Contacts of the helix formed by residues 267 - 280 (chain K) in PDB entry 5LS6
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 267 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264K ARG* 4.2 14.9 + - - -
265K ILE* 3.1 1.8 - - - +
266K ASN* 1.3 85.4 + - - +
268K LYS* 1.3 65.6 + - - +
269K ARG* 3.7 7.7 + - - +
270K MET* 3.4 25.1 + - - +
271K MET* 2.9 23.7 + - - +
298K ASP* 5.9 1.3 - - - -
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Residues in contact with LYS 268 (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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266K ASN 3.8 1.2 + - - -
267K SER* 1.3 72.0 - - - +
269K ARG* 1.3 59.0 + - - +
271K MET* 3.6 5.8 + - - +
272K ASN* 2.8 40.2 + - - +
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Residues in contact with ARG 269 (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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267K SER* 3.1 8.6 - - - +
268K LYS* 1.3 80.5 - - - +
270K MET* 1.3 61.6 + - + +
272K ASN* 3.6 6.8 - - - +
273K ALA* 3.1 24.1 + - - +
292K GLN* 2.6 43.6 + - + +
293K LYS 3.5 23.2 + - - +
294K ILE* 3.8 30.4 - - - +
590L GLU* 4.3 10.9 + - - +
594L GLU* 5.9 3.4 + - - +
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Residues in contact with MET 270 (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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217K LEU* 3.9 23.6 - - + -
226K VAL* 4.1 9.9 - - + -
227K ALA* 3.5 34.8 - - + -
229K PHE* 3.9 13.2 - - + -
264K ARG 4.1 14.1 - - - +
265K ILE* 3.6 24.7 - - + +
267K SER* 3.2 14.5 + - - +
269K ARG* 1.3 79.3 - - + +
271K MET* 1.3 57.6 + - - +
272K ASN 3.2 1.8 - - - -
273K ALA* 2.9 2.4 + - - +
274K ILE* 2.7 40.5 + - + +
292K GLN* 4.4 6.3 - - - -
294K ILE* 3.9 23.8 - - + -
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Residues in contact with MET 271 (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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265K ILE 3.7 8.5 + - - +
266K ASN* 3.1 39.9 - - + +
267K SER 2.9 15.8 + - - +
268K LYS* 4.0 5.2 - - - +
270K MET* 1.3 70.1 - - - +
272K ASN* 1.3 61.5 + - - +
274K ILE* 4.1 10.3 - - + +
275K LYS* 3.2 22.0 + - - +
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Residues in contact with ASN 272 (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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268K LYS* 2.8 32.7 + - - +
269K ARG* 3.6 8.5 - - - +
271K MET* 1.3 75.7 - - - +
273K ALA* 1.3 53.3 + - - +
275K LYS* 2.8 16.7 + - - +
276K GLU* 2.7 48.1 + - - +
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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
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226K VAL* 3.8 17.5 - - + +
269K ARG 3.1 12.4 + - - +
270K MET* 2.9 13.6 + - - +
272K ASN* 1.3 75.7 - - - +
274K ILE* 1.3 66.6 + - - +
276K GLU* 3.6 4.8 + - - +
277K SER* 3.0 23.2 + - - -
289K PHE* 3.6 9.8 - - + -
292K GLN* 3.6 28.3 - - + +
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Residues in contact with ILE 274 (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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199K HIS* 5.7 1.8 - - - +
202K ASP* 4.5 1.1 - - - +
205K LEU* 3.7 38.6 - - + -
217K LEU* 4.1 16.8 - - + -
226K VAL* 3.7 21.1 - - + -
265K ILE* 4.4 20.6 - - + +
270K MET* 2.7 30.9 + - + +
271K MET* 4.1 9.2 - - + +
273K ALA* 1.3 72.9 - - - +
275K LYS* 1.3 63.4 - - - +
277K SER* 2.5 23.7 + - - -
278K TYR* 3.4 17.9 + - + -
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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
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271K MET 3.2 13.3 + - - +
272K ASN* 2.8 19.9 + - - +
274K ILE* 1.3 78.6 - - - +
276K GLU* 1.3 76.5 + - - +
278K TYR* 3.0 24.3 + - + +
279K ASP* 3.0 38.8 + - - +
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Residues in contact with GLU 276 (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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272K ASN* 2.7 30.8 + - - +
273K ALA* 4.2 4.7 - - - +
275K LYS* 1.3 90.3 + - - +
277K SER* 1.3 56.7 + - - +
279K ASP* 3.2 11.0 + - + +
280K TYR* 3.0 23.9 + - - +
287K ARG* 5.6 4.3 + - - -
289K PHE* 3.5 15.7 - - + -
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Residues in contact with SER 277 (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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219K ASN* 2.8 24.9 + - - +
222K THR* 3.0 21.8 + - - +
224K THR* 3.4 18.7 + - - -
226K VAL* 3.7 13.0 - - - +
273K ALA 3.0 15.3 + - - -
274K ILE* 2.5 21.8 + - - +
276K GLU* 1.3 73.6 - - - +
278K TYR* 1.3 63.1 + - - +
280K TYR* 3.5 8.7 + - - +
289K PHE* 3.4 19.2 - - - -
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Residues in contact with TYR 278 (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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202K ASP* 2.5 42.4 + - - -
204K ASN* 3.4 17.3 + - - +
205K LEU* 4.2 2.7 - - + +
219K ASN* 3.1 32.9 + - - +
221K GLN* 3.7 29.4 - - + -
222K THR* 3.4 15.4 - - + +
274K ILE* 3.8 26.0 - - + -
275K LYS* 3.0 14.3 + - + +
277K SER* 1.3 82.1 + - - +
279K ASP* 1.3 67.2 + - - +
280K TYR 3.3 3.5 + - - +
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Residues in contact with ASP 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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275K LYS* 3.0 39.3 + - - +
276K GLU* 3.2 13.6 + - + +
278K TYR* 1.3 79.9 - - - +
280K TYR* 1.3 62.7 + - - +
281K ASN* 3.4 3.8 + - - +
284K LYS* 6.1 0.2 - - - +
287K ARG* 5.6 1.4 + - - -
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Residues in contact with TYR 280 (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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222K THR* 3.9 15.0 - - - +
223K ASP 5.6 1.3 - - - -
224K THR* 3.6 19.7 - - + -
276K GLU 3.0 7.1 + - - +
277K SER 3.7 11.4 - - - +
278K TYR 3.2 8.9 - - - +
279K ASP* 1.3 75.7 - - - +
281K ASN* 1.3 64.5 + - - +
282K PRO* 3.6 31.9 - - + +
285K THR* 3.9 16.4 - - + -
287K ARG* 3.3 36.6 + - - +
288K PRO* 3.5 10.9 - - - +
289K PHE* 3.3 53.8 + + + -
575L ARG* 3.5 14.0 + - - -
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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
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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