Contacts of the helix formed by residues 405 - 417 (chain H) in PDB entry 5GJQ
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 405 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365H GLU* 2.6 19.7 - - - +
368H ILE* 3.9 2.7 - - - -
401H ARG* 4.2 21.5 + - - +
403H ILE* 4.7 4.7 - - + +
404H ALA* 1.3 69.1 - - - +
406H GLU* 1.3 68.2 + - - +
407H LYS* 3.5 18.5 + - + +
408H ASP* 2.2 62.8 + - - +
409H PHE* 3.2 12.0 + - - -
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Residues in contact with GLU 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365H GLU* 3.0 7.7 + - - -
368H ILE* 2.6 51.5 - - + +
369H ARG* 3.8 29.6 + - - +
372H LEU* 3.9 17.0 - - - +
373H LEU* 4.3 5.4 - - - +
405H THR* 1.3 73.7 - - - +
407H LYS* 1.3 54.1 + - + +
409H PHE* 2.7 11.6 + - - +
410H LEU* 2.7 62.2 + - + +
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Residues in contact with LYS 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401H ARG* 6.1 2.1 - - - +
405H THR* 3.9 14.7 - - - +
406H GLU* 1.3 79.3 - - + +
408H ASP* 1.3 59.4 + - - +
410H LEU* 3.6 19.3 - - + -
411H GLU* 2.5 54.3 + - + +
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Residues in contact with ASP 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392H ALA* 4.0 12.9 - - + +
395H PHE* 4.5 17.8 - - + +
396H ALA* 5.1 4.7 - - - -
401H ARG* 4.2 16.2 + - - -
403H ILE 4.4 0.3 - - - +
404H ALA* 3.1 20.9 - - + -
405H THR* 2.2 56.2 + - - +
407H LYS* 1.3 78.6 - - - +
409H PHE* 1.3 55.8 + - - +
411H GLU* 4.0 13.1 - - - +
412H ALA* 3.1 24.9 + - - +
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Residues in contact with PHE 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H PHE* 5.1 2.9 - + - -
362H MET* 3.9 21.5 - - + -
364H VAL* 4.1 6.3 - - + -
368H ILE* 3.0 34.5 - - + -
370H PHE* 3.5 30.7 - + - -
373H LEU* 3.8 19.1 - - + -
388H VAL* 4.5 12.6 - - + -
389H CYS* 4.1 26.5 - - - -
392H ALA* 4.2 12.3 - - + -
404H ALA* 4.2 15.0 - - + -
405H THR 3.2 13.4 + - - -
406H GLU* 2.7 12.5 + - - +
408H ASP* 1.3 72.3 - - - +
410H LEU* 1.3 54.1 + - - +
412H ALA* 3.0 4.1 + - - +
413H VAL* 2.5 42.3 + - - +
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Residues in contact with LEU 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372H LEU* 4.1 13.2 - - + -
373H LEU* 3.1 34.1 - - + -
376H LEU* 4.2 8.7 - - + -
406H GLU* 2.7 42.3 + - + +
407H LYS* 2.9 25.5 + - + +
409H PHE* 1.3 72.6 - - - +
411H GLU* 1.3 52.2 + - + +
413H VAL* 3.0 4.8 + - - +
414H ASN* 2.6 47.8 + - - +
207l GLU* 5.1 18.4 - - + -
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Residues in contact with GLU 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395H PHE* 3.5 35.8 - - + -
407H LYS* 2.5 46.0 + - + +
408H ASP* 4.0 10.4 - - - +
410H LEU* 1.3 71.0 - - + +
412H ALA* 1.3 52.7 + - - +
414H ASN* 2.9 7.3 + - - +
415H LYS* 2.2 44.1 + - + +
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Residues in contact with ALA 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H VAL* 3.1 30.7 - - + +
391H GLU* 3.8 25.8 - - + -
392H ALA* 4.1 3.6 - - - +
395H PHE* 4.5 2.2 - - + -
408H ASP 3.1 14.6 + - - +
409H PHE* 3.0 6.8 + - - +
411H GLU* 1.3 77.3 - - - +
413H VAL* 1.3 53.5 + - - +
415H LYS* 3.7 8.3 - - - -
416H VAL* 2.5 38.1 + - - +
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Residues in contact with VAL 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H PHE* 4.9 3.1 - - + -
373H LEU* 3.6 33.0 - - + +
376H LEU* 4.0 28.9 - - + +
377H CYS* 5.2 0.9 - - - -
388H VAL* 3.9 14.1 - - + -
409H PHE 2.5 20.1 + - - +
410H LEU* 3.2 9.9 - - - +
412H ALA* 1.3 71.0 - - - +
414H ASN* 1.3 68.8 + - - +
417H ILE* 2.9 62.3 + - + +
418H LYS* 5.6 2.2 - - - +
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Residues in contact with ASN 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376H LEU* 5.6 5.5 - - - +
410H LEU* 2.6 28.1 + - - +
411H GLU* 3.6 5.1 - - - +
413H VAL* 1.3 79.8 - - - +
415H LYS* 1.3 61.5 - - - +
416H VAL 3.4 0.2 - - - -
418H LYS* 3.4 47.8 + - + +
419H SER* 3.6 4.3 + - - -
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Residues in contact with LYS 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391H GLU* 4.1 13.4 + - - +
395H PHE* 3.6 29.6 - - + -
398H ARG* 4.2 6.9 - - - +
411H GLU* 2.2 35.6 + - + +
412H ALA* 3.6 6.3 - - - +
414H ASN* 1.3 71.5 - - - +
416H VAL* 1.3 60.3 + - + +
419H SER* 3.0 31.9 - - - +
420H TYR* 3.2 28.2 + - + -
196I GLU* 3.0 29.3 + - - +
349I ARG* 5.0 1.0 - - - +
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Residues in contact with VAL 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H GLU* 4.3 19.3 - - + +
387H SER* 2.7 42.4 - - - +
388H VAL* 4.1 6.5 - - + +
391H GLU* 3.8 27.8 - - + +
412H ALA 2.5 22.1 + - - +
415H LYS* 1.3 73.1 - - - +
417H ILE* 1.3 80.3 + - + +
420H TYR* 2.8 39.6 + - + +
344I PRO* 5.8 0.9 - - + -
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Residues in contact with ILE 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376H LEU 4.3 13.0 - - - +
377H CYS* 4.5 16.6 - - + -
378H PRO* 5.8 4.9 - - + -
380H SER* 4.8 12.6 - - - +
384H GLU* 4.1 18.1 - - + +
388H VAL* 4.7 8.5 - - + -
413H VAL* 2.9 46.8 + - + +
416H VAL* 1.3 99.8 - - + +
418H LYS* 1.3 82.7 + - + +
420H TYR 3.1 3.5 - - - +
421H ALA* 3.1 15.8 + - + -
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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