Contacts of the helix formed by residues 339 - 354 (chain M) in PDB entry 6D6Q
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 ARG 339 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330M LEU* 3.2 37.6 - - + +
331M VAL* 2.5 29.1 + - - +
333M ASP* 3.7 21.8 + - - +
337M ASP* 3.0 41.4 + - - +
338M PHE* 1.3 74.4 - - - +
340M GLU* 1.3 60.4 + - - +
341M ASP* 3.2 18.8 + - + +
342M ASN* 3.8 10.6 + - - +
343M PHE 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338M PHE* 3.7 28.2 + - + -
339M ARG* 1.3 70.5 - - - +
341M ASP* 1.3 56.7 + - - +
342M ASN 3.3 0.4 - - - -
343M PHE* 3.3 18.2 - - + -
344M ASN* 2.4 57.9 + - - +
545M PRO* 3.6 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 341 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M ARG* 3.2 13.5 - - + +
340M GLU* 1.3 81.8 - - - +
342M ASN* 1.3 61.9 + - - +
344M ASN* 3.1 12.6 + - - +
345M THR* 2.9 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 342 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329M HIS* 3.6 15.1 - - + +
330M LEU* 2.9 50.4 + - - +
339M ARG* 3.8 11.4 + - - +
340M GLU 3.3 0.2 - - - -
341M ASP* 1.3 80.1 - - - +
343M PHE* 1.3 55.8 + - - +
345M THR* 3.3 10.1 + - - -
346M ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 343 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320M ILE* 3.3 31.6 - - + -
329M HIS* 5.4 0.2 - - - -
330M LEU 3.8 2.8 + - - -
331M VAL* 3.9 15.9 - - + -
338M PHE* 4.7 11.7 - + + -
340M GLU* 2.9 31.8 + - + +
342M ASN* 1.3 79.8 - - - +
344M ASN* 1.3 59.2 + - - +
346M ALA* 3.2 4.9 + - - +
347M MET* 2.8 64.4 + - + +
543M MET* 3.4 20.9 - - + -
544M SER 4.3 4.0 - - - -
545M PRO* 3.8 30.1 - - + -
548M GLY* 4.5 17.0 - - - -
552M LEU* 5.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340M GLU* 2.4 56.2 + - - +
341M ASP* 3.5 11.4 + - - +
343M PHE* 1.3 71.1 - - - +
345M THR* 1.3 58.2 + - - +
347M MET* 3.2 8.6 + - - +
348M GLN* 2.9 40.4 + - - +
545M PRO* 4.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329M HIS* 3.8 21.5 - - + +
341M ASP 2.9 15.0 + - - -
342M ASN* 3.5 13.2 + - - -
344M ASN* 1.3 76.0 - - - +
346M ALA* 1.3 57.9 + - - +
348M GLN* 3.2 17.6 + - + +
349M VAL* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320M ILE* 4.8 14.6 - - + -
322M PRO* 4.4 3.1 - - + +
329M HIS* 3.9 26.4 - - + +
342M ASN 2.9 14.3 + - - +
343M PHE* 3.2 11.6 + - - +
345M THR* 1.3 77.5 - - - +
347M MET* 1.3 65.6 + - + +
349M VAL* 3.1 8.1 + - - +
350M LEU* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 347 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320M ILE* 4.7 5.2 - - + -
343M PHE* 2.8 70.2 + - + +
344M ASN* 3.6 10.5 - - - +
346M ALA* 1.3 81.6 - - + +
348M GLN* 1.3 58.3 + - + +
350M LEU* 3.2 33.6 + - + +
351M ARG* 2.9 39.1 + - + +
539M VAL* 4.9 7.6 - - + -
542M LYS* 6.0 0.9 - - - -
543M MET* 3.9 26.7 - - + +
544M SER* 5.5 1.8 - - - -
545M PRO* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 348 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344M ASN* 2.9 26.1 + - - +
345M THR* 3.4 19.3 + - + +
347M MET* 1.3 75.0 - - - +
349M VAL* 1.3 58.9 + - + +
351M ARG* 3.2 19.4 + - - +
352M ASP* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322M PRO* 3.8 21.5 - - + -
323M ALA 5.3 2.9 - - - +
325M GLY* 4.0 19.1 - - - +
329M HIS* 4.2 18.6 - - + +
345M THR* 2.9 26.3 + - + +
346M ALA 3.1 7.8 + - - +
348M GLN* 1.3 73.3 - - + +
350M LEU* 1.3 66.4 + - - +
352M ASP* 3.1 10.1 + - + +
353M ALA* 2.9 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322M PRO* 3.4 27.4 - - + -
323M ALA 5.7 0.4 - - - +
346M ALA* 2.8 36.6 + - + +
347M MET* 3.2 28.9 + - + +
349M VAL* 1.3 78.4 - - - +
351M ARG* 1.3 64.0 + - + +
353M ALA* 3.1 17.8 + - - +
354M GLY* 3.7 3.5 + - - -
539M VAL* 4.1 12.8 - - + +
540M ASP* 4.7 1.3 - - - -
541M GLU 2.8 46.0 - - - +
542M LYS* 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 351 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M MET* 2.9 22.8 + - - +
348M GLN* 3.6 19.5 - - - +
350M LEU* 1.3 77.3 - - + +
352M ASP* 1.3 56.1 + - - +
354M GLY* 2.7 28.9 + - - +
542M LYS* 4.4 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 352 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348M GLN* 2.9 28.9 + - - +
349M VAL* 3.1 10.7 + - + +
351M ARG* 1.3 77.4 - - - +
353M ALA* 1.3 65.8 + - - +
354M GLY 3.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323M ALA* 4.2 22.7 - - + +
349M VAL* 2.9 13.6 + - + +
350M LEU* 3.1 13.9 + - - +
352M ASP* 1.3 76.1 - - - +
354M GLY* 1.3 56.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350M LEU 3.7 3.6 + - - -
351M ARG 2.7 26.0 + - - +
352M ASP* 3.0 7.4 - - - +
353M ALA* 1.3 80.2 - - - +
----------------------------------------------------------
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