Contacts of the strand formed by residues 341 - 347 (chain F) in PDB entry 3HU1
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 VAL 341 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239F ARG* 4.3 12.6 - - - +
293F ALA* 3.9 30.1 - - + +
294F GLU* 4.1 9.2 - - + +
297F ALA 4.9 0.7 - - - +
299F ALA* 3.5 11.7 - - + +
301F ILE* 3.9 33.2 - - + -
335F LEU* 3.9 34.0 - - + +
339F ALA* 3.4 18.0 - - + +
340F HIS* 1.3 82.6 - - - +
342F ILE* 1.3 66.0 + - - +
343F VAL 4.3 0.5 + - - -
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Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F MET 3.9 10.3 - - - +
220F VAL* 4.2 24.2 - - + +
223F PRO* 4.6 13.7 - - + -
224F LEU* 3.8 28.3 - - + -
237F PRO* 5.0 4.9 - - + -
238F PRO 3.4 22.2 - - - +
239F ARG* 3.7 10.1 - - + +
241F ILE* 3.6 28.5 - - + -
299F ALA 3.1 6.8 + - - +
300F ILE* 3.4 5.5 - - - +
301F ILE 3.0 23.0 + - - -
341F VAL* 1.3 78.7 - - - +
343F VAL* 1.3 67.9 + - - +
344F MET* 3.8 1.6 + - + -
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Residues in contact with VAL 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F ARG 3.0 14.0 + - - +
240F GLY* 3.3 3.5 - - - -
241F ILE 3.0 24.4 + - - -
290F PHE* 4.4 9.4 - - + -
301F ILE* 3.4 26.7 - - + +
303F ILE* 3.8 19.5 - - + -
332F MET* 3.8 22.4 - - + -
335F LEU* 4.2 20.4 - - + -
341F VAL* 4.8 0.2 - - + -
342F ILE* 1.3 75.5 - - - +
344F MET* 1.3 61.6 + - - +
363F PHE* 3.4 26.8 - - + -
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Residues in contact with MET 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F ILE* 4.2 20.4 - - + -
220F VAL* 3.8 31.0 - - + -
241F ILE* 3.3 10.3 - - + +
243F LEU* 3.9 29.6 - - + -
254F ILE* 5.2 0.7 - - + -
258F VAL* 4.6 15.3 - - + -
300F ILE* 4.0 19.3 - - + -
301F ILE 2.6 13.0 + - - +
302F PHE* 3.5 37.7 - - + -
303F ILE* 2.8 31.7 + - - +
342F ILE* 3.8 2.2 + - + -
343F VAL* 1.3 79.1 - - - +
345F ALA* 1.3 56.7 + - - +
363F PHE* 4.1 0.4 - - - -
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Residues in contact with ALA 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F ILE 2.8 7.5 + - - +
242F LEU* 3.3 8.7 - - + -
243F LEU* 2.6 35.2 + - - +
302F PHE* 4.4 4.5 - - - -
303F ILE* 3.3 16.8 - - + +
306F LEU* 3.9 24.7 - - + -
344F MET* 1.3 76.4 - - - +
346F ALA* 1.3 55.8 + - - +
363F PHE* 3.6 22.2 - - + -
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Residues in contact with ALA 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F LEU* 4.8 0.7 - - - -
243F LEU* 3.3 8.1 - - + +
251F LYS* 3.8 25.6 - - + -
302F PHE* 3.7 17.2 - - + -
303F ILE 3.2 6.9 + - - -
304F ASP* 3.6 20.0 - - - +
305F GLU 3.0 24.9 + - - -
306F LEU* 3.1 9.5 + - - -
345F ALA* 1.3 76.7 - - - +
347F THR* 1.3 59.8 + - - +
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Residues in contact with THR 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F LEU* 4.0 14.8 - - + -
243F LEU 2.9 9.8 + - - +
244F TYR* 3.3 22.7 - - + +
245F GLY 3.5 0.5 + - - -
251F LYS* 3.4 11.8 - - - +
305F GLU* 5.0 0.9 - - - +
306F LEU 4.7 0.2 - - - -
307F ASP* 2.6 31.6 + - - +
346F ALA* 1.3 76.7 - - - +
348F ASN* 1.3 59.3 + - - +
349F ARG 3.2 11.1 + - - -
350F PRO* 3.6 31.6 - - + -
353F ILE* 3.6 16.8 - - + -
800F AGS 4.9 0.7 - - - -
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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