Contacts of the helix formed by residues 20 - 29 (chain 6) in PDB entry 4E2I
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 GLU 20 (chain 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186 ASP* 5.4 1.4 + - - -
196 CYS* 1.3 79.0 - - - +
216 GLU* 1.3 67.5 + - - +
226 ALA* 3.8 21.1 + - - +
236 LEU* 3.0 35.5 + - + +
246 ILE* 3.0 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206 GLU* 1.3 74.8 - - - +
226 ALA* 1.3 60.0 + - - +
246 ILE* 3.7 8.9 + - + +
256 GLU* 3.1 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206 GLU* 3.1 21.0 + - + +
216 GLU* 1.3 78.8 - - - +
236 LEU* 1.3 64.6 + - + +
256 GLU* 4.1 9.8 - - - +
266 LYS* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186 ASP 4.3 1.6 - - - +
196 CYS* 3.5 28.7 - - + -
206 GLU* 3.0 38.4 + - + +
226 ALA* 1.3 78.5 - - + +
246 ILE* 1.3 64.8 + - - +
266 LYS* 3.1 23.3 - - + +
276 LEU* 3.1 15.0 - - + +
576 LEU 3.9 17.3 - - - +
586 THR* 3.6 22.9 - - - +
596 SER* 3.4 26.0 - - - +
626 LEU* 5.4 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 ALA* 3.5 35.9 - - + +
86 LEU* 4.6 4.5 - - + +
96 ALA* 3.9 24.9 - - + +
126 LEU* 3.8 17.0 - - + -
196 CYS* 3.2 29.2 - - + +
206 GLU 3.0 14.5 + - - +
216 GLU* 4.2 7.4 - - + +
236 LEU* 1.3 75.5 - - - +
256 GLU* 1.3 61.2 + - - +
266 LYS 3.1 0.2 - - - -
276 LEU* 3.3 16.4 + - - +
286 VAL* 3.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 ALA* 4.4 14.1 - - + -
216 GLU* 3.1 32.1 + - + +
226 ALA* 4.1 8.0 - - - +
246 ILE* 1.3 75.7 - - - +
266 LYS* 1.3 62.5 + - - +
276 LEU 3.2 0.2 - - - -
286 VAL* 3.4 24.5 + - + +
296 GLU* 3.7 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226 ALA 3.4 12.7 + - - +
236 LEU* 3.1 19.5 + - + +
246 ILE 3.1 0.6 - - - -
256 GLU* 1.3 80.7 - - - +
276 LEU* 1.3 60.4 + - + +
296 GLU* 3.6 30.9 + - - +
306 LEU* 4.0 7.2 + - + +
596 SER* 4.8 12.8 - - - +
626 LEU* 3.2 35.9 + - + +
636 ASN* 3.4 28.2 + - - +
666 GLU* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86 LEU* 3.5 32.1 - - + -
126 LEU* 5.8 4.7 - - + -
196 CYS* 5.7 5.2 - - - -
236 LEU* 3.1 20.2 - - + +
246 ILE* 3.3 8.2 + - - +
256 GLU 3.2 0.4 - - - -
266 LYS* 1.3 78.0 - - + +
286 VAL* 1.3 65.5 + - - +
296 GLU 3.0 2.5 - - - -
306 LEU* 3.0 44.1 + - + +
316 CYS* 3.3 11.6 - - - -
416 MET* 4.6 8.0 - - + +
426 VAL* 6.5 0.2 - - - -
456 LEU* 4.1 12.8 - - + -
626 LEU* 3.5 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26 SER* 4.0 13.0 - - - -
36 ALA* 3.6 29.6 - - + +
46 SER 4.4 1.8 - - - +
56 ALA* 3.6 28.0 - - + +
86 LEU* 4.8 3.8 - - + -
246 ILE 3.2 17.3 - - - +
256 GLU* 3.4 20.9 - - + +
276 LEU* 1.3 78.0 - - - +
296 GLU* 1.3 61.6 + - + +
316 CYS* 3.3 15.5 + - - +
326 VAL* 3.2 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256 GLU 3.7 13.5 - - - +
266 LYS* 3.6 31.1 + - - +
276 LEU 3.0 0.4 - - - -
286 VAL* 1.3 76.2 - - + +
306 LEU* 1.3 54.1 + - - +
316 CYS 3.1 0.4 - - - -
326 VAL* 3.0 7.8 + - - +
336 GLN* 2.8 48.9 + - + +
666 GLU* 5.4 5.8 - - - +
----------------------------------------------------------
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