Contacts of the strand formed by residues 257 - 267 (chain L) in PDB entry 3GHG
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 THR 257 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249L GLU* 4.5 11.7 - - - +
250L LEU 3.2 19.5 - - - +
251L GLU* 3.3 32.3 - - + +
256L ARG* 1.3 77.9 - - - +
258L SER* 1.3 68.3 + - - +
259L THR* 6.4 0.2 - - - -
285L ASP* 4.3 6.1 - - - +
372L TRP* 4.0 4.9 - - - -
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Residues in contact with SER 258 (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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249L GLU* 3.6 1.9 - - - +
250L LEU* 3.0 30.6 + - - +
257L THR* 1.3 79.7 - - - +
259L THR* 1.3 69.3 + - - +
285L ASP* 2.9 25.1 - - - -
286L ALA* 3.6 16.5 - - - +
372L TRP* 3.3 37.8 - - - -
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Residues in contact with THR 259 (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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247L ARG* 3.5 32.2 + - - +
248L VAL* 3.7 4.7 - - - +
249L GLU* 3.2 27.6 - - + +
250L LEU 4.8 0.2 - - - +
258L SER* 1.3 87.3 - - - +
260L ALA* 1.3 58.3 + - - +
261L ASP* 4.1 0.7 - - - -
284L GLY* 3.0 19.7 - - - +
285L ASP* 3.2 10.5 + - - -
286L ALA* 2.7 29.4 + - - +
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Residues in contact with ALA 260 (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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248L VAL* 3.2 30.7 + - + +
259L THR* 1.3 77.8 - - - +
261L ASP* 1.3 64.1 + - - +
262L TYR* 3.6 12.2 - - + -
281L PHE* 3.7 13.5 - - + -
284L GLY* 4.5 0.9 - - - -
286L ALA* 3.9 2.9 - - + -
287L GLY 3.2 26.2 - - - +
369L TRP* 3.7 20.2 - - + -
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Residues in contact with ASP 261 (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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191L TRP* 5.5 0.7 - - - -
246L LEU 3.3 13.0 - - - +
247L ARG* 3.0 47.9 + - - +
259L THR* 4.1 0.5 - - - -
260L ALA* 1.3 80.4 + - - +
262L TYR* 1.3 57.4 + - - +
281L PHE* 3.1 13.1 - - - -
282L ALA* 2.8 38.7 + - + -
283L GLY 3.5 17.5 + - - +
392L LEU* 4.8 18.7 - - + +
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Residues in contact with TYR 262 (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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245L ALA* 3.6 4.2 - - - +
246L LEU* 2.9 48.4 + - + +
248L VAL* 4.8 0.9 - - + -
260L ALA 3.6 19.3 - - - -
261L ASP* 1.3 76.5 - - - +
263L ALA* 1.3 62.0 + - - +
265L PHE 5.0 0.2 - - - -
278L TYR* 3.3 59.2 - + + -
280L TYR 3.7 3.1 - - - -
281L PHE* 3.8 18.6 - + + -
282L ALA* 4.7 2.7 - - - -
288L ASP* 2.4 36.7 + - - -
289L ALA 3.7 4.5 + - - -
290L PHE* 3.1 39.9 + + - +
369L TRP* 3.7 11.7 - + - -
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Residues in contact with ALA 263 (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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244L TYR 4.5 1.3 - - - -
245L ALA* 4.8 4.0 - - + +
262L TYR* 1.3 72.1 - - - +
264L MET* 1.3 65.7 + - - +
265L PHE 3.1 2.2 - - - -
278L TYR* 3.1 4.9 - - - +
279L ALA* 2.7 28.7 + - - -
280L TYR* 3.1 42.4 + - + +
282L ALA* 4.5 6.7 - - + +
389L PHE* 3.9 21.3 - - + -
392L LEU* 6.4 1.1 - - + -
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Residues in contact with MET 264 (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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243L PRO* 3.7 27.8 - - + -
244L TYR 3.3 8.6 + - - -
263L ALA* 1.3 74.6 - - + +
265L PHE* 1.3 63.3 + - - +
266L LYS* 3.5 6.4 + - + +
277L THR* 3.2 4.7 + - - +
278L TYR* 2.9 17.2 - - - -
279L ALA* 3.6 20.0 - - + +
280L TYR* 4.8 9.0 - - + +
389L PHE* 3.4 39.7 - - + -
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Residues in contact with PHE 265 (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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194L PHE* 4.4 16.8 - + - -
233L ILE* 4.5 7.4 - - + -
237L SER* 4.3 4.1 - - - -
244L TYR* 2.9 23.7 + - - +
246L LEU* 3.5 51.8 - - + +
262L TYR 4.6 1.1 - - - +
263L ALA 3.1 1.4 - - - -
264L MET* 1.3 78.1 - - - +
266L LYS* 1.3 71.0 + - - +
267L VAL* 3.6 30.7 - - + -
276L LEU* 3.3 36.6 - - + -
277L THR 3.3 2.7 - - - -
278L TYR* 4.2 7.9 - + + -
335L TRP* 5.2 3.8 - + - -
384L MET* 6.0 0.4 - - + -
386L ILE* 3.7 32.8 - - + -
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Residues in contact with LYS 266 (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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237L SER* 3.4 27.2 + - - +
238L THR* 4.6 15.4 + - + +
241L ALA* 3.7 29.6 + - - +
242L ILE 4.4 13.7 - - - -
243L PRO* 4.8 7.9 - - - -
244L TYR 5.5 0.7 - - - +
264L MET* 4.4 7.0 - - + +
265L PHE* 1.3 86.0 - - - +
267L VAL* 1.3 65.3 + - - +
275L ARG 3.8 1.4 - - - +
276L LEU* 3.8 3.5 - - - +
277L THR* 2.8 47.8 + - - +
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Residues in contact with VAL 267 (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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230L ASN* 3.7 10.8 - - + +
233L ILE* 4.3 11.2 - - + -
234L HIS* 2.6 48.6 + - + +
237L SER* 3.1 13.9 + - - +
238L THR* 3.2 10.0 - - - +
265L PHE* 3.6 30.5 - - + -
266L LYS* 1.3 74.6 - - - +
268L GLY* 1.3 64.2 + - - +
274L TYR* 3.9 16.6 - - + +
275L ARG 3.5 2.7 - - - +
276L LEU* 5.1 1.3 - - + -
335L TRP* 4.2 20.4 - - + -
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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