Contacts of the helix formed by residues 367 - 379 (chain A) in PDB entry 6F0X
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 SER 367 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.5 27.4 - - - -
356A LEU* 4.1 3.5 - - - +
359A ILE* 3.8 17.5 - - - +
362A ILE 3.3 16.1 + - - -
364A ASN* 2.3 45.1 + - - -
366A VAL* 1.3 67.2 - - - +
368A LYS* 1.3 62.9 + - - -
369A LEU 3.3 1.8 - - - -
370A SER* 3.3 6.2 + - - -
371A LEU* 3.1 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU* 2.9 42.4 - - - +
364A ASN* 3.5 7.8 + - - +
365A ASN* 4.9 9.4 - - - +
366A VAL 3.2 2.2 - - - -
367A SER* 1.3 77.2 - - - +
369A LEU* 1.3 75.5 + - + +
371A LEU* 2.9 14.8 + - + +
372A LEU* 2.9 17.6 + - + +
408A GLU* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLN* 4.9 15.3 - - + -
349A GLN 5.3 7.2 - - - +
350A LEU* 5.1 14.1 - - + -
366A VAL 5.0 8.7 - - - +
367A SER 3.3 1.0 - - - -
368A LYS* 1.3 86.4 - - + +
370A SER* 1.3 59.2 + - - +
372A LEU* 3.2 10.9 + - + +
373A LEU* 2.9 27.4 + - - +
407A ILE* 4.2 17.0 - - + -
408A GLU* 3.0 44.4 - - + +
411A LEU* 3.8 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.6 5.9 - - - -
332A LEU* 5.3 0.5 - - - +
349A GLN 4.6 1.6 + - - -
350A LEU* 3.7 10.0 - - - +
351A LEU* 3.0 42.6 + - - +
356A LEU* 3.6 25.1 - - - +
366A VAL 5.4 0.2 + - - -
367A SER 3.3 9.2 + - - -
368A LYS 3.2 0.6 - - - -
369A LEU* 1.3 74.7 - - - +
371A LEU* 1.3 60.7 + - - +
373A LEU* 3.2 10.1 + - - +
374A ASN* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 4.0 15.5 - - + -
361A PHE* 3.4 59.7 - - + +
362A ILE 4.1 3.4 - - - +
363A GLU* 3.2 36.6 - - + +
367A SER* 3.1 14.7 + - - +
368A LYS* 2.9 7.2 + - - +
370A SER* 1.3 77.1 - - - +
372A LEU* 1.3 61.7 + - - +
374A ASN* 3.2 8.6 + - - +
375A ASP* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LYS* 2.9 17.0 + - + +
369A LEU* 3.4 14.1 - - + +
371A LEU* 1.3 77.6 - - - +
373A LEU* 1.3 56.4 + - - +
375A ASP* 3.1 15.0 + - + +
376A ILE* 2.9 48.2 + - + +
379A LYS* 5.5 4.7 - - - +
408A GLU* 5.7 3.1 - - + -
411A LEU* 3.7 40.4 - - + -
412A GLN* 5.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.5 22.7 - - + +
331A TYR* 3.5 45.3 - - + -
332A LEU* 3.7 22.7 - - + +
335A LEU* 3.8 22.2 - - + -
350A LEU* 5.4 3.1 - - + -
369A LEU 2.9 13.8 + - - +
370A SER* 3.5 11.4 - - - +
372A LEU* 1.3 75.3 - - - +
374A ASN* 1.3 63.6 + - - +
376A ILE* 3.1 17.1 + - + +
377A SER* 2.9 26.5 + - - -
411A LEU* 5.2 6.1 - - + -
414A LEU* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 5.5 1.4 - - - +
328A PHE* 3.9 9.5 - - - -
353A LEU* 3.4 27.3 - - + +
356A LEU* 4.7 0.4 - - + +
361A PHE* 3.3 38.6 - - - -
370A SER 2.9 13.8 + - - +
371A LEU* 3.3 13.9 - - - +
373A LEU* 1.3 76.4 - - - +
375A ASP* 1.3 65.5 + - - +
377A SER* 3.1 5.1 + - - -
378A ARG* 2.9 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.0 20.4 + - - +
372A LEU* 3.1 15.7 + - + +
374A ASN* 1.3 78.0 + - - +
376A ILE* 1.3 58.3 + - + +
378A ARG* 3.4 18.3 + - - +
379A LYS* 2.9 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 3.4 24.2 - - + +
372A LEU* 2.9 47.2 + - + +
373A LEU* 3.4 14.4 - - + +
375A ASP* 1.3 77.0 - - - +
377A SER* 1.3 56.7 + - - +
379A LYS* 3.1 29.2 - - - +
380A SER* 2.1 38.5 + - - +
411A LEU* 4.5 13.5 - - + +
414A LEU* 3.7 29.6 - - + -
415A SER* 5.1 5.2 - - - +
418A VAL* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 3.9 15.3 - - - -
327A ILE* 3.6 32.4 - - - +
328A PHE* 3.3 18.9 + - - +
331A TYR* 3.1 24.2 - - - -
353A LEU* 5.9 0.2 - - - -
373A LEU 2.9 9.4 + - - -
374A ASN* 3.4 9.9 - - - -
376A ILE* 1.3 76.1 - - - +
378A ARG* 1.3 65.9 + - - +
380A SER* 2.8 19.8 + - - -
381A GLU* 3.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 4.6 17.9 - - + +
353A LEU* 5.7 1.8 - - - +
357A GLU* 5.1 3.8 + - - -
361A PHE* 3.5 21.8 - - - -
374A ASN* 2.9 51.3 + - - +
375A ASP* 3.6 18.9 + - - +
377A SER* 1.3 76.4 - - - +
379A LYS* 1.3 58.6 + - - +
380A SER 2.9 5.7 + - - -
381A GLU* 3.3 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 5.5 4.6 - - - +
375A ASP* 2.9 21.9 + - + +
376A ILE* 3.1 37.5 - - - +
378A ARG* 1.3 74.0 - - - +
380A SER* 1.3 58.0 + - - +
381A GLU* 3.5 2.3 + - - -
415A SER* 3.0 33.8 + - - +
418A VAL* 4.5 5.9 - - + +
419A ASP* 5.3 8.2 + - - +
422A PHE* 3.6 17.5 - - - -
----------------------------------------------------------
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