Contacts of the helix formed by residues 319 - 326 (chain M) in PDB entry 3FKS
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 ASP 319 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293L ARG* 3.3 20.4 + - - -
279M VAL* 4.6 1.8 - - - +
281M TYR* 2.7 28.5 + - - -
313M PRO* 3.5 17.5 - - + +
314M ALA* 5.7 0.2 - - - +
316M ASP* 3.2 20.8 + - + +
317M LEU 3.2 1.2 - - - -
318M THR* 1.3 78.1 + - - +
320M PRO* 1.3 76.6 - - - +
321M ALA 2.8 11.8 + - - -
322M PRO* 3.0 17.3 - - + +
323M ALA* 2.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 320 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J ARG* 5.8 5.8 - - - +
278M ALA* 4.1 11.9 - - + +
279M VAL* 3.5 37.7 - - + -
281M TYR* 4.1 10.8 - - + -
285M LEU* 4.0 11.1 - - + +
318M THR 3.4 5.8 - - - +
319M ASP* 1.3 92.9 - - - +
321M ALA* 1.3 59.1 + - - +
323M ALA* 4.2 5.4 - - + -
324M THR* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M PHE* 3.5 20.2 - - + -
262M THR* 4.5 6.7 - - + -
281M TYR* 3.3 33.4 - - + +
285M LEU* 4.0 11.6 - - + +
289M MET* 4.1 6.7 - - + +
319M ASP* 2.8 8.5 + - - -
320M PRO* 1.3 77.3 - - - +
322M PRO* 1.3 68.4 - - + +
324M THR* 4.0 3.3 - - - -
325M THR* 2.9 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 322 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M PHE* 3.6 15.5 - - + -
259M PHE* 5.0 0.9 - - + -
310M VAL* 4.4 4.9 - - + -
311M TYR 3.3 25.4 - - - +
312M VAL* 4.0 12.3 - - + -
313M PRO* 3.4 16.4 - - + -
316M ASP 4.6 0.2 - - - +
317M LEU* 4.7 7.9 - - - +
319M ASP* 3.0 30.3 - - + +
321M ALA* 1.3 89.7 - - + +
323M ALA* 1.3 65.1 + - - +
325M THR* 3.0 23.3 + - - +
326M PHE* 3.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J GLU* 5.7 0.7 - - - +
332J GLN* 4.3 22.5 + - - +
317M LEU 3.9 15.0 + - - +
318M THR 4.4 5.2 - - - +
319M ASP 2.9 22.3 + - - +
320M PRO* 3.9 5.8 - - + +
322M PRO* 1.3 78.5 - - - +
324M THR* 1.3 63.6 + - - +
325M THR 3.1 1.4 + - - -
326M PHE* 3.2 23.6 + - - +
327M ALA 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285M LEU* 3.6 20.9 - - + +
286M ALA* 4.6 18.8 - - + +
289M MET* 4.4 11.7 - - + -
320M PRO* 3.0 19.3 + - - +
321M ALA 4.0 3.4 - - - -
322M PRO 3.4 0.2 - - - -
323M ALA* 1.3 78.8 - - - +
325M THR* 1.3 62.8 + - - +
326M PHE 3.4 0.5 + - - -
327M ALA* 3.7 12.8 + - - +
328M HIS* 3.7 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M PHE* 4.3 4.0 - - + -
258M ILE* 4.9 7.4 - - + +
289M MET* 3.5 26.2 - - - +
293M GLN* 5.0 7.6 - - - +
308M GLN* 5.1 0.9 - - - +
310M VAL* 3.7 35.8 - - + +
321M ALA 2.9 16.5 + - - -
322M PRO* 3.0 15.3 + - - +
324M THR* 1.3 79.5 - - - +
326M PHE* 1.3 62.9 + - - +
328M HIS* 2.9 21.0 + - + +
329M LEU* 3.8 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 326 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J ARG* 3.4 57.2 - - + -
174J GLN* 4.4 11.1 + - - +
156M PHE* 3.4 49.4 - + - -
317M LEU* 3.9 19.7 - - + -
322M PRO 3.5 18.3 + - - -
323M ALA* 3.2 16.1 + - - +
325M THR* 1.3 77.1 - - - +
327M ALA* 1.3 57.4 + - - +
328M HIS 2.8 6.8 + - - -
329M LEU* 2.9 24.9 + - - +
332M THR* 3.8 21.1 - - + +
334M VAL* 4.5 7.2 - - + -
352M ASP* 5.4 0.4 - - - -
----------------------------------------------------------
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