Contacts of the helix formed by residues 368 - 379 (chain B) in PDB entry 5F2R
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 ILE 368 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE* 3.9 32.5 - - + -
296B LYS* 5.0 1.3 - - + -
300B SER* 3.7 4.0 - - - +
327B PHE* 4.0 33.0 - - + -
328B GLU* 5.7 0.9 - - + -
335B PHE* 4.1 11.9 - - + -
365B SER* 3.2 21.8 - - - +
366B THR 3.1 0.6 - - - -
367B ARG* 1.3 76.0 - - - +
369B PRO* 1.3 71.9 - - + +
370B LYS* 3.8 13.2 - - + +
371B ILE* 2.9 26.8 + - + +
372B GLN* 3.1 12.0 + - - +
501B ACP 3.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU 4.4 2.9 - - - +
300B SER* 3.6 29.6 - - - +
324B ARG* 4.0 30.7 - - + +
328B GLU* 5.2 1.6 - - - +
367B ARG 3.1 9.6 - - - +
368B ILE* 1.3 85.6 - - + +
370B LYS* 1.3 56.8 + - - +
372B GLN* 3.3 15.3 + - - +
373B GLN* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 3.6 39.1 + - + +
332B MET* 3.8 22.2 - - + +
335B PHE* 3.6 30.3 - - + -
368B ILE* 3.2 4.7 - - + +
369B PRO* 1.3 79.0 - - - +
371B ILE* 1.3 57.9 + - - +
373B GLN* 2.9 35.7 + - - +
374B LEU* 2.9 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 4.0 24.5 - - + -
225B LEU* 3.8 19.5 - - + -
335B PHE* 3.4 43.7 - - + +
338B THR* 5.0 4.3 - - + +
339B MET* 5.0 1.1 - - + +
361B LEU* 5.6 0.4 - - + -
365B SER 3.6 16.6 - - - +
366B THR* 3.9 21.5 - - + -
368B ILE* 2.9 22.7 + - + +
370B LYS* 1.3 73.3 - - - +
372B GLN* 1.3 68.4 + - - +
374B LEU* 3.2 5.8 + - + +
375B VAL* 3.0 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 3.8 25.6 - - + +
366B THR 3.0 26.9 + - - +
367B ARG* 3.7 18.4 + - - +
368B ILE 3.1 5.7 + - - +
369B PRO* 3.5 13.3 - - - +
371B ILE* 1.3 78.0 - - - +
373B GLN* 1.3 63.1 + - - +
375B VAL* 3.3 3.6 + - - +
376B LYS* 3.0 24.0 + - - +
384B PRO* 5.7 3.7 - - + +
386B ARG* 4.6 20.1 + - - +
390B PRO* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PRO 2.9 13.8 + - - +
370B LYS* 2.9 45.2 + - - +
371B ILE 3.3 0.2 - - - -
372B GLN* 1.3 77.2 - - - +
374B LEU* 1.3 59.4 + - - +
376B LYS* 3.2 9.2 + - - +
377B GLU* 2.8 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B MET* 4.4 6.3 - - - -
335B PHE* 3.6 39.7 - - + -
336B ARG* 3.4 38.8 - - + +
339B MET* 3.6 19.4 - - + +
370B LYS* 2.9 41.4 + - + +
371B ILE* 3.2 4.7 + - + +
373B GLN* 1.3 73.9 - - + +
375B VAL* 1.3 58.1 + - - +
377B GLU* 3.5 19.8 + - + +
378B PHE* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PHE* 3.8 46.7 - - + -
339B MET* 4.0 8.3 - - + -
359B ILE* 3.9 22.0 - - + -
361B LEU* 3.9 24.7 - - + -
371B ILE* 3.0 22.0 + - + +
372B GLN 3.7 3.8 - - - +
374B LEU* 1.3 72.3 - - - +
376B LYS* 1.3 67.2 + - - +
378B PHE* 3.3 4.3 + - - +
379B PHE* 3.2 33.6 + - + -
384B PRO* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLN 3.0 16.8 + - - +
373B GLN* 3.5 8.5 - - - +
375B VAL* 1.3 79.3 - - - +
377B GLU* 1.3 60.9 + - + +
379B PHE 3.3 8.7 + - - -
381B GLY* 2.9 49.7 + - - +
382B LYS 3.6 20.9 + - - +
383B GLU* 3.5 36.4 + - - +
384B PRO* 4.9 6.9 - - + +
386B ARG* 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ARG* 5.1 3.1 + - - -
353B LYS* 5.2 0.3 + - - -
373B GLN* 2.8 52.5 + - + +
374B LEU* 3.8 23.8 - - + +
376B LYS* 1.3 75.3 - - + +
378B PHE* 1.3 65.4 - - - +
380B ASN* 3.2 18.3 + - - +
381B GLY 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B MET* 3.8 43.1 - - + -
342B VAL* 3.4 28.5 - - + -
343B GLN* 3.7 26.7 - - + -
346B LEU* 4.2 6.7 - - + -
353B LYS* 3.0 61.0 + - - +
374B LEU 2.9 17.9 + - - +
375B VAL* 3.3 5.8 + - - +
377B GLU* 1.3 75.4 - - - +
379B PHE* 1.3 84.9 + + + +
380B ASN* 3.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 4.0 24.0 - - + -
223B PHE* 6.0 0.7 - + - -
342B VAL* 3.9 17.0 - - + -
346B LEU* 4.7 2.5 - - + -
353B LYS* 4.1 26.7 - - + -
356B ILE* 3.8 24.9 - - + -
359B ILE* 3.3 39.0 - - + -
375B VAL* 3.2 36.0 + - + +
376B LYS 3.3 2.2 - - - +
377B GLU 3.2 0.2 - - - -
378B PHE* 1.3 102.0 - + + +
380B ASN* 1.3 70.1 + - - +
381B GLY 3.3 2.5 - - - -
382B LYS* 3.2 21.4 + - + +
----------------------------------------------------------
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