Contacts of the helix formed by residues 393 - 404 (chain F) in PDB entry 5JLH
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 ASP 393 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377F ASN 4.6 6.4 - - - +
378F ILE* 5.6 0.4 - - - -
379F ALA* 3.5 21.6 + - - +
381F LYS* 5.9 0.8 - - - +
391F MET* 3.3 28.1 - - - +
392F PRO* 1.3 76.4 - - - +
394F ASN* 1.3 63.0 + - - +
395F THR* 4.0 20.4 - - + +
396F ALA* 4.2 12.9 + - - +
397F ALA 4.8 0.2 + - - -
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Residues in contact with ASN 394 (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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391F MET* 4.4 12.3 - - + -
392F PRO 3.7 5.4 + - - +
393F ASP* 1.3 71.3 - - - +
395F THR* 1.3 62.5 + - - +
396F ALA 3.2 1.5 + - - -
397F ALA* 3.5 1.9 + - - +
398F GLN* 2.7 49.8 + - - +
408F VAL* 4.8 13.4 - - + +
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Residues in contact with THR 395 (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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393F ASP* 4.0 21.8 - - + +
394F ASN* 1.3 86.7 + - - +
396F ALA* 1.3 77.1 + - + +
398F GLN* 3.3 7.1 - - - +
399F LYS* 2.9 23.6 + - - +
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Residues in contact with ALA 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374F GLN* 4.6 6.3 - - - +
377F ASN* 3.8 42.0 - - + +
378F ILE* 4.1 7.4 - - - +
391F MET* 6.0 0.4 - - - -
393F ASP* 4.2 11.5 + - - +
394F ASN 3.2 0.8 - - - -
395F THR* 1.3 83.5 - - + +
397F ALA* 1.3 57.0 + - - +
399F LYS* 2.7 36.8 + - - +
400F LEU* 2.9 6.7 + - - +
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Residues in contact with ALA 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F ILE* 4.4 7.5 - - + +
391F MET* 3.5 37.0 - - + -
394F ASN 3.5 2.1 + - - +
396F ALA* 1.3 79.1 - - - +
398F GLN* 1.3 55.9 + - - +
400F LEU* 3.2 11.3 + - + +
401F CYS* 2.9 34.8 + - - -
408F VAL* 4.8 4.7 - - + -
411F PHE* 4.1 23.8 - - + -
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Residues in contact with GLN 398 (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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394F ASN* 2.7 39.2 + - + +
395F THR* 3.3 8.5 - - - +
397F ALA* 1.3 70.4 - - - +
399F LYS* 1.3 58.7 + - - +
401F CYS* 3.2 13.0 + - - +
402F ARG* 2.9 41.9 + - + +
408F VAL* 3.7 29.2 - - + +
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Residues in contact with LYS 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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319F LEU 4.8 0.2 - - - -
320F LEU* 2.9 57.8 + - + +
322F GLU* 3.9 24.5 + - - +
374F GLN* 3.2 36.5 - - - +
377F ASN* 5.1 2.4 - - - +
395F THR* 2.9 13.1 + - - +
396F ALA* 2.7 21.2 + - - +
398F GLN* 1.3 72.4 - - - +
400F LEU* 1.3 54.2 + - - +
402F ARG* 3.1 13.7 + - + +
403F LEU* 2.9 30.2 + - + +
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Residues in contact with LEU 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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371F ALA* 4.5 16.8 - - + +
374F GLN* 5.0 13.8 + - + +
375F PHE* 4.5 28.3 - - + -
378F ILE* 5.9 5.4 - - + -
396F ALA 2.9 5.9 + - - +
397F ALA* 3.2 17.5 - - + +
399F LYS* 1.3 77.5 - - - +
401F CYS* 1.3 58.6 + - - +
403F LEU* 2.9 8.5 + - - +
404F LEU* 2.8 53.1 + - + +
406F LEU* 5.1 5.4 - - + -
411F PHE* 3.8 39.7 - - + -
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Residues in contact with CYS 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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397F ALA 2.9 22.3 + - - -
398F GLN* 3.4 17.3 - - - +
400F LEU* 1.3 75.1 - - - +
402F ARG* 1.3 57.6 + - - +
404F LEU 2.5 26.6 - - - +
405F GLY 4.3 0.2 - - - -
406F LEU* 3.0 39.0 - - - +
407F GLY 3.8 2.9 - - - -
408F VAL* 3.3 36.3 - - - +
411F PHE* 4.6 9.6 - - - -
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Residues in contact with ARG 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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318F ASP 5.3 1.4 + - - -
320F LEU* 3.4 40.1 - - - +
367F ARG* 5.9 0.7 - - - -
398F GLN* 2.9 33.2 + - - +
399F LYS* 3.1 15.0 + - + +
401F CYS* 1.3 75.5 - - - +
403F LEU* 1.3 62.9 - - - +
404F LEU 3.2 6.7 + - - +
631F ASP* 4.9 2.6 - - - +
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Residues in contact with LEU 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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318F ASP 5.2 1.8 - - - +
319F LEU* 4.5 15.0 - - - +
367F ARG* 3.3 69.2 - - + +
370F SER* 3.7 13.5 - - - +
371F ALA* 3.5 26.7 - - + +
374F GLN* 3.9 12.6 - - + +
399F LYS* 2.9 13.7 + - + +
400F LEU* 2.9 12.4 + - - +
402F ARG* 1.3 76.8 - - - +
404F LEU* 1.3 70.0 + - + +
631F ASP* 4.0 8.7 - - - +
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Residues in contact with LEU 404 (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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368F MET* 5.2 8.5 - - + -
371F ALA* 4.8 13.5 - - + -
375F PHE* 5.2 7.4 - - + -
400F LEU* 2.8 35.3 + - + +
401F CYS 2.5 21.8 - - - +
402F ARG 3.4 7.1 - - - +
403F LEU* 1.3 89.4 - - + +
405F GLY* 1.3 59.5 + - - +
406F LEU* 4.1 14.8 - - + +
626F LEU* 3.9 26.2 - - + -
629F SER* 5.2 0.2 - - - +
630F THR* 4.7 2.1 - - - +
631F ASP* 4.1 12.3 - - - +
634F THR* 3.8 32.8 - - + +
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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