Contacts of the helix formed by residues 389 - 405 (chain B) in PDB entry 1F1J
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 GLY 389 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASN* 1.3 72.3 - - - +
390B THR* 1.3 62.3 + - - +
391B ASP 3.4 0.4 - - - -
392B LYS* 3.4 9.7 + - - +
393B ASP* 3.4 15.7 + - - -
533B ARG* 4.8 2.0 - - - -
534B SER 4.1 5.8 - - - -
535B PRO* 3.2 21.2 + - - -
538B GLY* 3.6 13.4 - - - -
1202B SO4 2.8 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN* 2.8 25.2 + - - +
376B LYS* 3.3 38.4 - - + -
387B ARG* 2.9 49.8 + - - +
388B ASN 3.3 0.6 + - - -
389B GLY* 1.3 76.2 - - - +
391B ASP* 1.3 65.5 + - - +
393B ASP* 2.9 13.1 + - - +
394B ALA 2.9 24.9 + - - -
442B LEU* 4.0 5.9 - - - +
533B ARG* 4.7 1.7 - - - +
1202B SO4 3.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN* 3.1 25.3 + - - +
376B LYS* 3.6 20.1 + - - +
390B THR* 1.3 71.0 - - - +
392B LYS* 1.3 60.8 + - - +
394B ALA* 3.2 4.1 + - - +
395B GLU* 3.0 25.1 + - - +
1202B SO4 2.7 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLY* 3.5 7.5 - - - +
391B ASP* 1.3 76.7 - - - +
393B ASP* 1.3 58.4 + - - +
395B GLU* 3.4 8.6 + - - +
396B ALA* 2.9 30.5 + - - +
535B PRO 2.9 24.4 + - - -
536B GLY* 3.0 32.2 - - - +
537B ARG* 4.1 16.6 - - - +
538B GLY 4.5 0.4 - - - +
1202B SO4 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 4.9 2.9 + - - -
389B GLY 3.4 9.5 + - - +
390B THR* 2.9 16.2 + - - +
392B LYS* 1.3 78.5 - - - +
394B ALA* 1.3 60.4 + - - +
396B ALA* 3.4 2.4 + - - +
397B LEU* 2.9 36.6 + - - +
442B LEU* 4.3 11.3 - - + +
484B GLN* 4.9 1.0 - - - +
533B ARG* 5.1 0.9 - - - -
537B ARG 4.4 1.6 - - - +
538B GLY* 3.4 7.8 - - - -
539B SER* 2.9 47.9 + - - +
542B VAL* 3.2 28.2 - - + +
543B GLN* 4.6 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 4.2 5.7 - - + +
374B ASN* 3.6 39.0 - - + +
390B THR 2.9 5.8 + - - +
391B ASP* 3.6 7.6 - - - +
393B ASP* 1.3 75.6 - - - +
395B GLU* 1.3 57.1 + - - +
397B LEU* 4.0 3.6 - - - +
398B PHE* 2.9 30.7 + - - +
410B VAL* 4.6 13.4 - - + +
442B LEU* 4.0 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASP 3.0 16.7 + - - +
392B LYS* 3.6 7.5 - - - +
394B ALA* 1.3 74.7 - - - +
396B ALA* 1.3 77.0 + - - +
398B PHE* 3.2 11.6 + - + -
399B LYS* 2.9 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LYS 2.9 17.7 + - - +
393B ASP* 3.8 5.4 - - - +
395B GLU* 1.3 85.2 + - - +
397B LEU* 1.3 58.1 + - - +
399B LYS* 3.8 4.5 - - - +
400B CYS* 2.9 31.2 + - - +
542B VAL* 4.9 2.9 - - + -
546B CYS* 3.6 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 3.9 14.4 - - + -
393B ASP 2.9 21.2 + - - +
394B ALA* 4.0 0.9 - - - +
396B ALA* 1.3 74.5 - - - +
398B PHE* 1.3 56.6 + - - +
400B CYS* 4.1 0.4 - - - -
401B PHE* 2.7 53.1 + - + +
440B ILE* 3.5 33.0 - - + -
442B LEU* 3.8 23.8 - - + -
542B VAL* 3.8 17.0 - - + -
545B LEU* 3.8 26.0 - - + -
546B CYS* 3.7 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ILE* 3.7 9.3 - - - +
394B ALA 2.9 17.4 + - - +
395B GLU* 3.5 17.7 - - + -
397B LEU* 1.3 74.5 - - - +
399B LYS* 1.3 89.8 + - + +
402B ARG* 2.9 68.5 + - - +
408B VAL* 3.7 29.2 - - + +
410B VAL* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU* 2.9 53.3 + - - +
396B ALA* 3.8 4.5 - - - +
398B PHE* 1.3 99.8 - - + +
400B CYS* 1.3 62.9 + - - +
402B ARG* 3.1 24.0 + - - +
403B SER* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ALA 2.9 20.8 + - - +
397B LEU* 3.6 3.4 - - - +
399B LYS* 1.3 77.7 - - - +
401B PHE* 1.3 61.6 + - + +
403B SER* 3.6 8.3 + - - -
404B LEU* 3.4 21.2 + - - +
546B CYS* 3.9 25.6 - - + -
549B LEU* 3.5 44.2 - - - -
550B GLU* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B CYS* 3.4 32.3 - - + -
397B LEU* 2.7 39.4 + - + +
398B PHE* 4.2 1.1 - - - +
400B CYS* 1.3 75.9 - - + +
402B ARG* 1.3 61.5 + - - +
404B LEU* 3.3 8.3 + - + -
405B GLY 3.3 2.8 + - - -
406B PHE* 3.1 55.3 + + + +
408B VAL* 4.2 6.7 - - + -
438B ALA* 4.5 5.2 - - + -
440B ILE* 3.8 24.5 - - + -
480B LEU* 5.8 0.2 - - + -
482B PHE* 3.9 31.4 - + - -
545B LEU* 4.5 2.2 - - + -
549B LEU* 3.6 29.8 - - + -
601B PHE* 5.7 3.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B PHE* 2.9 56.6 + - - +
399B LYS* 3.3 28.7 + - - +
401B PHE* 1.3 73.5 - - - +
403B SER* 1.3 62.7 + - - +
405B GLY* 2.8 23.6 + - - -
406B PHE 3.9 7.9 + - - +
408B VAL* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LYS 3.0 14.6 + - - -
400B CYS* 3.6 12.4 - - - -
401B PHE 3.4 0.2 - - - -
402B ARG* 1.3 78.5 + - - +
404B LEU* 1.3 61.3 + - - +
405B GLY* 3.5 0.3 + - - -
554B LYS* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 3.3 14.3 - - + +
400B CYS* 3.4 14.5 + - - +
401B PHE* 3.3 18.1 + - + +
402B ARG 3.1 0.6 - - - -
403B SER* 1.3 80.7 - - - +
405B GLY* 1.3 56.9 + - - +
406B PHE* 3.8 25.4 - - + -
549B LEU* 4.2 27.4 - - + +
553B GLY* 3.6 36.1 - - - +
554B LYS* 4.0 20.2 - - + +
601B PHE* 4.1 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 5.4 1.7 - - - +
367B LEU* 3.3 24.7 + - - +
368B GLY 4.3 1.0 + - - -
402B ARG 2.8 11.4 + - - -
403B SER 3.2 0.8 - - - -
404B LEU* 1.3 81.4 - - - +
406B PHE* 1.3 65.4 + - - +
407B ASP* 4.1 4.9 + - - +
----------------------------------------------------------
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