Contacts of the strand formed by residues 392 - 403 (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 VAL 392 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95F ASN 5.1 8.1 - - - +
361F TRP* 4.6 13.9 - - + -
376F MET 4.4 0.7 - - - -
377F ILE* 3.3 8.1 - - - +
378F TRP* 2.9 47.8 + - + -
390F PHE* 3.8 1.6 - - - -
391F SER* 1.3 88.6 - - - +
394F LYS* 1.3 72.7 + - - +
395F GLN* 4.7 4.5 - - + +
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Residues in contact with LYS 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F ARG* 4.5 4.4 - - - +
366F LYS* 4.4 2.2 - - - +
375F GLU* 3.0 44.3 + - + +
376F MET 3.4 3.6 - - - +
377F ILE* 3.8 20.3 - - + +
390F PHE* 4.1 22.9 - - + -
391F SER 4.2 0.4 + - - -
392F VAL* 1.3 84.6 - - - +
395F GLN* 1.3 61.7 + - - +
396F ASP* 4.1 16.5 + - - +
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Residues in contact with GLN 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F GLY* 3.6 5.1 - - - -
97F TRP* 2.8 65.9 - - - +
361F TRP* 4.8 2.7 - - + -
375F GLU* 3.4 1.7 - - - -
376F MET* 2.8 45.3 + - + +
392F VAL* 4.7 6.4 - - + +
394F LYS* 1.3 74.1 - - - +
396F ASP* 1.3 68.4 + - - +
397F ILE* 3.0 12.2 - - + +
446F PHE* 5.4 2.1 - - - -
453F THR* 3.6 13.2 + - - -
454F VAL* 3.4 14.5 - - - +
455F GLY* 3.9 14.4 - - - +
458F TRP* 5.8 0.5 - - - -
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Residues in contact with ASP 396 (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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366F LYS* 2.5 33.8 + - + +
374F PHE 4.0 4.3 - - - -
375F GLU* 4.2 1.7 - - - +
394F LYS* 4.2 14.7 + - - +
395F GLN* 1.3 76.6 - - - +
397F ILE* 1.3 68.7 + - - +
398F VAL 4.9 1.8 - - - +
455F GLY* 3.4 12.3 - - - -
456F TRP* 3.3 32.4 + - - +
458F TRP* 4.4 2.4 - - - -
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Residues in contact with ILE 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F TRP* 5.5 0.9 - - + -
374F PHE* 2.9 29.7 + - + +
376F MET* 4.0 20.6 - - + +
395F GLN* 3.0 32.3 - - + +
396F ASP* 1.3 91.4 - - - +
398F VAL* 1.3 79.1 + - + +
422F PHE* 4.1 10.5 - - + -
424F VAL* 4.5 3.1 - - + -
444F ILE* 3.9 16.2 - - + -
446F PHE* 3.9 30.1 - - + -
456F TRP 3.5 7.2 - - - -
458F TRP* 3.2 25.9 + - - +
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Residues in contact with VAL 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F LYS* 3.1 8.9 - - - +
373F GLY* 2.9 21.0 - - - +
374F PHE* 2.8 38.3 + - + +
396F ASP* 5.7 0.9 - - - -
397F ILE* 1.3 101.0 - - + +
399F ALA* 1.3 66.1 + - - +
402F ASP* 3.7 18.2 - - + +
403F TRP 4.0 11.7 - - - +
404F SER* 4.6 1.6 - - - -
424F VAL* 5.2 0.7 - - + -
426F LEU* 4.2 9.9 - - + -
444F ILE* 3.8 16.8 - - + -
456F TRP 3.8 2.1 + - - -
457F SER* 3.7 6.7 - - - +
458F TRP 4.1 9.9 - - - +
459F PRO* 4.8 3.8 - - + -
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Residues in contact with ALA 399 (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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366F LYS* 4.3 4.9 - - - +
373F GLY* 3.2 7.4 - - - -
396F ASP* 6.4 0.2 - - - -
398F VAL* 1.3 77.2 - - - +
400F ILE* 1.3 58.6 + - - +
401F THR* 3.0 19.5 - - + +
402F ASP* 2.9 24.3 + - - +
456F TRP 4.9 0.2 + - - -
457F SER* 2.8 27.9 + - - +
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Residues in contact with ILE 400 (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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366F LYS* 3.7 39.2 - - + +
367F SER* 4.1 20.0 - - - +
372F SER* 3.3 24.1 - - - -
373F GLY* 4.0 8.3 - - - -
398F VAL 3.6 1.4 + - - -
399F ALA* 1.3 72.9 - - + +
401F THR* 1.3 61.7 + - + +
402F ASP 3.1 1.1 - - - -
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Residues in contact with THR 401 (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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372F SER* 5.6 0.2 - - - -
399F ALA* 3.7 10.0 - - + +
400F ILE* 1.3 81.1 - - + +
402F ASP* 1.3 75.8 + - - +
403F TRP* 5.7 2.6 + - - -
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Residues in contact with ASP 402 (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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372F SER* 3.5 4.7 - - - -
373F GLY* 2.7 33.8 + - - -
398F VAL* 3.7 6.7 - - + +
399F ALA* 2.9 19.1 + - - +
400F ILE 3.1 0.6 - - - -
401F THR* 1.3 100.6 + - - +
403F TRP* 1.3 59.3 + - - +
457F SER* 4.3 2.4 + - - -
459F PRO* 3.6 36.9 - - + +
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Residues in contact with TRP 403 (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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370F SER* 4.0 10.8 - - - -
371F ARG* 3.4 20.0 - - + +
372F SER* 3.6 18.8 - - - -
398F VAL* 4.0 4.7 - - - +
401F THR 5.7 2.6 + - - -
402F ASP* 1.3 77.5 - - - +
404F SER* 1.3 60.6 + - - +
426F LEU* 3.6 20.0 - - - +
427F ILE 3.5 20.6 - - - +
428F ARG* 3.5 31.2 - - - -
432F LYS* 3.5 51.4 - - + -
433F GLU* 3.3 24.4 + - + +
460F ASP* 5.1 4.7 + - + +
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Residues in contact with SER 404 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F THR* 4.1 6.1 - - - +
371F ARG* 2.9 26.3 + - - +
372F SER 3.4 0.7 + - - -
373F GLY* 2.8 33.4 + - - -
374F PHE* 4.6 4.3 - - - -
398F VAL* 4.6 2.2 - - - -
403F TRP* 1.3 73.6 - - - +
405F GLY* 1.3 62.7 + - - -
424F VAL* 4.6 9.0 - - - -
425F GLU 3.0 11.4 - - - -
426F LEU* 3.9 10.5 - - - -
427F ILE* 2.9 29.2 + - - +
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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