Contacts of the helix formed by residues 200 - 209 (chain A) in PDB entry 4EQU
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 ALA 200 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP 3.6 1.0 + - - -
199A MET* 1.3 73.9 - - - +
201A PRO* 1.3 73.9 - - + +
202A GLU* 3.3 26.9 - - - +
203A VAL* 3.0 20.8 + - + +
204A VAL* 3.1 11.1 + - - +
218B ALA* 3.9 13.6 + - - +
221B TRP* 3.4 27.9 - - + -
222B SER* 4.5 2.2 + - - -
282B ARG* 3.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 1.3 84.4 - - + +
202A GLU* 1.3 58.6 + - - +
204A VAL* 3.2 6.0 + - + +
205A MET* 2.9 31.7 + - - +
221B TRP* 3.4 45.1 - - + -
249B ILE* 3.9 20.0 - - + +
250B ALA* 4.7 2.1 - - - +
277B LYS* 4.0 32.8 - - + +
282B ARG* 4.4 0.2 - - - +
405B 1PE 4.1 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ALA* 3.3 16.3 - - - +
201A PRO* 1.3 75.8 - - - +
203A VAL* 1.3 63.2 + - + +
205A MET* 3.5 1.6 + - - +
206A CYS* 3.0 34.0 + - - -
209B MET* 4.0 23.1 - - + -
214B TYR 4.7 2.6 - - - +
217B LYS* 4.3 0.7 - - - +
218B ALA* 3.9 11.1 + - - +
277B LYS 4.2 1.2 - - - +
279B PRO* 3.5 18.9 - - + +
282B ARG* 2.8 42.5 + - - -
405B 1PE 3.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE 4.4 0.2 - - - +
199A MET* 4.1 19.1 - - + -
200A ALA* 3.0 18.0 + - + +
202A GLU* 1.3 81.3 - - + +
204A VAL* 1.3 66.3 + - - +
206A CYS* 3.8 3.7 - - - +
207A GLU* 2.9 31.1 + - + +
156B ARG* 3.4 44.2 - - - +
218B ALA* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET* 3.8 24.0 - - + -
200A ALA 3.1 13.8 + - - +
201A PRO* 3.5 8.1 - - + +
203A VAL* 1.3 76.8 - - - +
205A MET* 1.3 57.1 + - - +
207A GLU* 3.4 3.4 + - - +
208A THR* 2.8 41.3 + - - +
246B LEU* 3.4 50.7 - - + +
249B ILE* 4.1 20.4 - - + -
250B ALA* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO 2.9 19.5 + - - +
202A GLU* 3.8 5.8 - - - +
203A VAL 3.2 0.2 - - - -
204A VAL* 1.3 78.4 - - - +
206A CYS* 1.3 56.1 + - - +
208A THR* 3.4 8.1 + - + -
209A MET* 3.0 55.4 + - + +
279A PRO* 6.4 0.4 - - + -
280A GLU* 5.6 4.7 - - - +
250B ALA* 3.8 24.2 - - + -
251B LYS* 5.1 11.0 - - - +
405B 1PE 3.7 58.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU 3.0 22.7 + - - +
203A VAL* 4.2 3.6 - - - +
205A MET* 1.3 76.0 - - - +
207A GLU* 1.3 64.8 + - - +
209A MET* 4.0 5.2 + - - +
210A LYS* 3.3 30.2 + - - +
206B CYS* 2.1 59.9 - - + +
209B MET* 4.4 11.0 - - + -
210B LYS* 5.9 2.5 - - - -
405B 1PE 3.8 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE* 3.9 27.8 - - + +
199A MET* 5.0 6.1 - - + -
203A VAL* 2.9 25.8 + - + +
204A VAL* 3.8 4.3 - - - +
206A CYS* 1.3 79.1 - - - +
208A THR* 1.3 64.7 + - - +
209A MET 3.2 0.2 - - - -
210A LYS* 3.2 47.4 + - - +
211A ASP* 3.9 9.5 + - - +
156B ARG* 4.1 11.6 + - - -
246B LEU* 6.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 2.8 37.7 + - - +
205A MET* 3.8 10.9 - - + -
207A GLU* 1.3 72.7 - - - +
209A MET* 1.3 65.5 + - + +
210A LYS 3.2 0.7 - - - -
211A ASP* 3.1 22.2 - - - +
214A TYR* 3.3 40.2 - - + +
246B LEU* 5.4 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A MET* 3.0 39.9 + - + +
206A CYS* 4.1 8.5 - - - +
207A GLU 3.2 0.6 - - - -
208A THR* 1.3 83.3 - - + +
210A LYS* 1.3 58.0 + - + +
211A ASP 3.5 0.4 - - - -
214A TYR* 3.3 46.8 - - + +
215A ASP* 3.2 27.6 - - - +
279A PRO* 3.6 28.7 - - + -
202B GLU* 4.1 20.2 - - + +
206B CYS* 4.3 15.3 - - + -
405B 1PE 4.6 7.9 - - - +
----------------------------------------------------------
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