Contacts of the helix formed by residues 337 - 343 (chain E) in PDB entry 5I4V
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 LYS 337 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325E GLU 4.5 1.0 + - - -
336E SER* 1.3 73.7 - - - +
338E ASP* 1.3 71.4 + - - +
340E PHE* 3.0 15.1 + - - +
341E HIS* 3.1 11.8 + - - +
350E ILE* 3.9 14.9 - - + +
351E ASN* 3.0 33.8 + - - +
354E PHE* 3.6 45.2 - - + +
358E ARG* 4.1 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E SER* 3.2 7.8 + - - +
337E LYS* 1.3 84.3 - - - +
339E ASP* 1.3 58.5 + - - +
341E HIS* 3.0 10.4 + - - +
342E ARG* 2.8 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E TRP* 3.7 20.9 + - + -
271E PHE* 4.8 1.1 - - - -
334E THR 4.2 2.6 - - - +
335E TYR* 3.4 29.2 - - + -
336E SER* 2.9 38.5 + - - +
338E ASP* 1.3 76.2 - - - +
340E PHE* 1.3 61.6 + - - +
342E ARG* 2.9 25.2 + - - +
343E ALA* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E PHE* 4.0 16.8 - + - -
327E ILE* 3.7 24.5 - - + -
329E PHE* 4.0 19.7 - + - -
335E TYR* 3.8 29.6 - - + -
336E SER 3.1 22.1 + - - -
337E LYS 3.0 9.8 + - - +
339E ASP* 1.3 77.7 - - - +
341E HIS* 1.3 61.2 + - - +
343E ALA* 3.2 13.0 + - - +
345E LEU* 3.4 35.8 + - + +
350E ILE* 3.7 20.4 - - + -
353E ILE* 4.7 11.4 - - + -
354E PHE* 4.1 19.7 - + - -
501E 67S 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E LYS 3.1 8.8 + - - +
338E ASP* 3.0 13.1 + - - +
340E PHE* 1.3 75.6 - - - +
342E ARG* 1.3 64.0 + - + +
344E GLY* 3.0 19.9 + - - -
345E LEU 3.4 18.7 + - - +
346E GLN* 4.5 1.6 - - - -
347E VAL* 4.2 27.7 - - + +
350E ILE* 3.4 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E TRP* 5.3 0.4 - - - -
264E SER* 4.5 12.6 + - - +
267E ARG* 3.6 46.6 + - - +
336E SER* 4.7 1.2 + - - -
338E ASP* 2.8 47.2 + - - +
339E ASP* 2.9 38.8 + - - +
341E HIS* 1.3 75.8 - - - +
343E ALA* 1.3 59.1 + - - +
344E GLY* 3.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E TRP* 4.2 2.2 - - + -
264E SER 5.2 0.9 - - - -
267E ARG* 3.8 15.0 - - - +
268E PHE* 3.3 31.9 - - - +
271E PHE* 3.6 42.4 - - + +
339E ASP 2.9 12.6 + - - +
340E PHE 3.4 11.2 - - - +
341E HIS 3.1 0.4 - - - -
342E ARG* 1.3 76.3 - - - +
344E GLY* 1.3 55.5 + - - +
345E LEU* 3.6 4.5 + - + +
501E 67S 5.4 0.2 - - - -
----------------------------------------------------------
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