Contacts of the helix formed by residues 336 - 341 (chain E) 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 SER 336 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E VAL* 3.5 1.5 - - - +
334E VAL* 3.6 9.9 + - - +
335E LEU* 1.3 76.8 - - - +
337E ARG* 1.3 62.5 + - - +
338E GLY* 3.0 16.5 + - - -
339E ILE* 3.8 20.4 + - - +
340E SER 3.6 3.1 + - - -
347E ALA* 3.2 28.2 + - - +
349E ASP* 4.0 14.6 + - - +
352E ASP* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 5.8 6.9 - - - +
158E GLY* 5.2 3.4 - - - +
159E ALA 2.8 32.3 + - - +
160E GLY* 4.1 18.1 + - - +
161E VAL* 3.8 10.5 - - + +
336E SER* 1.3 73.6 + - - +
338E GLY* 1.3 58.4 + - - +
339E ILE 3.3 0.9 - - - -
340E SER* 3.7 6.3 - - - +
341E GLU* 2.9 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E SER* 3.0 10.3 + - - -
337E ARG* 1.3 79.6 - - - +
339E ILE* 1.3 65.9 - - - +
341E GLU* 3.5 22.4 - - - +
342E LEU* 3.7 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E SER* 3.8 12.0 + - - +
337E ARG 3.3 0.2 - - - -
338E GLY* 1.3 79.0 - - - +
340E SER* 1.3 66.1 + - - +
341E GLU 3.2 0.2 - - - -
342E LEU* 3.2 20.1 + - + +
344E ILE* 3.4 43.2 + - + +
347E ALA* 3.7 21.3 - - - +
348E VAL 3.7 25.1 - - - +
349E ASP* 3.7 29.6 - - + +
350E PRO* 4.6 7.4 - - + -
411E GLN* 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E GLY 3.6 18.3 + - - -
161E VAL* 4.6 1.5 - - - -
336E SER 3.6 7.3 + - - -
337E ARG* 3.6 13.7 + - - +
338E GLY 3.4 0.2 - - - -
339E ILE* 1.3 77.3 - - - +
341E GLU* 1.3 61.4 + - - +
343E GLY* 2.8 20.6 + - - -
344E ILE 4.1 7.4 - - - +
345E TYR* 4.0 19.4 + - - -
347E ALA* 3.6 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 5.1 13.4 - - + +
398A GLN* 5.5 5.3 + - - -
337E ARG* 2.9 20.1 + - - +
338E GLY* 3.5 15.6 - - - +
339E ILE 3.2 0.2 - - - -
340E SER* 1.3 78.4 - - - +
342E LEU* 1.3 60.7 + - + +
343E GLY* 3.2 3.1 + - - -
----------------------------------------------------------
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