Contacts of the helix formed by residues 272 - 288 (chain L) in PDB entry 6Y5D
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 272 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265L PHE* 2.8 22.4 + - - +
267L GLU* 4.1 17.2 + - - -
270L ILE 3.3 1.8 + - - -
271L LEU* 1.3 70.8 - - - +
273L ALA* 1.3 61.7 + - - +
274L SER* 3.3 2.3 + - - -
275L LYS* 2.9 34.9 + - - +
276L MET* 3.1 23.6 + - - +
373L GLU* 2.9 25.2 + - - -
375L TRP* 4.0 1.8 - - - -
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Residues in contact with ALA 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271L LEU 3.3 5.5 + - - -
272L SER* 1.3 72.5 - - - +
274L SER* 1.3 55.5 + - - +
276L MET* 3.5 0.7 + - - +
277L LEU* 2.9 40.5 + - + +
361L PRO* 3.9 18.6 - - + -
362L LYS 4.5 1.6 - - - +
372L GLU 4.1 10.1 - - - +
373L GLU* 2.6 11.8 + - - +
374L THR 3.8 22.0 - - - +
375L TRP* 3.5 18.6 - - + +
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Residues in contact with SER 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L SER* 3.6 2.9 - - - -
273L ALA* 1.3 78.9 - - - +
275L LYS* 1.3 54.5 + - - +
277L LEU* 3.9 7.0 - - - +
278L SER* 2.7 39.2 + - - -
372L GLU* 4.3 9.9 + - - +
373L GLU* 2.7 27.5 + - - -
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Residues in contact with LYS 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264L GLN 4.0 10.4 + - - +
265L PHE* 3.6 35.2 - - + +
266L LEU 2.8 25.6 + - - -
267L GLU* 4.5 14.4 - - - +
272L SER* 2.9 22.6 + - - +
274L SER* 1.3 74.3 - - - +
276L MET* 1.3 67.5 + - - +
278L SER* 3.3 6.0 + - - -
279L LYS* 2.9 25.8 + - - +
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Residues in contact with MET 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L PHE* 3.6 14.1 - - + -
232L LEU* 3.9 20.9 - - + -
262L LEU* 4.4 5.2 - - + -
265L PHE* 3.6 31.8 - - + -
271L LEU* 3.8 32.5 - - + -
272L SER 3.1 13.8 + - - +
273L ALA 4.1 2.0 - - - +
275L LYS* 1.3 79.4 - - - +
277L LEU* 1.3 58.5 + - - +
279L LYS 3.4 0.2 + - - -
280L PHE* 2.8 31.6 + - - +
322L LEU* 3.6 28.0 - - + -
324L LEU* 3.9 11.4 - - + -
361L PRO* 5.7 0.2 - - + -
375L TRP* 3.7 16.8 - - + -
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Residues in contact with LEU 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L ALA* 2.9 29.1 + - + +
274L SER* 3.9 6.3 - - - +
276L MET* 1.3 75.8 - - - +
278L SER* 1.3 63.0 + - - +
280L PHE* 3.6 5.9 - - - +
281L ARG* 3.2 27.6 + - - +
301L LYS* 4.5 11.8 + - - +
304L GLY* 4.3 20.4 - - - +
307L ALA* 3.3 39.4 - - + +
322L LEU* 5.1 3.1 - - + -
361L PRO* 3.7 35.0 - - + +
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Residues in contact with SER 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L SER* 2.7 27.3 + - - -
275L LYS* 3.6 6.3 - - - -
277L LEU* 1.3 77.7 - - - +
279L LYS* 1.3 58.4 + - - +
281L ARG* 3.2 14.9 - - - +
282L LYS* 3.0 25.8 + - - +
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Residues in contact with LYS 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200L ASP* 3.4 34.2 + - - -
201L SER* 4.5 3.6 + - - -
202L ALA* 3.7 2.8 - - + +
203L PHE* 4.1 1.3 - - + -
264L GLN* 2.7 26.1 + - - +
265L PHE* 3.7 29.4 - - + -
275L LYS 2.9 16.3 + - - +
278L SER* 1.3 75.0 - - - +
280L PHE* 1.3 61.0 + - - +
282L LYS* 3.0 18.6 + - + -
283L ILE* 2.8 39.3 + - + +
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Residues in contact with PHE 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L LEU* 3.7 33.0 - - + -
203L PHE* 3.8 23.9 - + + -
206L VAL* 5.1 1.3 - - + -
230L PHE* 3.4 30.1 - + + -
276L MET 2.8 19.4 + - - +
277L LEU* 3.6 7.6 - - - +
279L LYS* 1.3 76.0 - - - +
281L ARG* 1.3 57.4 + - - +
283L ILE* 3.4 3.1 + - - +
284L ILE* 3.0 53.4 + - + +
307L ALA* 3.8 23.1 - - + -
308L VAL* 3.8 9.0 - - + -
320L ILE* 3.8 19.3 - - + -
322L LEU* 4.0 25.1 - - + -
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Residues in contact with ARG 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J A 6.4 0.2 - - - -
47J A 5.2 7.7 + - - -
277L LEU 3.2 11.1 + - - +
278L SER* 3.2 21.1 - - - +
280L PHE* 1.3 77.9 - - - +
282L LYS* 1.3 57.1 + - - +
284L ILE* 4.1 3.1 - - - -
285L LYS* 2.5 49.6 + - - +
298L MET* 3.3 32.9 - - - +
299L LYS 4.7 7.1 + - - -
300L ARG* 6.0 0.6 - - - +
301L LYS* 4.7 25.4 - - - +
307L ALA 5.0 2.1 + - - +
308L VAL* 3.9 22.8 - - + +
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Residues in contact with LYS 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L SER 3.0 19.8 + - - +
279L LYS* 3.0 24.4 + - + +
281L ARG* 1.3 78.8 - - - +
283L ILE* 1.3 58.9 + - + +
285L LYS* 3.4 29.6 - - - +
286L GLU* 3.2 42.5 - - - +
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Residues in contact with ILE 283 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L ARG* 3.8 30.2 - - + +
197L LEU* 3.9 21.3 - - + -
200L ASP* 3.3 37.7 - - + +
203L PHE* 3.3 33.4 - - + -
279L LYS* 2.8 23.1 + - + +
280L PHE 3.9 3.6 - - - +
282L LYS* 1.3 77.1 - - + +
284L ILE* 1.3 60.8 + - - +
286L GLU* 3.5 7.5 + - - +
287L GLU* 3.0 27.0 + - + +
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Residues in contact with ILE 284 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L LEU* 4.0 24.5 - - + -
197L LEU* 4.5 14.1 - - + -
230L PHE* 5.0 0.7 - - + -
280L PHE* 3.0 63.4 + - + +
281L ARG* 3.2 2.7 + - - +
283L ILE* 1.3 74.4 - - - +
285L LYS* 1.3 59.7 + - - +
286L GLU 3.1 1.6 - - - -
287L GLU* 4.3 4.7 - - - -
288L ILE* 2.8 46.1 + - + +
298L MET* 3.6 18.8 - - + -
308L VAL* 3.8 11.9 - - + -
310L LEU* 4.2 7.4 - - + -
320L ILE* 4.9 3.4 - - + -
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Residues in contact with LYS 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J A 4.7 15.4 + - - +
281L ARG* 2.5 33.8 + - - +
282L LYS* 3.4 34.9 - - - +
284L ILE* 1.3 73.6 - - - +
286L GLU* 1.3 79.5 + - + +
288L ILE* 3.5 14.0 - - - +
289L ASN* 3.3 20.4 + - - +
298L MET* 3.5 25.0 - - + +
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Residues in contact with GLU 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L ARG* 5.5 4.9 + - - -
282L LYS* 3.2 33.0 - - - +
283L ILE* 3.5 8.4 + - - +
284L ILE 3.1 0.2 - - - -
285L LYS* 1.3 100.0 + - + +
287L GLU* 1.3 65.1 + - - +
289L ASN* 3.5 21.6 + - - +
290L ASP* 4.0 9.1 + - - +
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Residues in contact with GLU 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L HIS* 2.7 48.9 + - + +
193L LEU* 3.7 20.2 - - + -
196L ARG* 3.2 46.4 + - + +
283L ILE* 3.0 20.8 + - + +
284L ILE 3.2 0.2 + - - -
286L GLU* 1.3 73.9 - - - +
288L ILE* 1.3 59.3 + - - +
289L ASN 3.1 2.0 - - - -
290L ASP* 2.8 37.4 + - - +
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Residues in contact with ILE 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L LEU* 3.7 17.7 - - + -
284L ILE* 2.8 35.6 + - + +
285L LYS* 3.5 15.3 - - - +
287L GLU* 1.3 72.9 - - - +
289L ASN* 1.3 65.3 + - - +
290L ASP 3.0 0.2 - - - -
291L ILE* 2.9 38.0 + - + +
296L VAL* 3.7 49.9 + - + +
298L MET* 3.9 31.4 - - + +
310L LEU* 4.2 9.0 - - + -
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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
------------------------------------------------------------
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