Contacts of the helix formed by residues 370 - 384 (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 ASN 370 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369X PHE* 1.3 76.4 - - - +
371X ARG* 1.3 67.5 + - - +
372X ALA* 3.4 29.5 - - + +
373X ASP* 3.1 21.2 + - + +
374X SER* 2.9 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369X PHE 3.6 2.6 + - - -
370X ASN* 1.3 75.7 - - - +
372X ALA* 1.3 64.2 + - - +
374X SER* 3.1 12.5 + - - -
375X ASP* 3.0 54.0 + - - +
421X GLU* 4.1 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370X ASN* 3.1 18.7 - - + +
371X ARG* 1.3 80.0 - - - +
373X ASP* 1.3 63.1 + - - +
375X ASP* 3.2 17.4 - - - +
376X ALA* 3.2 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369X PHE* 4.5 6.5 - - + -
370X ASN* 3.1 27.3 + - + +
372X ALA* 1.3 78.7 - - - +
374X SER* 1.3 63.2 + - - +
376X ALA* 3.3 6.1 + - - +
377X LEU* 3.0 29.4 + - + +
463X PRO* 5.8 0.5 - - - +
465X ILE* 4.3 15.9 - - - +
466X ALA* 4.3 17.0 - - + +
469X ILE* 3.7 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369X PHE* 3.7 28.9 - - - -
370X ASN 2.9 13.0 + - - -
371X ARG* 3.1 18.5 + - - -
373X ASP* 1.3 76.5 - - - +
375X ASP* 1.3 68.2 + - - +
377X LEU* 3.1 11.7 + - - +
378X ALA 2.9 22.2 + - - -
420X TYR* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 375 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371X ARG* 3.0 54.4 + - - +
372X ALA* 3.2 10.9 + - - +
374X SER* 1.3 82.0 + - - +
376X ALA* 1.3 60.1 + - - +
378X ALA* 3.5 13.1 - - + +
379X ASN* 3.0 31.1 + - - +
382X ARG* 4.9 0.2 + - - -
420X TYR 5.0 1.8 - - - +
421X GLU* 4.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 376 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372X ALA 3.2 16.8 + - - +
373X ASP* 3.6 5.8 - - - +
374X SER 3.2 0.8 - - - -
375X ASP* 1.3 79.3 + - - +
377X LEU* 1.3 67.2 + - + +
379X ASN* 3.2 13.7 + - - +
380X VAL* 3.2 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373X ASP* 3.0 20.6 + - + +
374X SER* 3.2 9.4 - - - +
376X ALA* 1.3 75.4 - - + +
378X ALA* 1.3 62.6 + - - +
380X VAL* 3.4 12.6 + - + -
381X TRP* 3.4 8.8 + - - -
420X TYR* 4.0 24.9 - - + -
456X TYR* 2.8 30.8 + - - +
460X LEU* 4.3 12.8 - - + -
463X PRO* 4.5 6.1 - - + -
466X ALA* 3.8 30.1 - - + -
469X ILE* 4.0 14.1 - - + -
470X VAL* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374X SER 2.9 7.1 + - - +
375X ASP* 3.5 15.3 - - - +
377X LEU* 1.3 73.9 - - - +
379X ASN* 1.3 64.4 + - - +
381X TRP* 3.1 9.9 + - - +
382X ARG* 2.9 29.8 + - - +
417X ILE* 4.0 11.8 - - + +
420X TYR* 3.8 26.5 - - + +
421X GLU* 4.3 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 379 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375X ASP* 3.0 24.0 + - - +
376X ALA* 3.2 16.4 + - - +
378X ALA* 1.3 75.5 - - - +
380X VAL* 1.3 62.7 + - + +
382X ARG* 3.0 26.0 + - - +
383X SER* 3.0 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376X ALA 3.2 14.8 + - - +
377X LEU* 3.6 15.0 - - + +
378X ALA 3.3 0.4 - - - -
379X ASN* 1.3 75.4 - - + +
381X TRP* 1.3 60.8 + - - +
383X SER* 2.7 25.0 + - - +
384X ILE* 3.2 16.5 + - + +
456X TYR* 3.7 21.1 - - + -
459X SER* 4.9 2.7 - - - +
460X LEU* 3.7 23.6 - - + -
461X GLY 4.7 8.3 - - - +
463X PRO* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 381 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377X LEU 3.4 5.6 + - - -
378X ALA 3.1 8.0 + - - +
380X VAL* 1.3 78.2 - - - +
382X ARG* 1.3 63.4 + - - +
384X ILE* 3.1 21.4 + - + +
389X MET* 4.2 21.1 - - + -
409X VAL* 5.0 0.7 - - + -
412X VAL* 4.0 19.5 - - + -
413X ARG* 3.1 54.1 + - + +
416X SER* 3.4 29.9 - - - -
417X ILE* 3.7 16.6 - - + -
420X TYR* 3.6 24.8 - + - -
452X THR* 4.3 13.0 - - + -
453X LEU* 4.4 8.5 - - + -
456X TYR* 3.4 58.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 382 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375X ASP 4.9 0.2 + - - -
378X ALA* 2.9 12.9 + - - +
379X ASN* 3.0 43.1 + - - +
381X TRP* 1.3 76.0 - - - +
383X SER* 1.3 59.6 + - - +
384X ILE 3.5 1.6 + - - +
413X ARG* 3.1 29.2 + - - +
417X ILE* 3.9 20.8 - - + +
421X GLU* 2.5 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 383 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379X ASN 3.0 10.4 + - - -
380X VAL* 2.7 27.0 + - - +
382X ARG* 1.3 75.0 - - - +
384X ILE* 1.3 64.3 + - - +
385X ASP* 3.5 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 384 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380X VAL* 3.2 20.1 + - + +
381X TRP* 3.1 17.9 + - + +
382X ARG 4.1 1.2 - - - +
383X SER* 1.3 81.5 + - - +
385X ASP* 1.3 73.9 + - - +
386X ALA* 3.6 2.3 + - - +
389X MET* 3.9 37.2 - - + -
409X VAL* 5.7 0.4 - - + -
413X ARG* 3.1 33.3 + - - -
456X TYR* 3.7 29.4 - - + -
459X SER* 4.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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