Contacts of the helix formed by residues 214 - 222 (chain A) in PDB entry 3PEI
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 MSE 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.9 23.6 - - - -
209A MSE 3.0 40.6 + - + +
212A LEU* 4.2 11.7 - - + -
213A GLY* 1.3 72.5 - - - +
215A GLY* 1.3 55.6 + - - +
217A ALA* 4.7 0.7 - - + -
218A LEU* 3.0 31.2 + - - +
230A THR* 3.6 20.0 - - - +
321A MSE 3.7 27.1 - - + +
341A ASP* 3.0 49.2 - - + +
342A THR* 3.9 9.9 - - - +
345A TYR* 4.2 7.0 - - + -
508A PEG 3.7 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLY 2.8 10.9 + - - -
214A MSE 1.3 70.8 - - - +
216A CYS* 1.3 65.5 + - - +
219A ALA* 3.2 24.1 + - - +
318A LEU* 4.0 4.8 - - - +
319A LYS 3.2 18.4 + - - -
341A ASP* 3.1 1.0 + - - -
508A PEG 3.3 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLY* 1.3 72.9 - - - +
217A ALA* 1.3 60.8 + - - +
219A ALA* 3.3 11.6 + - - +
220A VAL* 3.6 16.5 + - - +
318A LEU* 3.9 20.0 - - - +
319A LYS 3.9 1.0 + - - -
320A SER* 3.6 30.7 - - - -
326A VAL* 3.9 20.2 - - - -
337A LEU* 3.4 27.8 - - + +
340A CYS* 3.6 13.7 - - - -
341A ASP* 2.6 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MSE 3.7 23.3 - - + -
214A MSE 4.2 1.8 - - + +
216A CYS* 1.3 69.3 - - - +
218A LEU* 1.3 66.3 + - - +
220A VAL* 3.2 15.8 + - - +
221A GLY 3.7 0.3 + - - -
228A ASN* 2.9 19.2 + - - +
337A LEU 3.6 4.9 + - - -
338A VAL* 3.9 30.4 - - + +
341A ASP* 2.9 24.4 + - + +
342A THR* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLN* 3.9 19.6 - - + +
209A MSE 4.0 20.4 - - + -
210A ALA* 3.6 42.8 - - + +
214A MSE 3.0 22.1 + - - +
217A ALA* 1.3 76.5 - - - +
219A ALA* 1.3 57.1 + - - +
221A GLY* 3.6 2.3 + - - -
222A ARG* 3.0 27.7 + - - +
228A ASN* 4.0 25.1 - - + +
508A PEG 3.9 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLY 3.2 19.1 + - - +
216A CYS 3.6 1.6 - - - +
217A ALA 3.1 1.2 - - - -
218A LEU* 1.3 76.7 - - - +
220A VAL* 1.3 64.9 + - + +
222A ARG* 3.3 34.9 + - - +
223A GLY 4.9 0.2 + - - -
312A TYR* 4.1 14.4 - - + +
318A LEU* 3.5 34.8 - - + -
334A GLU* 5.1 1.1 - - - -
337A LEU* 5.7 0.4 - - + -
508A PEG 3.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A CYS 3.6 14.4 - - - +
217A ALA 3.2 7.7 + - - +
219A ALA* 1.3 79.0 - - - +
221A GLY* 1.3 59.0 + - - +
223A GLY 5.0 1.2 + - - -
252A LEU* 4.0 22.4 - - + -
303A ALA* 4.4 3.4 - - + -
304A GLU 3.2 9.0 - - - +
305A ASN* 4.2 6.2 - - - +
312A TYR* 5.3 5.0 - - - -
334A GLU* 3.3 57.0 - - + +
337A LEU* 3.7 20.2 - - + -
338A VAL* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLN* 5.5 0.2 - - - -
217A ALA 3.7 4.6 + - - -
218A LEU 3.6 4.7 + - - -
220A VAL* 1.3 79.8 - - - +
222A ARG* 1.3 65.1 + - - +
223A GLY 3.1 2.9 - - - -
224A SER* 2.7 18.8 + - - -
226A MSE 5.4 0.2 - - - -
228A ASN* 3.4 19.1 + - - +
303A ALA* 4.5 2.2 - - - +
304A GLU 3.4 15.3 - - - -
497A K 3.1 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.0 13.2 + - + +
219A ALA* 3.3 27.7 + - - +
221A GLY* 1.3 75.2 - - - +
223A GLY* 1.3 60.3 + - - +
224A SER 3.5 3.6 + - - +
312A TYR* 3.6 34.0 - - + +
313A ARG* 5.4 2.8 - - - +
316A ASP* 3.8 12.7 + - - +
318A LEU* 4.3 10.5 - - - +
508A PEG 3.3 36.9 + - - -
----------------------------------------------------------
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