Contacts of the helix formed by residues 389 - 405 (chain F) in PDB entry 3HX0
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 ARG 389 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387F MET 3.9 0.2 + - - -
388F PRO* 1.3 71.6 - - - +
390F GLU* 1.3 56.5 + - + +
392F ALA* 3.2 8.9 + - - +
393F THR* 2.9 33.7 + - - -
418F TYR* 2.7 62.4 + - + +
419F ARG* 4.6 2.4 - - - +
421F GLY* 3.8 13.6 - - - +
422F LYS 3.4 21.5 + - - +
423F ALA* 3.0 22.2 + - - +
424F THR* 4.4 0.2 - - - +
425F CYS* 4.6 3.5 - - - -
11Q T 3.8 27.9 - - - +
12Q G 3.1 41.9 + - - +
1R C 4.0 9.9 - - - +
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Residues in contact with GLU 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F PRO* 3.7 22.2 - - + +
389F ARG* 1.3 78.3 - - + +
391F GLU* 1.3 63.0 + - - +
393F THR* 3.2 13.9 + - - -
394F GLU* 3.3 16.3 + - - +
1R C 3.4 54.3 + - + +
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Residues in contact with GLU 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F MET* 3.6 12.8 - - + +
388F PRO* 3.0 19.5 + - + +
390F GLU* 1.3 76.5 - - - +
392F ALA* 1.3 66.7 + - - +
393F THR 3.1 0.4 - - - -
394F GLU* 3.2 10.1 + - - +
395F ILE* 3.1 31.8 + - + +
479F LEU* 3.8 18.1 + - + +
484F ARG* 3.4 29.8 + - - +
485F ARG 4.4 5.2 + - - +
487F ARG* 2.7 49.7 + - - +
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Residues in contact with ALA 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F MET* 4.0 12.9 - - - -
388F PRO 3.0 13.2 + - - +
389F ARG* 3.2 13.7 + - - +
391F GLU* 1.3 77.6 - - - +
393F THR* 1.3 61.8 + - - +
395F ILE* 3.6 3.5 + - - +
396F GLU* 3.3 21.1 + - - +
418F TYR* 3.6 25.0 - - + -
425F CYS* 3.9 18.4 - - + -
428F VAL* 3.9 12.4 - - + +
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Residues in contact with THR 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F ARG 2.9 15.3 + - - -
390F GLU 3.4 9.9 - - - -
391F GLU 3.1 0.2 - - - -
392F ALA* 1.3 74.0 - - - +
394F GLU* 1.3 61.7 + - + +
395F ILE 3.1 1.6 - - - -
396F GLU* 3.0 8.3 + - - +
397F GLN* 2.8 43.1 + - + +
418F TYR* 3.0 25.1 + - - +
12Q G 3.5 34.1 + - + +
1R C 3.7 11.3 + - - +
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Residues in contact with GLU 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F GLU 3.3 11.8 + - - +
391F GLU* 3.2 6.4 + - - +
393F THR* 1.3 78.8 - - + +
395F ILE* 1.3 56.9 + - - +
397F GLN* 3.5 9.3 + - - +
398F THR* 2.9 32.6 + - - -
479F LEU* 3.5 23.7 - - + +
480F PRO* 5.6 1.9 - - - +
484F ARG* 3.4 29.7 + - - -
1R C 5.7 5.5 + - - +
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Residues in contact with ILE 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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387F MET* 3.6 20.0 - - - -
391F GLU* 3.1 14.4 + - + +
392F ALA 3.7 4.7 - - - +
393F THR 3.1 0.2 - - - -
394F GLU* 1.3 74.3 - - - +
396F GLU* 1.3 66.1 + - - +
398F THR* 3.3 4.7 + - - -
399F VAL* 3.2 21.3 + - - +
428F VAL* 3.5 30.3 - - + -
456F PHE* 3.9 20.4 - - + -
477F CYS* 4.1 5.8 - - - -
479F LEU* 4.0 17.5 - - + -
487F ARG* 3.8 24.9 - - + -
489F LEU* 3.8 23.6 - - + -
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Residues in contact with GLU 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F ALA 3.3 10.1 + - - +
393F THR* 3.0 11.6 + - - +
395F ILE* 1.3 76.7 - - - +
397F GLN* 1.3 64.2 + - - +
399F VAL* 3.2 3.2 + - - +
400F GLN* 2.8 58.7 + - - +
412F CYS* 3.9 16.3 - - - +
413F VAL 4.7 0.9 - - - -
414F ALA* 3.5 39.6 + - + +
418F TYR* 5.3 5.4 + - + -
428F VAL* 4.3 4.0 - - + -
430F VAL* 4.2 20.9 - - + -
12Q G 5.2 9.2 - - - +
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Residues in contact with GLN 397 (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 THR* 2.8 33.3 + - + +
394F GLU* 3.5 9.4 - - + +
396F GLU* 1.3 80.3 - - - +
398F THR* 1.3 62.3 + - - +
400F GLN* 3.2 24.5 + - - +
401F LYS* 2.9 60.6 + - - +
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Residues in contact with THR 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 GLU 2.9 18.5 + - - -
395F ILE 3.4 8.7 - - - -
396F GLU 3.2 0.2 - - - -
397F GLN* 1.3 76.7 - - - +
399F VAL* 1.3 64.5 + - - +
401F LYS* 3.9 6.3 - - - +
402F ALA* 3.0 26.9 + - - +
451F LEU* 3.9 9.2 - - + -
454F GLU* 4.2 13.7 - - - +
456F PHE* 3.7 45.8 - - + -
479F LEU* 3.9 6.2 - - - +
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Residues in contact with VAL 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F ILE 3.4 13.9 - - - +
396F GLU 3.2 6.7 + - - +
398F THR* 1.3 75.6 - - - +
400F GLN* 1.3 65.4 + - - +
402F ALA* 3.8 1.9 - - - +
403F ALA* 3.0 24.4 + - - +
412F CYS* 5.0 0.2 - - - -
430F VAL* 3.9 34.3 - - + -
432F ILE* 4.2 15.0 - - + -
447F LEU* 4.1 6.8 - - + +
451F LEU* 4.5 11.7 - - + -
456F PHE* 4.5 6.7 - - + -
489F LEU* 4.2 17.3 - - + -
491F ILE* 4.0 27.8 - - + -
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Residues in contact with GLN 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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396F GLU* 2.8 42.9 + - - +
397F GLN* 3.2 24.0 + - - +
399F VAL* 1.3 72.0 - - - +
401F LYS* 1.3 52.9 + - + +
403F ALA* 2.8 7.6 + - - +
404F GLN* 2.7 70.5 + - + +
412F CYS* 3.8 28.4 + - + +
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Residues in contact with LYS 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 GLN* 2.9 56.4 + - - +
398F THR* 3.9 4.9 - - - +
400F GLN* 1.3 75.3 - - + +
402F ALA* 1.3 58.7 + - - +
404F GLN* 3.3 9.6 + - - +
405F ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 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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398F THR 3.0 18.6 + - - +
399F VAL 3.8 2.7 - - - +
401F LYS* 1.3 76.4 - - - +
403F ALA* 1.3 57.3 + - - +
405F ALA* 3.4 11.8 - - - +
406F PHE* 3.0 22.0 - - - -
447F LEU* 4.0 4.8 - - + +
450F SER* 3.9 18.6 + - - +
451F LEU* 3.4 28.0 - - + -
454F GLU* 4.4 7.4 - - - +
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Residues in contact with ALA 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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399F VAL 3.0 13.1 + - - +
400F GLN 2.8 10.1 + - - +
402F ALA* 1.3 75.3 - - - +
404F GLN* 1.3 58.8 + - - +
405F ALA 2.8 9.5 + - - -
406F PHE* 3.3 21.7 + - - -
407F ASN 3.7 4.7 + - - -
410F LEU* 3.8 23.2 - - + +
412F CYS* 4.1 18.4 - - - -
432F ILE* 4.6 7.2 - - + -
447F LEU* 3.8 15.7 - - + -
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Residues in contact with GLN 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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400F GLN* 2.7 55.6 + - + +
401F LYS* 4.1 8.6 + - - +
403F ALA* 1.3 72.7 - - + +
405F ALA* 1.3 63.8 + - - +
406F PHE 3.4 0.2 - - - -
407F ASN 3.2 11.0 - - - -
408F SER* 3.0 39.6 + - - +
410F LEU* 4.0 23.2 + - - +
411F LEU* 5.8 4.0 - - - +
412F CYS* 5.2 2.4 - - - +
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Residues in contact with ALA 405 (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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401F LYS 2.9 17.5 + - - +
402F ALA* 3.4 16.4 - - - +
403F ALA 2.8 1.2 + - - -
404F GLN* 1.3 79.5 - - - +
406F PHE* 1.3 61.5 + - + +
407F ASN 3.4 1.9 + - - -
408F SER 5.0 0.2 + - - -
450F SER* 5.5 2.7 - - - +
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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