Contacts of the strand formed by residues 372 - 379 (chain F) in PDB entry 2HU4
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 372 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365F THR* 3.5 1.6 - - - -
366F LYS* 2.9 18.9 + - - +
367F SER* 3.4 15.0 + - - -
370F SER* 2.7 32.4 + - - -
371F ARG* 1.3 75.0 - - - +
373F GLY* 1.3 68.7 + - - +
400F ILE* 3.3 26.0 - - - -
401F THR 5.6 0.2 - - - -
402F ASP 3.5 8.5 - - - -
403F TRP* 3.6 12.1 - - - +
404F SER* 3.4 0.9 + - - -
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Residues in contact with GLY 373 (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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365F THR* 3.2 9.0 - - - -
366F LYS* 3.6 7.9 - - - -
372F SER* 1.3 80.1 - - - +
374F PHE* 1.3 62.1 + - - +
398F VAL* 2.9 23.3 - - - -
399F ALA 3.2 13.6 + - - -
400F ILE* 4.0 0.2 - - - -
402F ASP 2.7 14.1 + - - -
404F SER* 2.8 18.5 + - - -
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Residues in contact with PHE 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F PHE* 4.0 2.9 - + - -
363F GLY* 3.7 10.1 - - - -
364F ARG* 3.3 41.5 - - - -
365F THR* 4.1 3.6 - - + -
366F LYS* 3.5 6.6 + - - +
373F GLY* 1.3 76.8 - - - -
375F GLU* 1.3 84.1 + - - +
376F MET* 4.2 2.9 - - - -
397F ILE* 2.9 49.3 + - + -
398F VAL* 2.8 19.7 + - + +
404F SER* 4.6 7.0 - - - -
405F GLY 4.7 6.1 - - - -
407F SER* 3.4 38.4 - - - -
422F PHE* 4.0 20.2 - + - -
424F VAL* 4.1 17.0 - - + -
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Residues in contact with GLU 375 (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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327F ARG* 4.6 0.7 + - - -
362F ILE 3.5 5.0 - - - +
363F GLY* 3.7 2.6 - - - -
364F ARG* 3.1 61.2 + - + +
365F THR 4.1 3.6 - - - +
366F LYS* 2.8 39.5 + - - +
374F PHE* 1.3 83.3 - - - +
376F MET* 1.3 63.0 + - - +
377F ILE* 3.5 7.5 - - + +
394F LYS* 3.0 35.8 + - + -
395F GLN 3.4 13.7 - - - +
396F ASP* 4.3 1.3 - - - +
397F ILE* 4.2 1.8 - - - +
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Residues in contact with MET 376 (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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97F TRP* 3.4 58.3 - - + +
352F PHE* 3.9 28.7 - - + -
361F TRP* 3.7 20.5 - - + -
362F ILE 3.5 16.4 - - - +
363F GLY* 3.9 2.7 - - - -
374F PHE* 4.2 2.5 - - - -
375F GLU* 1.3 77.7 - - - +
377F ILE* 1.3 61.3 + - - +
394F LYS* 3.4 1.7 - - - -
395F GLN* 2.8 42.0 + - + +
397F ILE* 4.0 7.2 - - + -
422F PHE* 3.7 29.2 - - + -
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Residues in contact with ILE 377 (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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321F VAL* 4.0 12.1 - - + -
360F VAL 3.5 2.3 - - - +
361F TRP* 3.5 5.7 - - - -
362F ILE* 2.8 46.2 + - + +
364F ARG* 3.5 41.5 - - + +
375F GLU* 3.5 18.2 - - + +
376F MET* 1.3 76.8 - - - +
378F TRP* 1.3 61.2 + - - +
379F ASP* 3.8 3.4 + - + +
390F PHE* 3.5 41.5 - - + -
392F VAL 3.3 3.4 - - - +
394F LYS* 3.8 22.9 - - + +
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Residues in contact with TRP 378 (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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356F TYR* 4.0 23.6 - + + -
359F GLY* 3.8 16.8 - - - -
360F VAL* 3.1 45.1 - - - -
361F TRP* 3.7 50.1 - + + -
377F ILE* 1.3 70.9 - - - +
379F ASP* 1.3 58.6 - - - +
380F PRO* 3.5 26.3 - - + +
390F PHE* 3.6 2.8 - - - +
391F SER* 2.9 43.4 + - - -
392F VAL* 2.9 25.6 + - + -
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Residues in contact with ASP 379 (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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319F SER* 2.8 24.5 + - - +
321F VAL* 4.1 6.0 - - + +
359F GLY* 3.2 1.0 - - - -
360F VAL* 2.9 40.9 + - + +
362F ILE* 4.8 5.4 - - + -
377F ILE* 3.8 3.0 + - + -
378F TRP* 1.3 72.5 - - - +
380F PRO* 1.3 93.9 - - - +
381F ASN 3.6 1.9 - - - +
382F GLY* 3.3 20.0 + - - -
387F ASP* 3.8 9.9 - - - +
389F SER 3.3 26.2 - - - +
390F PHE* 3.9 8.7 - - + -
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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