Contacts of the helix formed by residues 267 - 280 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264E ARG* 4.7 13.6 + - - -
265E ILE* 3.2 1.8 - - - +
266E ASN* 1.3 84.0 + - - +
268E LYS* 1.3 65.7 + - - +
269E ARG* 3.4 9.0 + - - +
270E MET* 3.2 20.6 + - - +
271E MET* 3.1 22.0 + - - +
298E ASP* 5.7 2.7 - - - -
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Residues in contact with LYS 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684C MET 4.8 7.9 + - - -
685C GLN 4.7 19.0 + - - -
266E ASN 3.8 1.0 + - - -
267E SER* 1.3 74.4 - - - +
269E ARG* 1.3 64.9 + - - +
270E MET 3.1 1.0 + - - -
271E MET* 3.2 6.4 + - - +
272E ASN* 3.2 34.1 + - - +
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Residues in contact with ARG 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E SER* 3.3 9.0 + - - +
268E LYS* 1.3 79.2 - - - +
270E MET* 1.3 64.9 + - + +
272E ASN* 3.8 6.2 + - - +
273E ALA* 3.3 20.6 + - - +
292E GLN* 2.8 36.6 + - + +
293E LYS 3.5 16.4 + - - -
294E ILE* 4.1 22.1 - - - +
295E HIS 5.8 0.4 - - - +
590F GLU* 3.3 31.5 + - - -
594F GLU* 5.8 5.9 - - - +
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Residues in contact with MET 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E LEU* 3.8 16.6 - - + -
226E VAL* 3.5 30.5 - - + -
227E ALA* 3.6 23.8 - - + -
229E PHE* 4.1 4.3 - - + -
264E ARG 4.1 9.4 - - - +
265E ILE* 3.4 38.1 - - + +
267E SER* 3.2 8.6 + - - +
269E ARG* 1.3 78.7 - - + +
271E MET* 1.3 67.8 + - - +
272E ASN 3.2 0.2 - - - -
273E ALA* 2.9 10.5 + - - +
274E ILE* 2.9 30.6 + - + +
292E GLN* 4.5 2.5 - - - -
294E ILE* 4.0 21.8 - - + -
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Residues in contact with MET 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E ILE 3.5 9.0 - - - +
266E ASN* 3.3 26.2 - - - +
267E SER 3.1 17.9 + - - +
268E LYS* 3.7 6.3 - - - +
270E MET* 1.3 77.1 - - - +
272E ASN* 1.3 63.5 + - - +
274E ILE* 3.3 18.1 + - + +
275E LYS* 3.1 21.2 + - - +
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Residues in contact with ASN 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LYS* 3.2 25.3 + - - +
269E ARG* 4.0 5.1 - - - +
271E MET* 1.3 79.7 - - - +
273E ALA* 1.3 57.8 + - - +
275E LYS* 3.2 14.3 + - - +
276E GLU* 2.9 52.3 + - - +
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Residues in contact with ALA 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E VAL* 4.2 14.8 - - + +
269E ARG 3.3 8.7 + - - +
270E MET* 2.9 13.6 + - - +
272E ASN* 1.3 78.5 - - - +
274E ILE* 1.3 56.8 + - - +
276E GLU* 3.8 8.0 + - - -
277E SER* 3.1 26.5 + - - -
289E PHE* 3.8 11.8 - - + -
292E GLN* 3.5 35.6 - - + +
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Residues in contact with ILE 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E HIS* 5.9 0.9 - - - +
202E ASP* 4.7 1.8 - - - +
205E LEU* 3.8 36.8 - - + -
217E LEU* 4.9 4.5 - - + -
226E VAL* 3.9 19.3 - - + -
265E ILE* 4.6 19.1 - - + +
270E MET* 2.9 31.8 + - + +
271E MET* 3.5 20.4 - - + +
273E ALA* 1.3 75.0 - - - +
275E LYS* 1.3 62.4 - - - +
277E SER* 2.4 26.4 + - - -
278E TYR* 3.2 27.5 - - + -
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Residues in contact with LYS 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E MET 3.1 13.5 + - - +
272E ASN* 3.2 15.6 + - - +
274E ILE* 1.3 76.9 - - - +
276E GLU* 1.3 71.5 + - - +
278E TYR* 3.5 14.5 - - + +
279E ASP* 2.8 56.9 + - - +
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Residues in contact with GLU 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ASN* 2.9 36.8 + - - +
273E ALA* 4.2 6.8 - - - +
275E LYS* 1.3 88.7 + - - +
277E SER* 1.3 65.0 + - - +
278E TYR 3.3 0.2 - - - -
279E ASP* 3.8 9.2 - - + +
280E TYR* 3.2 17.7 + - - +
289E PHE* 3.4 19.1 - - + -
292E GLN* 5.9 0.9 + - - -
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Residues in contact with SER 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ASN* 3.4 14.4 + - - +
222E THR* 3.2 13.0 + - - -
224E THR* 3.4 19.7 + - - -
226E VAL* 3.8 17.0 - - - +
273E ALA 3.1 14.8 + - - -
274E ILE* 2.4 31.7 + - - +
276E GLU* 1.3 76.6 - - - +
278E TYR* 1.3 63.9 + - - +
280E TYR* 3.4 16.6 - - - +
289E PHE* 3.6 15.2 - - - -
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Residues in contact with TYR 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ASP* 2.6 37.7 + - - -
204E ASN* 4.2 4.5 + - - -
205E LEU* 4.6 1.5 - - + +
219E ASN* 3.3 30.5 + - - +
221E GLN* 3.9 29.8 - - - -
222E THR* 3.3 12.8 - - + +
274E ILE* 3.2 35.9 - - + -
275E LYS* 3.5 16.5 + - + +
277E SER* 1.3 81.2 + - - +
279E ASP* 1.3 66.1 + - - +
280E TYR 3.0 11.1 + - - +
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Residues in contact with ASP 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E LYS* 2.8 50.4 + - - +
276E GLU* 3.9 9.8 - - + +
277E SER 3.4 0.4 - - - -
278E TYR* 1.3 78.8 - - - +
280E TYR* 1.3 63.0 + - - +
281E ASN* 3.7 4.2 + - - +
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Residues in contact with TYR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E THR* 4.4 9.5 - - - +
224E THR* 3.7 19.7 - - + -
276E GLU 3.2 11.7 + - - +
277E SER 3.4 15.3 - - - +
278E TYR 3.0 10.7 + - - +
279E ASP* 1.3 80.7 - - - +
281E ASN* 1.3 69.8 + - - +
282E PRO* 3.7 31.9 - - + +
285E THR* 4.1 16.4 - - + -
287E ARG* 3.0 27.7 + - + +
288E PRO* 3.5 8.7 - - - +
289E PHE* 3.4 43.7 - + + -
575F ARG* 2.7 31.2 + - - -
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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