Contacts of the helix formed by residues 406 - 421 (chain X) in PDB entry 5G04
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 406 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247X HIS* 6.0 3.8 - - - -
279X ASP* 5.0 4.8 + - - +
282X PHE* 5.5 3.0 - - + -
283X ARG* 3.3 62.9 - - + +
310X VAL* 5.1 9.5 - - - +
373X VAL* 4.8 14.2 - - + +
374X GLN* 4.5 13.9 + - - -
403X ALA* 4.1 18.4 - - + +
404X PRO 3.3 11.5 + - - +
405X CYS* 1.3 81.7 - - - +
407X LEU* 1.3 63.6 + - - +
408X ASP* 3.3 4.5 - - + +
409X CYS* 2.9 38.7 + - + +
410X TYR* 2.9 11.2 - - - -
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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
----------------------------------------------------------
249X GLY 4.6 0.4 - - - +
251X ASN* 3.8 19.1 - - - +
283X ARG* 3.0 33.8 - - + +
284X ALA* 4.4 10.5 - - - +
285X GLY* 5.8 0.4 - - - -
405X CYS 4.3 9.9 - - - +
406X ARG* 1.3 70.4 - - - +
408X ASP* 1.3 63.2 + - - +
410X TYR* 3.3 10.9 + - - +
411X GLU* 3.2 22.6 + - - +
433X VAL* 5.8 1.6 - - - -
437X LEU* 3.5 31.0 - - + -
443X THR* 3.4 41.1 - - + +
447X LEU* 5.3 4.9 - - + +
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Residues in contact with ASP 408 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282X PHE* 3.8 30.7 - - + -
283X ARG* 5.5 3.5 + - - +
313X TYR* 4.2 20.5 + - - -
374X GLN* 3.9 11.5 + - - +
377X LEU* 4.4 14.1 - - + +
406X ARG* 5.0 4.0 - - + -
407X LEU* 1.3 79.3 - - - +
409X CYS* 1.3 61.2 + - - +
411X GLU* 3.0 45.8 + - - +
412X GLY* 3.4 5.0 + - - -
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Residues in contact with CYS 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377X LEU* 4.6 19.7 - - + +
396X PHE* 5.6 2.3 - - - -
399X ALA* 5.4 2.5 - - + +
400X ILE* 3.9 20.7 - - + +
403X ALA* 3.2 45.3 - - + -
406X ARG* 2.9 33.6 + - + +
408X ASP* 1.3 78.5 - - - +
410X TYR* 1.3 73.5 + - - +
412X GLY* 3.7 2.0 + - - -
413X LEU 3.6 14.0 + - - -
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Residues in contact with TYR 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400X ILE* 5.2 9.5 + - + -
403X ALA 4.2 2.9 + - - -
404X PRO* 3.7 8.7 - - - +
405X CYS* 3.1 35.9 + - - -
406X ARG 2.9 29.3 + - - -
407X LEU* 3.3 8.2 + - - +
408X ASP 3.2 0.4 - - - -
409X CYS* 1.3 84.3 - - - +
411X GLU* 1.3 64.1 + - - +
413X LEU* 3.4 19.3 + - + +
414X ILE* 3.1 26.3 + - - +
429X MET 5.6 1.6 - - - -
432X ASN 6.1 0.2 - - - -
433X VAL* 3.5 49.1 - - + -
436X THR* 4.6 9.9 - - + +
437X LEU* 4.9 3.8 - - + -
447X LEU* 5.0 4.3 - - + -
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Residues in contact with GLU 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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313X TYR* 5.2 1.7 + - - -
407X LEU 3.2 11.5 + - - +
408X ASP* 3.0 39.4 + - - +
410X TYR* 1.3 74.9 - - - +
412X GLY* 1.3 59.4 + - - +
414X ILE* 3.2 11.0 - - - +
415X GLU* 2.9 54.8 + - + +
447X LEU* 3.9 16.3 - - + +
477X LYS* 3.5 28.3 + - - +
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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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384X ARG* 4.6 5.4 - - - -
396X PHE* 4.3 19.7 - - - -
408X ASP 3.4 5.9 + - - -
409X CYS* 3.7 3.8 + - - -
410X TYR 3.4 0.4 - - - -
411X GLU* 1.3 82.0 - - - +
413X LEU* 1.3 63.7 + - - +
415X GLU* 3.8 5.8 - - - +
416X CYS* 3.0 33.5 + - - -
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Residues in contact with LEU 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765H ASP* 4.8 0.9 - - - +
396X PHE* 4.6 9.9 - - + +
397X ARG* 4.4 15.9 - - + +
400X ILE* 3.7 52.5 - - + -
409X CYS 3.6 4.8 + - - +
410X TYR* 3.4 19.2 + - + +
411X GLU 3.4 0.2 - - - -
412X GLY* 1.3 78.0 - - - +
414X ILE* 1.3 61.5 + - - +
416X CYS* 3.4 4.8 + - - +
417X TYR* 3.1 49.4 + - + -
429X MET* 3.8 33.7 - - + +
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Residues in contact with ILE 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 TYR 3.1 12.1 + - - +
411X GLU* 3.2 24.5 - - - +
413X LEU* 1.3 80.9 - - + +
415X GLU* 1.3 62.5 + - + +
417X TYR* 3.4 7.6 + - - +
418X LEU* 3.2 20.9 + - + +
426X ALA* 4.0 29.0 - - + +
429X MET* 5.3 6.3 - - + -
430X ALA* 4.8 7.0 - - + +
447X LEU* 3.7 26.9 - - + +
450X VAL* 4.2 17.5 - - + -
451X CYS* 3.4 30.3 - - - +
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Residues in contact with GLU 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384X ARG* 2.8 49.0 + - - +
411X GLU* 2.9 47.8 + - - +
412X GLY* 3.8 0.9 - - - +
414X ILE* 1.3 72.5 - - + +
416X CYS* 1.3 64.9 + - - +
418X LEU* 3.3 13.9 - - + +
419X ALA* 3.3 17.7 + - - +
450X VAL* 6.0 5.8 - - + -
481X LYS* 5.9 2.2 + - - +
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Residues in contact with CYS 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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384X ARG* 4.2 17.9 - - - +
389X VAL* 5.1 2.4 - - - +
392X ALA* 5.7 1.1 - - - -
393X ILE* 4.1 26.7 - - + +
396X PHE* 3.4 42.4 - - + -
412X GLY 3.0 24.0 + - - +
413X LEU* 3.6 6.1 - - - +
414X ILE 3.4 0.2 - - - -
415X GLU* 1.3 74.7 - - - +
417X TYR* 1.3 61.1 + - + +
419X ALA* 3.2 10.5 + - - +
420X SER* 3.0 25.7 + - - -
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Residues in contact with TYR 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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764H MET* 5.3 2.5 + - + -
765H ASP* 3.1 28.1 + - - -
393X ILE* 4.9 11.2 - - + -
397X ARG* 3.8 18.1 + - + -
413X LEU* 3.1 44.4 + - + -
414X ILE 3.8 7.2 - - - +
415X GLU 3.3 0.4 - - - -
416X CYS* 1.3 77.2 - - + +
418X LEU* 1.3 54.8 + - - +
420X SER* 3.1 10.0 + - - -
421X ASN 2.8 29.8 + - - -
422X SER* 3.1 41.3 + - - +
425X GLU* 3.5 27.2 + - + -
426X ALA* 4.4 4.0 - - + -
429X MET* 3.5 30.0 - - + -
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Residues in contact with LEU 418 (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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384X ARG* 6.2 0.7 - - - +
414X ILE* 3.2 13.8 + - + +
415X GLU* 3.3 16.2 - - + +
417X TYR* 1.3 74.4 - - - +
419X ALA* 1.3 61.9 + - + +
421X ASN* 3.1 22.1 + - - +
426X ALA* 5.1 3.2 - - + +
450X VAL* 5.2 18.8 - - + +
453X GLU* 6.6 0.2 - - + -
454X ASP* 3.8 36.3 - - + +
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Residues in contact with ALA 419 (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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384X ARG* 5.5 7.0 - - - +
389X VAL* 4.4 21.8 - - + +
415X GLU 3.3 7.8 + - - +
416X CYS* 3.2 13.1 + - - +
418X LEU* 1.3 82.6 - - + +
420X SER* 1.3 60.4 + - - +
421X ASN* 3.4 2.8 + - - +
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Residues in contact with SER 420 (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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389X VAL* 5.8 1.3 - - - -
393X ILE* 4.0 20.1 - - - +
416X CYS 3.0 13.2 + - - -
417X TYR* 3.1 17.5 + - - -
419X ALA* 1.3 75.0 - - - +
421X ASN* 1.3 67.1 + - - +
422X SER* 3.8 13.2 + - - -
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Residues in contact with ASN 421 (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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417X TYR 2.8 6.5 + - - -
418X LEU* 3.1 17.1 + - - +
419X ALA 3.2 2.7 - - - +
420X SER* 1.3 80.1 - - - +
422X SER* 1.3 56.5 + - - +
423X ILE* 3.2 26.5 + - - +
454X ASP* 4.1 7.4 - - - +
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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