Contacts of the helix formed by residues 405 - 417 (chain X) in PDB entry 3F6B
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 PHE 405 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52X GLY* 4.8 7.3 - - - -
55X ASP* 3.6 28.5 - - + -
56X GLY* 4.8 1.8 - - - -
59X GLN* 3.7 21.3 - - - -
84X ASN* 3.7 29.6 - - + +
373X LEU* 4.4 3.6 - - + -
375X GLU* 3.1 6.7 + - - +
396X TYR* 3.9 28.5 - + + -
397X PHE* 4.2 2.9 - - - -
398X CYS* 3.6 30.7 - - + -
399X ALA 5.9 1.1 - - - -
402X GLY 3.8 0.4 + - - -
403X LEU 3.5 1.2 - - - -
404X GLY* 1.3 78.3 - - - +
406X ALA* 1.4 68.6 + - + +
407X LEU 3.3 0.8 + - - -
408X PRO* 3.4 4.1 - - - +
409X ALA* 2.8 55.4 + - + +
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Residues in contact with ALA 406 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373X LEU* 3.5 23.6 - - + +
374X ASN 4.2 7.4 - - - +
375X GLU* 2.9 38.0 + - + +
405X PHE* 1.4 84.1 - - + +
407X LEU* 1.3 58.4 + - - +
410X ALA* 2.9 33.1 + - - +
424X ALA* 4.4 0.2 - - - +
426X ILE* 4.2 11.9 - - + -
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Residues in contact with LEU 407 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375X GLU* 5.1 2.0 + - - +
404X GLY* 5.0 1.7 - - - -
406X ALA* 1.3 80.7 - - - +
408X PRO* 1.3 69.3 - - + +
410X ALA 3.5 4.5 + - - -
411X ILE* 3.6 12.0 - - + +
426X ILE* 3.7 22.7 - - + +
430X SER 6.0 0.7 - - - +
431X ALA* 3.8 31.2 - - + +
434X SER* 3.9 9.6 - - - +
435X ILE* 4.3 14.6 - - + -
437X ALA* 3.8 22.0 - - + -
438X LEU* 3.8 24.2 - - + +
450X PHE* 3.6 31.0 - - + -
452X ILE* 5.1 5.4 - - + -
518X LEU* 5.8 0.4 - - + -
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Residues in contact with PRO 408 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X ALA 4.3 0.7 - - - +
49X CYS* 3.5 26.5 - - - +
52X GLY* 4.1 9.9 - - - -
53X ILE* 3.3 21.1 - - + +
404X GLY 3.2 26.7 - - - +
405X PHE 3.4 7.9 - - - +
407X LEU* 1.3 91.9 - - + +
409X ALA* 1.3 63.2 + - - +
411X ILE* 3.0 13.0 + - + +
412X GLY 3.1 8.7 + - - -
434X SER* 3.6 18.4 - - - +
437X ALA* 3.7 18.2 - - + -
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Residues in contact with ALA 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X GLY 3.2 19.4 + - - +
56X GLY* 3.6 7.8 - - - -
373X LEU* 3.9 7.6 - - + -
405X PHE* 2.8 57.9 + - + +
408X PRO* 1.3 74.3 - - - +
410X ALA* 1.3 57.8 + - - +
412X GLY* 3.1 2.1 + - - +
413X VAL* 2.8 32.2 + - + +
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Residues in contact with ALA 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373X LEU* 3.5 27.3 - - + +
406X ALA 2.9 19.7 + - - +
407X LEU 3.7 4.9 - - - +
408X PRO 3.1 0.2 - - - -
409X ALA* 1.3 76.3 - - - +
411X ILE* 1.3 55.9 + - - +
413X VAL* 4.4 0.4 - - - -
414X GLN* 3.1 21.5 + - - +
422X VAL* 3.6 5.7 - - + +
424X ALA* 3.8 12.1 - - + -
448X THR* 3.2 30.4 + - + -
450X PHE* 4.5 0.9 - - + -
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Residues in contact with ILE 411 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X ILE* 4.3 8.5 - - + -
407X LEU 3.6 16.6 - - - +
408X PRO* 3.0 7.7 + - + +
410X ALA* 1.3 76.1 - - - +
412X GLY* 1.3 60.6 + - - +
414X GLN 3.3 0.9 + - - -
415X LEU* 3.0 27.5 + - - +
437X ALA* 3.1 40.4 - - + +
440X THR* 4.3 11.0 - - + -
441X ALA* 3.9 20.9 - - + +
446X ILE* 3.6 33.4 - - + +
448X THR* 3.6 7.4 - - - +
450X PHE* 3.8 20.2 - - + -
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Residues in contact with GLY 412 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X ILE* 3.3 32.6 - - - +
57X TYR* 3.5 20.0 - - - -
408X PRO 3.1 7.7 + - - -
409X ALA 3.1 5.5 + - - -
411X ILE* 1.3 75.1 - - - +
413X VAL* 1.3 63.7 + - - +
415X LEU* 3.3 7.3 + - - +
416X ALA 2.9 18.4 + - - -
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Residues in contact with VAL 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X GLY* 3.5 25.1 - - - +
60X ALA* 4.0 12.6 - - + -
371X ILE* 3.7 41.7 - - + -
373X LEU* 4.5 5.8 - - + -
396X TYR* 4.0 26.7 - - + -
409X ALA* 2.8 26.1 + - + +
410X ALA* 4.0 5.8 - - - +
412X GLY* 1.3 71.8 - - - +
414X GLN* 1.3 59.7 + - - +
416X ALA* 3.1 3.6 + - - +
417X GLU* 3.0 26.0 + - - +
422X VAL* 3.8 5.2 - - + -
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Residues in contact with GLN 414 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410X ALA 3.1 10.0 + - - +
411X ILE 3.3 0.2 + - - -
412X GLY 3.2 0.2 - - - -
413X VAL* 1.3 76.4 - - - +
415X LEU* 1.3 62.9 + - - +
417X GLU 3.0 30.1 + - - -
418X PRO* 3.4 15.6 + - - +
420X ARG 2.9 23.7 + - - +
421X GLN* 3.4 14.8 + - - +
422X VAL* 2.9 31.0 + - + +
446X ILE* 3.6 20.0 - - + -
447X PRO* 3.7 24.2 - - + +
448X THR* 3.3 22.2 - - - +
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Residues in contact with LEU 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X PHE* 3.9 24.0 - - + -
40X ARG* 4.2 27.4 + - - +
42X ILE* 4.3 20.9 - - + -
53X ILE* 5.3 1.6 - - + -
57X TYR* 3.9 23.8 - - + -
411X ILE 3.0 13.4 + - - +
412X GLY* 3.5 9.9 - - - +
413X VAL 3.2 0.2 - - - -
414X GLN* 1.3 78.6 - - - +
416X ALA* 1.3 59.7 + - - +
418X PRO* 3.8 10.6 - - - +
444X TYR* 6.1 0.2 - - + -
446X ILE* 4.1 28.6 - - + +
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Residues in contact with ALA 416 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X TYR* 3.7 27.5 - - + +
60X ALA* 3.7 24.5 - - + -
61X SER* 4.1 10.6 - - - +
412X GLY 2.9 13.0 + - - +
413X VAL 3.1 8.3 + - - +
415X LEU* 1.3 77.3 - - - +
417X GLU* 1.3 64.2 + - - +
418X PRO* 3.4 7.7 - - - +
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Residues in contact with GLU 417 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X ALA* 4.1 24.2 - - + +
62X ARG* 5.3 4.3 + - - -
371X ILE* 3.8 25.8 - - + -
413X VAL 3.0 13.7 + - - +
414X GLN* 3.0 21.5 + - - -
416X ALA* 1.3 85.1 - - + +
418X PRO* 1.4 64.4 - - - +
419X GLU* 3.0 6.1 + - - +
420X ARG* 3.1 36.0 + - + +
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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