Contacts of the strand formed by residues 346 - 355 (chain X) in PDB entry 1M6E
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 LYS 346 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213X ARG* 3.8 11.8 - - - +
220X THR 4.4 5.9 - - - +
221X GLU* 3.9 13.0 - - - +
281X GLU* 3.1 45.4 + - - +
282X ILE 3.2 17.0 - - - +
283X TYR* 3.7 28.9 + - + +
284X TRP* 3.2 22.8 + - - +
344X LYS 4.0 10.1 - - - +
345X THR* 1.3 75.9 - - - +
347X PHE* 1.3 59.8 + - - +
348X ILE* 4.3 11.0 - - + -
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Residues in contact with PHE 347 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X ILE* 4.8 16.8 - - + -
147X TYR* 4.0 11.0 - + - +
210X LEU* 3.4 29.6 - - + -
221X GLU 4.3 7.9 - - - -
222X CYS* 6.1 2.2 - - - -
224X LEU 5.4 0.4 - - - -
225X ILE* 4.6 15.9 - - + -
281X GLU* 3.2 5.9 - - - +
282X ILE* 2.8 43.1 + - + +
283X TYR 5.3 0.2 - - - -
284X TRP* 3.1 55.2 - + + -
286X SER* 5.7 1.6 - - - -
304X VAL* 5.6 3.4 - - + -
307X CYS* 6.4 0.9 - - - -
308X MET* 5.7 1.3 - - + -
346X LYS* 1.3 73.3 - - - +
348X ILE* 1.3 67.7 + - - +
2000X SAL 3.9 34.1 - + - -
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Residues in contact with ILE 348 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X LEU* 3.5 8.4 - - - +
211X GLY 2.9 35.4 + - - +
212X ARG* 3.2 36.8 - - - +
213X ARG* 3.9 26.5 - - + +
221X GLU* 4.4 25.2 + - + +
279X ALA* 4.1 16.4 - - + -
280X SER 3.4 7.9 - - - +
281X GLU* 4.2 9.2 - - + -
346X LYS* 4.3 15.7 - - + -
347X PHE* 1.3 86.6 - - - +
349X ASN* 1.3 65.4 + - - +
350X VAL 4.3 2.5 - - - +
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Residues in contact with ASN 349 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X VAL* 4.2 11.3 - - + +
147X TYR* 2.3 41.7 + - - -
208X THR* 4.3 10.1 - - + -
209X ILE 3.6 4.3 - - - -
279X ALA* 4.1 0.7 - - - -
280X SER* 2.6 33.6 + - - +
281X GLU* 4.0 2.2 - - - +
282X ILE* 3.3 28.5 - - - +
348X ILE* 1.3 75.1 - - - +
350X VAL* 1.3 59.1 + - - +
351X ILE* 2.6 45.3 - - + +
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Residues in contact with VAL 350 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X LEU 4.0 0.7 - - - +
208X THR* 3.6 1.4 - - - -
209X ILE* 2.9 41.7 + - + +
211X GLY* 4.4 1.3 - - - -
212X ARG 4.0 11.2 - - - +
258X SER 2.9 25.6 - - - +
259X PRO* 3.3 29.4 - - + +
262X VAL* 3.6 34.3 - - + -
277X ILE* 5.4 1.3 - - + -
278X GLU 3.4 9.4 - - - +
279X ALA* 4.1 6.7 - - + +
348X ILE* 3.9 1.0 + - + -
349X ASN* 1.3 70.3 - - - +
351X ILE* 1.3 58.6 + - - +
352X VAL* 4.4 8.1 - - + -
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Residues in contact with ILE 351 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X VAL* 6.1 0.4 - - + -
32X THR* 3.8 26.0 - - - +
35X ILE* 4.4 26.5 - - + -
206X VAL* 4.6 4.5 - - + -
207X LEU 3.5 9.2 - - - +
208X THR* 4.2 14.8 - - + +
276X HIS 6.1 0.4 - - - +
277X ILE* 3.3 1.1 - - - -
278X GLU* 2.8 47.2 + - + +
280X SER* 3.7 28.7 - - - +
349X ASN* 2.6 29.3 + - + +
350X VAL* 1.3 72.5 - - - +
352X VAL* 1.3 74.3 + - - +
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Residues in contact with VAL 352 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205X MET 3.6 1.0 - - - +
206X VAL* 3.4 4.4 - - - +
207X LEU* 2.9 38.5 + - + +
262X VAL* 3.9 22.2 - - + -
266X ILE* 4.0 6.3 - - + -
274X ILE* 4.7 0.9 - - + -
277X ILE* 3.7 31.6 - - + +
350X VAL* 4.4 6.5 - - + -
351X ILE* 1.3 86.2 - - - +
353X SER* 1.3 61.4 + - - +
354X LEU* 3.0 42.8 - - + -
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Residues in contact with SER 353 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ILE* 3.7 26.4 + - - +
39X ALA* 4.0 5.0 - - - +
204X ARG* 3.4 20.9 + - - +
205X MET 3.6 3.1 - - - -
206X VAL* 3.9 15.3 - - - +
275X ASP* 3.2 45.5 + - - -
276X HIS* 5.3 0.7 - - - -
277X ILE 4.8 0.4 - - - +
352X VAL* 1.3 76.2 - - - +
354X LEU* 1.3 69.1 + - - +
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Residues in contact with LEU 354 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X HIS* 6.5 0.4 - - + -
192X LEU* 4.7 4.0 - - + -
204X ARG* 3.4 16.0 + - - -
205X MET* 3.0 59.3 + - + +
207X LEU* 4.5 12.1 - - + -
266X ILE* 3.8 30.3 - - + -
272X PHE* 3.9 19.5 - - + -
274X ILE* 3.6 22.0 - - + +
352X VAL* 3.0 34.1 - - + -
353X SER* 1.3 79.6 + - - +
355X ILE* 1.3 67.1 + - - +
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Residues in contact with ILE 355 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201X PRO 4.7 0.9 - - - +
202X GLY* 3.4 25.8 - - - +
203X GLY 3.5 3.4 - - - +
204X ARG* 3.1 33.7 - - - +
272X PHE* 3.2 5.4 - - - -
273X LEU* 2.8 60.0 + - + +
274X ILE 4.9 1.8 - - - +
275X ASP* 4.5 11.7 - - + +
354X LEU* 1.3 79.7 - - - +
356X ARG* 1.3 73.5 + - - +
357X LYS 3.1 1.4 + - - -
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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