 1.3 75.2 - - - +
321B LEU* 1.3 65.4 + - - +
323B LYS* 3.5 18.0 + - - +
324B TYR* 3.2 20.3 + - - +
403B TYR* 4.3 8.5 - - + -
408B HIS* 3.7 33.4 - - + +
409B ALA* 4.9 2.7 - - + -
411B ILE* 4.0 15.6 - - + +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLU 2.9 20.6 + - - +
318B GLN 3.7 4.3 - - - +
319B HIS 3.3 0.2 - - - -
320B THR* 1.3 70.0 - - - +
322B ALA* 1.3 66.6 + - - +
324B TYR* 3.2 19.0 + - + +
325B LEU* 3.0 32.6 + - + +
351B ALA* 3.8 21.3 - - + -
354B ILE* 3.9 18.6 - - + -
355B LEU* 3.7 32.8 - - + -
411B ILE* 3.8 22.2 - - + +
414B LEU* 4.4 6.7 - - + -
417B LEU* 4.2 22.2 - - + -
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LEU* 3.6 27.1 - - + -
318B GLN 3.1 10.6 + - - +
319B HIS* 3.5 9.4 - - - +
321B LEU* 1.3 79.5 - - - +
323B LYS* 1.3 56.2 + - - +
325B LEU* 3.2 3.4 + - - +
326B MET* 3.0 32.1 + - - +
347B ALA* 3.6 28.9 - - - +
348B PHE* 4.2 8.1 - - + -
351B ALA* 4.0 2.2 - - + +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLN* 6.1 3.1 - - + -
223B TYR* 4.2 1.7 + - - -
302B LEU* 4.2 19.3 - - + -
305B LEU* 3.6 18.8 - - + +
319B HIS* 2.9 40.0 + - - +
320B THR* 3.6 23.5 + - - +
322B ALA* 1.3 77.0 - - - +
324B TYR* 1.3 57.6 + - - +
326B MET* 3.5 5.7 + - - +
327B GLU* 3.0 30.1 + - - +
403B TYR* 4.0 20.0 + - - +
408B HIS* 5.6 7.9 + - - -
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Residues in contact with TYR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B THR 3.2 10.0 + - - +
321B LEU* 3.2 24.1 + - + +
323B LYS* 1.3 76.9 - - - +
325B LEU* 1.3 70.8 + - + +
327B GLU* 3.2 3.5 + - - +
328B LEU* 3.1 44.8 + - + +
386B VAL* 5.1 3.5 - - + +
389B VAL* 3.6 17.0 - - - +
390B ASN* 4.5 2.8 + - - -
399B VAL* 3.9 3.4 - - + -
400B LYS* 3.3 42.1 - - - +
403B TYR* 3.7 40.7 - + + -
411B ILE* 3.9 4.0 - - + -
412B SER* 3.4 28.0 - - - -
417B LEU* 4.3 12.1 - - + -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LEU* 3.0 32.9 + - + +
322B ALA 3.6 5.8 - - - +
324B TYR* 1.3 84.4 - - + +
326B MET* 1.3 64.4 + - - +
328B LEU* 3.3 19.8 + - + +
329B THR* 3.5 1.0 - - - +
347B ALA* 3.6 30.5 - - + +
350B LEU* 4.1 23.1 - - + -
351B ALA* 4.0 13.0 - - + +
354B ILE* 5.3 2.0 - - + -
382B LEU* 3.3 25.8 - - + +
386B VAL* 3.7 30.3 - - + -
417B LEU* 4.6 5.2 - - + -
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Residues in contact with MET 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TYR* 3.3 21.2 + - + +
301B PRO* 3.6 39.9 - - + +
302B LEU* 3.8 15.0 - - + -
305B LEU* 3.6 23.8 - - + -
322B ALA 3.0 17.3 + - - +
323B LYS* 3.7 6.5 - - - +
325B LEU* 1.3 75.0 - - - +
327B GLU* 1.3 64.2 + - - +
329B THR* 2.6 32.6 + - - -
330B MET 3.9 0.7 + - - -
343B ILE* 4.1 10.3 - - + -
344B ALA* 3.7 25.6 - - - -
347B ALA* 3.7 16.1 - - + +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B VAL* 4.4 4.7 - - - +
212B GLN* 3.9 4.5 - - - +
219B GLN* 3.0 32.9 + - - +
223B TYR* 3.3 8.3 + - - +
323B LYS 3.0 16.6 + - - +
324B TYR* 3.2 6.5 + - - +
326B MET* 1.3 78.0 - - - +
328B LEU* 1.3 61.3 + - - +
329B THR 3.2 0.7 + - - -
330B MET* 3.3 33.1 + - + +
331B LEU* 4.1 5.0 - - - +
399B VAL* 4.0 14.7 - - + +
402B LYS* 2.7 31.3 + - - +
403B TYR* 2.6 38.9 + - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B TYR* 3.1 47.9 + - + +
325B LEU* 3.5 13.5 - - + +
326B MET 3.2 0.2 + - - -
327B GLU* 1.3 75.7 - - - +
329B THR* 1.3 62.1 + - + +
330B MET 3.3 0.5 + - - -
331B LEU* 3.4 20.5 + - + +
332B ASP 4.0 2.4 + - - -
382B LEU* 5.0 2.0 - - + +
385B ASN* 4.3 30.5 - - + +
386B VAL* 4.0 27.1 - - + +
389B VAL* 4.3 22.0 - - + -
396B HIS 5.9 0.9 - - - +
399B VAL* 3.8 23.1 - - + -
400B LYS 4.8 1.8 - - - +
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Residues in contact with THR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ARG* 5.3 0.7 + - - -
223B TYR* 5.3 2.6 - - - -
325B LEU 3.5 4.5 - - - +
326B MET 2.6 18.4 + - - +
328B LEU* 1.3 75.7 - - + +
330B MET* 1.3 66.8 + - - +
331B LEU 3.2 0.4 - - - -
332B ASP* 3.1 21.4 + - - +
335B MET* 3.5 37.2 - - + +
336B VAL* 5.9 0.2 - - - +
343B ILE* 3.8 25.2 - - + +
382B LEU* 3.3 33.4 - - + -
385B ASN* 5.0 1.1 - - - +
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Residues in contact with MET 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ARG* 3.0 30.6 + - - +
205B ILE* 3.4 15.6 - - + +
209B VAL* 3.7 17.0 - - + -
219B GLN* 3.9 4.3 - - - +
222B MET* 3.5 43.1 - - + +
223B TYR* 3.9 35.0 - - + -
226B VAL* 4.1 21.0 - - + +
327B GLU* 3.5 31.2 - - + +
328B LEU 3.2 0.2 - - - -
329B THR* 1.3 78.8 + - - +
331B LEU* 1.3 58.7 + - + +
399B VAL* 4.7 1.8 - - + -
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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