Contacts of the helix formed by residues 272 - 289 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265K PHE* 2.7 24.0 + - - +
267K GLU* 3.9 17.0 + - - -
270K ILE 3.3 1.8 + - - -
271K LEU* 1.3 71.0 - - - +
273K ALA* 1.3 63.0 - - - +
274K SER* 3.7 1.0 - - - -
275K LYS* 3.0 34.2 + - - +
276K MET* 3.1 23.0 + - - +
373K GLU* 2.8 26.3 + - - -
375K TRP* 3.9 2.1 - - - -
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Residues in contact with ALA 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271K LEU 3.3 5.3 + - - -
272K SER* 1.3 71.8 - - - +
274K SER* 1.3 56.0 + - - +
276K MET* 3.9 0.7 - - - +
277K LEU* 2.9 39.0 + - + +
361K PRO* 3.8 15.0 - - + +
362K LYS 4.4 2.0 - - - +
372K GLU 4.0 9.4 - - - +
373K GLU* 2.5 10.4 + - - +
374K THR 3.8 22.9 - - - +
375K TRP* 3.4 23.1 - - + +
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Residues in contact with SER 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K SER* 3.7 1.1 - - - -
273K ALA* 1.3 78.0 - - - +
275K LYS* 1.3 55.5 + - - +
277K LEU* 4.0 5.6 - - - +
278K SER* 2.7 39.4 + - - -
372K GLU* 3.6 17.7 + - - +
373K GLU* 2.7 27.9 + - - -
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Residues in contact with LYS 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264K GLN 3.8 12.1 + - - +
265K PHE* 3.7 35.2 - - + +
266K LEU 2.8 25.2 + - - -
267K GLU* 4.6 13.8 - - - +
272K SER* 3.0 24.1 + - - +
274K SER* 1.3 73.8 - - - +
276K MET* 1.3 67.9 + - - +
278K SER* 3.3 4.6 + - - -
279K LYS* 2.9 27.4 + - - +
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Residues in contact with MET 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K PHE* 3.7 13.9 - - + -
232K LEU* 4.0 20.9 - - + -
262K LEU* 4.9 3.1 - - + -
265K PHE* 3.6 32.5 - - + -
271K LEU* 3.9 33.0 - - + -
272K SER 3.1 12.8 + - - +
273K ALA 4.1 2.5 - - - +
275K LYS* 1.3 80.5 - - - +
277K LEU* 1.3 57.9 + - + +
279K LYS* 3.9 0.2 - - - -
280K PHE* 2.8 32.1 + - - +
322K LEU* 3.5 28.3 - - + -
324K LEU* 4.0 12.3 - - + -
361K PRO* 5.6 0.4 - - + -
375K TRP* 3.9 17.0 - - + -
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Residues in contact with LEU 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K ALA* 2.9 25.6 + - + +
274K SER* 4.0 5.4 - - - +
276K MET* 1.3 75.2 - - - +
278K SER* 1.3 63.8 + - - +
280K PHE* 3.5 4.9 - - - +
281K ARG* 3.1 28.2 + - - +
301K LYS* 4.2 21.9 - - + +
304K GLY* 3.8 29.8 - - - +
307K ALA* 3.4 34.6 - - + +
322K LEU* 5.0 4.0 - - + -
361K PRO* 3.6 35.2 - - + +
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Residues in contact with SER 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K SER* 2.7 26.4 + - - -
275K LYS* 3.7 4.9 - - - -
277K LEU* 1.3 76.3 - - - +
279K LYS* 1.3 58.8 + - - +
281K ARG* 3.3 14.9 - - - +
282K LYS* 3.1 27.2 + - - +
301K LYS* 5.6 4.2 - - - +
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Residues in contact with LYS 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K ASP* 3.7 29.3 + - - -
201K SER* 5.0 1.4 + - - -
202K ALA* 4.5 0.6 - - - +
264K GLN* 2.6 30.7 + - - -
265K PHE* 3.5 26.5 - - + -
275K LYS 2.9 16.7 + - - +
276K MET 4.0 0.2 - - - +
278K SER* 1.3 75.5 - - - +
280K PHE* 1.3 61.0 + - - +
282K LYS* 3.1 14.9 + - + +
283K ILE* 2.8 45.6 + - + +
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Residues in contact with PHE 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K LEU* 4.1 14.6 - - + -
203K PHE* 3.9 22.3 - + + -
206K VAL* 5.2 0.7 - - + -
230K PHE* 3.5 37.9 - + + -
276K MET 2.8 22.0 + - - +
277K LEU* 3.5 4.9 - - - +
279K LYS* 1.3 73.9 - - - +
281K ARG* 1.3 62.7 + - - +
283K ILE* 3.3 3.3 + - - +
284K ILE* 3.1 46.5 + - + +
307K ALA* 3.5 32.5 - - + -
308K VAL* 4.0 2.9 - - + -
320K ILE* 3.8 14.8 - - + -
322K LEU* 3.7 37.5 - - + -
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Residues in contact with ARG 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K LEU 3.1 12.8 + - - +
278K SER* 3.3 14.8 - - - +
280K PHE* 1.3 81.0 - - - +
282K LYS* 1.3 62.3 + - - +
285K LYS* 2.8 35.6 + - - +
298K MET* 3.3 26.0 + - - +
299K LYS 2.9 27.7 + - - -
300K ARG* 3.7 18.8 - - - +
301K LYS* 3.8 36.3 - - - +
307K ALA 4.3 3.2 + - - +
308K VAL* 3.5 27.9 - - + +
46V A 5.8 5.9 + - - -
47V A 5.1 9.1 + - - -
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Residues in contact with LYS 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278K SER 3.1 19.2 + - - +
279K LYS* 3.1 17.2 + - + +
281K ARG* 1.3 81.4 - - - +
283K ILE* 1.3 61.3 + - + +
285K LYS* 3.4 20.4 + - - +
286K GLU* 3.2 46.4 + - - +
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Residues in contact with ILE 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K ARG* 3.4 33.8 - - + +
197K LEU* 3.8 20.0 - - + +
200K ASP* 3.3 29.4 - - + +
203K PHE* 3.4 37.9 - - + -
279K LYS* 2.8 26.2 + - + +
280K PHE 3.7 4.3 - - - +
281K ARG 3.3 0.2 - - - -
282K LYS* 1.3 73.4 - - + +
284K ILE* 1.3 67.5 + - - +
286K GLU* 3.3 11.9 + - - +
287K GLU* 3.1 21.2 + - + +
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Residues in contact with ILE 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193K LEU* 3.6 34.5 - - + -
197K LEU* 4.7 13.2 - - + -
230K PHE* 4.5 5.4 - - + -
280K PHE* 3.1 54.3 + - + +
283K ILE* 1.3 74.1 - - + +
285K LYS* 1.3 55.6 + - - +
287K GLU* 3.0 2.4 + - - +
288K ILE* 2.7 40.7 + - + +
298K MET* 3.4 20.2 - - + -
308K VAL* 3.9 10.1 - - + -
310K LEU* 4.1 7.9 - - + -
320K ILE* 4.3 11.7 - - + -
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Residues in contact with LYS 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K ARG* 2.8 22.9 + - - +
282K LYS* 3.5 21.9 + - - +
284K ILE* 1.3 77.2 - - - +
286K GLU* 1.3 84.9 + - - +
288K ILE* 3.0 23.7 - - + +
289K ASN* 3.4 21.7 + - - +
298K MET* 3.3 23.3 - - + +
47V A 4.3 19.2 + - - +
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Residues in contact with GLU 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K ARG* 3.7 26.3 + - - +
282K LYS* 3.2 37.1 + - - +
283K ILE* 3.7 10.2 - - - +
284K ILE 3.2 0.2 - - - -
285K LYS* 1.3 97.6 + - - +
287K GLU* 1.3 62.4 + - - +
289K ASN* 3.5 17.5 + - - +
290K ASP* 3.9 11.0 + - - +
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Residues in contact with GLU 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K HIS* 2.9 67.4 + - + +
193K LEU* 3.8 15.3 - - + -
195K LEU* 5.1 2.3 - - - +
196K ARG* 3.6 40.0 + - + +
283K ILE 3.1 16.2 + - - +
284K ILE* 3.0 4.6 + - - +
286K GLU* 1.3 74.8 - - - +
288K ILE* 1.3 58.7 + - - +
289K ASN 3.1 2.2 - - - -
290K ASP* 2.8 29.9 + - - +
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Residues in contact with ILE 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193K LEU* 3.7 17.5 - - + -
284K ILE* 2.7 27.3 + - + +
285K LYS* 3.0 24.9 - - + +
287K GLU* 1.3 72.1 - - - +
289K ASN* 1.3 61.8 + - - +
290K ASP 3.0 0.2 - - - -
291K ILE* 2.8 39.3 + - + +
296K VAL* 3.6 49.8 + - + +
297K ILE* 4.1 0.4 - - - -
298K MET* 3.7 33.4 - - + +
310K LEU* 4.1 8.5 - - + -
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Residues in contact with ASN 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285K LYS* 3.4 29.8 + - - +
286K GLU* 3.5 11.7 + - - +
287K GLU 3.1 0.8 - - - -
288K ILE* 1.3 84.6 - - - +
290K ASP* 1.3 59.2 + - - +
291K ILE 3.4 3.6 + - - +
292K LYS* 2.9 21.8 + - - +
296K VAL 4.9 4.0 - - - +
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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
------------------------------------------------------------
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