Contacts of the helix formed by residues 405 - 423 (chain X) in PDB entry 3FEW
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 VAL 405 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390X ALA* 3.9 21.3 - - + +
393X LEU* 5.0 11.2 - - + -
400X PHE* 3.9 24.0 - - + +
401X LYS* 4.5 7.4 - - + -
402X PHE* 3.4 34.8 - - + +
403X ALA* 4.9 2.9 - - + -
404X ASP* 1.3 76.4 + - - +
406X VAL* 1.3 79.9 - - + +
407X MET 3.1 2.5 - - - -
408X LYS* 3.2 13.8 + - + +
409X VAL* 3.3 11.8 + - + +
448X VAL* 4.8 16.4 - - + -
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Residues in contact with VAL 406 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386X ALA* 3.9 11.2 - - + +
387X GLN* 3.5 61.5 - - + +
390X ALA* 4.0 15.3 - - + -
404X ASP 3.9 7.2 - - - +
405X VAL* 1.3 90.5 - - + +
407X MET* 1.3 53.4 + - + +
409X VAL* 3.1 3.4 + - - +
410X GLU* 2.7 38.2 + - + +
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Residues in contact with MET 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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404X ASP* 4.8 25.8 - - + +
405X VAL 3.1 1.7 - - - +
406X VAL* 1.3 80.6 - - + +
408X LYS* 1.3 60.8 + - + +
410X GLU* 3.6 6.9 + - - +
411X LYS* 3.2 35.8 + - + +
431X GLU* 5.5 0.2 - - - -
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Residues in contact with LYS 408 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402X PHE* 3.4 37.5 - - + -
404X ASP* 4.1 18.8 + - + +
405X VAL* 3.2 11.2 + - + +
407X MET* 1.3 74.8 - - + +
409X VAL* 1.3 61.5 + - - +
411X LYS* 3.5 4.1 + - - +
412X VAL* 3.0 33.5 + - - +
431X GLU* 4.9 0.9 - - - +
435X TRP* 3.6 62.3 - - + +
438X SER* 6.0 1.2 - - - -
440X ILE* 3.8 25.1 - - + +
448X VAL* 4.4 12.1 - - + -
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Residues in contact with VAL 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381X TRP* 5.0 0.6 - - + -
384X ILE* 5.7 0.7 - - + -
386X ALA* 3.8 29.2 - - + +
389X MET* 3.9 25.1 - - + -
390X ALA* 4.3 12.8 - - + +
393X LEU* 3.9 28.7 - - + -
405X VAL* 3.3 11.4 + - + +
406X VAL 3.1 7.8 + - - +
408X LYS* 1.3 76.8 - - + +
410X GLU* 1.3 55.7 + - - +
412X VAL* 3.0 3.1 + - - +
413X ARG* 2.7 36.0 + - + +
448X VAL* 5.6 1.3 - - + -
452X THR* 4.0 17.2 - - + +
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Residues in contact with GLU 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386X ALA* 4.1 19.3 - - + -
406X VAL* 2.7 22.8 + - + +
407X MET* 3.9 7.2 - - - +
408X LYS 3.4 0.2 - - - -
409X VAL* 1.3 72.8 - - - +
411X LYS* 1.3 59.4 - - + +
413X ARG* 3.4 11.9 + - - +
414X GLU* 3.0 31.5 + - - +
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Residues in contact with LYS 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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407X MET* 3.2 23.8 + - + +
408X LYS 3.8 3.6 - - - +
409X VAL 3.2 0.6 - - - -
410X GLU* 1.3 76.0 - - + +
412X VAL* 1.3 64.4 + - - +
414X GLU* 3.9 28.3 + - + +
415X LYS* 3.0 40.6 + - + +
431X GLU* 3.4 41.3 - - + +
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Residues in contact with VAL 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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381X TRP* 4.0 6.3 - - + -
408X LYS 3.0 20.4 + - - +
409X VAL 3.0 5.8 + - - +
411X LYS* 1.3 74.3 - - - +
413X ARG* 1.3 62.7 + - - +
416X SER* 2.8 35.4 + - - +
428X LEU* 4.1 14.3 - - + +
431X GLU* 5.3 2.0 - - + -
432X VAL* 5.8 0.4 - - + -
435X TRP* 3.9 24.7 - - + -
449X PHE* 4.5 11.9 - - + -
452X THR* 3.9 23.8 - - + +
453X LEU* 3.5 31.4 - - + -
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Residues in contact with ARG 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381X TRP* 3.1 41.8 + - + +
382X ARG* 3.1 33.0 + - - +
384X ILE* 3.1 31.2 + - - -
386X ALA* 4.8 14.4 - - - +
409X VAL* 2.7 18.4 + - + +
410X GLU* 3.4 16.2 + - - +
412X VAL* 1.3 74.1 - - - +
414X GLU* 1.3 63.1 + - - +
416X SER* 3.4 1.9 + - - -
417X ILE* 3.1 42.6 + - + +
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Residues in contact with GLU 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 GLU* 3.0 21.1 + - - +
411X LYS* 3.6 32.8 + - - +
413X ARG* 1.3 84.0 - - - +
415X LYS* 1.3 85.3 + - + +
417X ILE* 3.7 13.9 - - + +
418X GLU* 3.3 21.3 + - - +
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Residues in contact with LYS 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411X LYS* 3.0 30.8 + - - +
414X GLU* 1.3 102.8 - - + +
416X SER* 1.3 60.7 + - - +
417X ILE 3.4 0.4 - - - -
418X GLU* 3.4 24.0 - - - +
419X GLY* 2.9 22.9 + - - -
424X ASN 4.8 1.7 - - - +
427X PRO* 3.8 29.0 + - + +
428X LEU* 3.8 34.5 + - + +
431X GLU* 4.5 17.6 + - + +
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Residues in contact with SER 416 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381X TRP* 3.4 36.2 - - - -
412X VAL* 2.8 28.6 + - - +
413X ARG 3.8 0.7 - - - -
415X LYS* 1.3 74.7 - - - +
417X ILE* 1.3 55.4 + - - +
419X GLY* 3.1 0.7 + - - -
420X TYR* 2.7 44.5 + - - -
425X TRP* 3.9 15.6 - - - -
428X LEU* 4.1 13.5 - - - +
453X LEU* 4.7 2.3 - - - +
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Residues in contact with ILE 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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378X ALA* 4.0 15.9 - - + +
381X TRP* 3.7 15.5 - - + -
382X ARG* 3.9 37.5 - - + +
413X ARG* 3.1 42.2 + - + +
414X GLU* 3.7 11.2 - - + +
416X SER* 1.3 76.2 - - - +
418X GLU* 1.3 57.6 + - - +
420X TYR* 3.2 1.5 + - - +
421X GLU* 2.8 56.9 + - + +
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Residues in contact with GLU 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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414X GLU 3.3 10.8 + - - +
415X LYS* 3.4 30.3 - - - +
417X ILE* 1.3 80.5 - - - +
419X GLY* 1.3 55.1 + - - +
421X GLU* 4.7 5.2 - - - -
422X THR* 2.7 54.8 + - + +
424X ASN* 4.2 12.6 + - - +
427X PRO* 3.5 24.6 - - + +
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Residues in contact with GLY 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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369X PHE* 6.0 0.9 - - - -
415X LYS 2.9 15.7 + - - -
416X SER 3.1 4.0 + - - -
418X GLU* 1.3 74.6 - - - +
420X TYR* 1.3 56.4 + - - +
423X GLY* 2.8 32.4 + - - -
424X ASN 3.6 16.4 + - - -
425X TRP* 3.5 27.9 - - - -
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Residues in contact with TYR 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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369X PHE* 4.3 15.1 - + - -
374X SER* 3.1 43.0 + - - +
377X LEU* 4.0 26.0 - - + -
378X ALA* 3.8 17.9 - - + -
381X TRP* 3.6 34.7 + + - -
416X SER* 2.7 27.5 + - - +
417X ILE 3.9 0.2 - - - +
419X GLY* 1.3 73.7 - - - +
421X GLU* 1.3 60.8 + - - +
423X GLY* 4.4 1.7 + - - -
425X TRP* 3.7 23.6 - + - -
456X TYR* 4.1 9.6 - - - -
469X ILE* 4.9 0.2 - - + -
470X VAL* 3.5 25.1 - - - +
473X LEU* 3.8 20.8 - - + +
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Residues in contact with GLU 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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371X ARG* 4.1 19.4 + - - +
374X SER* 5.1 0.4 - - - -
375X ASP* 4.9 11.2 - - + -
378X ALA* 4.3 11.4 - - + -
382X ARG* 2.5 34.5 + - - -
417X ILE* 2.8 32.9 + - - +
418X GLU* 4.1 1.8 - - - +
420X TYR* 1.3 74.7 - - - +
422X THR* 1.3 71.0 - - + +
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Residues in contact with THR 422 (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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418X GLU* 2.7 37.2 + - + +
421X GLU* 1.3 87.8 - - + +
423X GLY* 1.3 58.7 + - - +
424X ASN* 3.1 26.2 + - - +
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Residues in contact with GLY 423 (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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362X LEU* 4.8 5.2 - - - +
369X PHE* 6.4 2.2 - - - -
419X GLY 2.8 17.4 + - - -
420X TYR 4.4 1.4 + - - -
421X GLU 3.7 1.2 - - - -
422X THR* 1.3 75.6 - - - +
424X ASN* 1.3 56.4 + - - +
425X TRP* 3.3 21.8 + - - -
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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
------------------------------------------------------------
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