Contacts of the helix formed by residues 406 - 417 (chain F) in PDB entry 5UHE
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 THR 406 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400F ALA* 3.6 5.4 - - - +
404F ASP* 3.0 36.8 + - - +
405F ILE* 1.3 76.3 + - - +
407F PRO* 1.3 64.3 - - + +
408F GLU* 3.2 24.4 + - + +
409F LYS* 3.5 30.2 + - + -
410F VAL* 3.6 3.5 - - - +
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Residues in contact with PRO 407 (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 PRO* 5.0 3.0 - - + +
397F GLU* 4.8 18.6 - - + +
400F ALA* 3.5 18.3 - - + -
401F LYS* 6.2 2.0 - - + -
405F ILE 3.5 10.3 - - - +
406F THR* 1.3 82.4 - - - +
408F GLU* 1.3 84.9 + - - +
409F LYS 3.5 0.3 + - - -
410F VAL* 3.6 7.2 + - + +
411F LEU* 3.4 23.2 + - - +
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Residues in contact with GLU 408 (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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406F THR* 3.2 18.5 - - + +
407F PRO* 1.3 94.5 - - - +
409F LYS* 1.3 63.0 + - + +
411F LEU* 3.8 14.0 + - + +
412F GLU* 3.5 20.4 + - - +
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Residues in contact with LYS 409 (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 MET* 5.4 9.5 - - - +
404F ASP* 3.7 17.7 - - - +
406F THR* 3.5 20.0 + - + +
407F PRO 3.3 0.4 - - - -
408F GLU* 1.3 79.8 - - + +
410F VAL* 1.3 52.6 + - - +
411F LEU 3.2 0.7 - - - -
412F GLU* 2.9 28.4 + - - +
413F ILE* 2.7 51.0 + - + +
416F TYR* 6.3 1.5 - - - -
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Residues in contact with VAL 410 (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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379F LEU* 4.0 30.7 - - + -
396F PRO* 4.5 17.5 - - + +
399F LEU* 4.6 6.3 - - + -
400F ALA* 3.6 35.2 - - + +
403F MET* 5.4 2.9 - - + -
404F ASP* 3.7 10.3 - - - +
406F THR 3.6 5.2 - - - +
407F PRO 3.6 6.7 + - - +
408F GLU 3.5 0.6 - - - -
409F LYS* 1.3 73.7 - - - +
411F LEU* 1.3 66.0 + - + +
413F ILE* 3.8 11.2 - - + +
414F GLN* 3.1 35.9 + - - +
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Residues in contact with LEU 411 (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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855C ARG* 3.3 34.1 - - - +
861C LEU 5.9 2.5 - - - +
863C ALA* 3.5 33.2 - - + +
396F PRO* 3.7 35.0 - - + -
407F PRO 3.4 16.4 - - - +
408F GLU* 3.9 13.9 - - + +
409F LYS 3.2 0.2 - - - -
410F VAL* 1.3 76.5 - - + +
412F GLU* 1.3 62.3 + - - +
414F GLN* 3.4 18.1 + - - +
415F GLN* 3.5 5.4 + - - +
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Residues in contact with GLU 412 (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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863C ALA* 5.5 0.4 - - - -
408F GLU 3.5 13.5 + - - +
409F LYS* 2.9 32.2 + - - +
411F LEU* 1.3 77.9 - - - +
413F ILE* 1.3 62.8 + - + +
415F GLN* 3.4 7.9 + - - +
416F TYR* 3.2 56.0 + - + -
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Residues in contact with ILE 413 (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 MET* 4.8 10.8 - - - -
375F VAL* 3.6 26.7 - - + -
376F ILE* 3.6 27.8 - - + +
379F LEU* 3.7 22.4 - - + -
403F MET* 5.6 5.6 - - + -
404F ASP* 5.1 4.7 - - + +
409F LYS* 2.7 39.9 + - + +
410F VAL* 3.8 13.2 - - + +
411F LEU 3.4 0.2 - - - -
412F GLU* 1.3 74.5 - - + +
414F GLN* 1.3 56.9 + - - +
415F GLN 3.1 0.4 - - - -
416F TYR* 3.0 26.7 + - + +
417F ALA* 3.2 11.6 + - - +
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Residues in contact with GLN 414 (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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863C ALA* 5.6 3.1 - - + -
379F LEU* 3.9 16.0 - - + +
383F GLN* 4.8 7.3 + - - -
396F PRO* 5.6 6.8 - - - +
399F LEU* 4.2 23.0 - - - +
410F VAL* 3.1 28.5 + - - +
411F LEU* 3.8 13.5 - - - +
412F GLU 3.3 0.2 - - - -
413F ILE* 1.3 75.8 - - - +
415F GLN* 1.3 58.0 + - - +
417F ALA* 4.0 8.9 + - - +
418F ARG* 3.6 23.3 + - - +
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Residues in contact with GLN 415 (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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863C ALA* 4.0 24.6 + - + +
332D GLY 4.4 6.3 + - - -
333D GLY* 4.5 19.7 - - - +
334D ARG* 4.5 3.5 - - - +
411F LEU 3.5 9.4 + - - +
412F GLU* 3.4 9.8 + - - +
413F ILE 3.1 0.6 - - - -
414F GLN* 1.3 75.0 - - - +
416F TYR* 1.3 69.5 + - + +
417F ALA 3.2 1.6 - - - -
418F ARG* 3.0 58.9 + - - +
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Residues in contact with TYR 416 (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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36D TYR* 3.6 38.9 + + + -
37D ARG* 3.9 19.6 - - - +
364F ARG* 5.7 1.4 + - - -
368F ILE* 4.7 16.4 - - + +
372F MET* 4.0 30.3 - - + -
376F ILE* 4.4 13.7 - - + +
409F LYS* 6.3 1.6 - - - -
412F GLU* 3.2 46.6 + - + -
413F ILE* 3.0 17.9 + - + +
415F GLN* 1.3 83.2 - - + +
417F ALA* 1.3 58.8 + - - +
418F ARG 3.6 4.2 + - - +
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Residues in contact with ALA 417 (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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364F ARG* 6.1 2.2 - - - +
368F ILE* 6.0 0.2 - - - -
376F ILE* 3.8 31.9 - - + -
413F ILE* 3.2 11.5 + - + +
414F GLN* 4.0 9.6 - - - +
415F GLN 3.2 0.6 - - - -
416F TYR* 1.3 76.6 - - - +
418F ARG* 1.3 64.5 + - - +
419F GLU* 3.2 14.7 + - - +
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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