Contacts of the helix formed by residues 202 - 214 (chain A) in PDB entry 4COO
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 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 3.7 1.3 - - - -
195A ALA* 4.0 8.1 - - - -
196A ARG 3.5 14.8 - - - -
197A PHE 2.7 27.7 + - - -
199A SER* 3.3 8.1 + - - -
201A GLU* 1.3 81.2 - - - +
203A HIS* 1.3 59.7 + - - +
204A VAL* 3.2 3.4 - - - +
205A GLY 2.9 16.6 + - - -
206A VAL* 2.9 28.4 + - - +
1553A EDO 3.5 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO* 3.5 10.5 - - + +
146A THR 3.6 31.6 - - - -
147A SER* 5.7 0.4 - - - -
168A VAL* 3.4 21.8 - - + +
170A PRO* 4.1 14.9 - - + +
191A THR* 3.4 26.5 + - - +
202A SER* 1.3 72.7 - - - +
204A VAL* 1.3 72.7 + - + +
207A ALA* 3.1 29.5 + - - +
223A TYR* 2.9 24.5 + + - -
308A TYR* 4.0 12.7 + + - -
310A PHE* 4.9 1.3 - + - -
1553A EDO 3.4 37.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
43A TRP* 4.2 14.4 - - + -
46A PRO* 4.3 18.8 - - + -
145A PRO* 3.9 11.9 - - + -
197A PHE* 3.2 19.3 - - + +
202A SER* 3.2 12.6 - - - +
203A HIS* 1.3 95.6 + - + +
205A GLY* 1.3 68.1 + - - +
207A ALA* 3.4 1.9 + - - +
208A TRP* 3.0 37.8 + - + +
223A TYR* 3.8 28.0 - - + -
310A PHE* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 4.9 11.0 - - - -
197A PHE 5.2 0.7 - - - -
199A SER 4.3 5.6 - - - -
200A PRO* 3.7 14.6 - - - -
202A SER* 2.9 18.5 + - - -
204A VAL* 1.3 78.8 - - - +
206A VAL* 1.3 57.3 + - - +
208A TRP* 3.4 3.9 + - - +
209A ARG* 3.1 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 3.9 16.6 - - + -
189A VAL* 3.9 20.2 - - + -
191A THR* 3.7 16.8 - - + -
200A PRO 3.5 13.7 - - - +
201A GLU* 3.9 8.3 - - - -
202A SER 2.9 19.7 + - - +
205A GLY* 1.3 72.1 - - - +
207A ALA* 1.3 67.8 + - - +
209A ARG* 3.2 15.4 + - - +
210A LEU* 2.9 32.9 + - + +
507B HIS* 3.9 11.4 - - + -
526B ALA* 5.7 0.2 - - + -
527B ILE* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.9 16.7 - - + +
145A PRO* 3.9 29.2 - - + -
168A VAL* 4.0 12.0 - - + +
203A HIS 3.1 18.5 + - - +
204A VAL 3.7 5.4 - - - +
206A VAL* 1.3 77.6 - - - +
208A TRP* 1.3 61.6 + - + +
210A LEU* 3.3 3.0 + - - +
211A LYS* 3.0 23.0 + - - +
219A ILE* 3.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.1 46.2 - + + +
44A ILE* 3.4 37.0 + - + -
46A PRO* 6.2 0.4 - - - +
145A PRO* 5.7 2.6 - - + +
204A VAL* 3.0 30.4 + - + +
205A GLY 3.9 5.6 - - - +
206A VAL 3.3 0.2 - - - -
207A ALA* 1.3 76.1 - - + +
209A ARG* 1.3 64.9 + - + +
211A LYS* 3.1 40.5 + - - +
212A ASN* 3.0 35.3 + - - +
219A ILE* 3.4 28.8 - - + +
221A ASP* 3.8 19.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PRO* 2.8 50.6 + - - +
201A GLU* 4.4 3.2 - - - +
205A GLY* 3.1 22.9 + - - +
206A VAL* 3.2 10.0 + - - +
208A TRP* 1.3 76.8 - - + +
210A LEU* 1.3 64.5 + - - +
212A ASN* 3.5 14.3 + - - +
213A GLU* 3.6 18.9 + - - +
507B HIS* 5.3 3.4 + - - -
525B THR* 5.5 2.0 + - - -
527B ILE* 3.2 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 4.1 12.8 - - + -
166A ILE* 4.1 13.0 - - + -
168A VAL* 3.8 28.9 - - + -
189A VAL* 4.1 15.3 - - + -
206A VAL* 2.9 25.2 + - + +
207A ALA 3.6 5.8 - - - +
209A ARG* 1.3 72.8 - - - +
211A LYS* 1.3 67.0 + - - +
213A GLU* 2.9 14.6 + - - +
214A ILE* 3.3 18.6 + - + +
1554A EDO 4.0 11.2 - - - +
526B ALA* 4.8 4.3 - - + +
527B ILE* 3.9 25.1 - - + +
530B LEU* 3.4 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.5 10.0 - - + +
207A ALA 3.0 13.4 + - - +
208A TRP* 3.1 44.6 + - - +
210A LEU* 1.3 78.8 - - - +
212A ASN* 1.3 80.7 + - - +
213A GLU 3.1 1.4 + - - -
214A ILE 3.1 13.2 + - - +
217A SER* 3.2 40.5 + - - +
218A HIS* 4.2 1.1 - - - -
219A ILE* 3.5 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TRP* 3.0 29.9 + - - +
209A ARG* 3.9 10.6 - - - +
210A LEU 3.2 0.4 - - - -
211A LYS* 1.3 94.7 + - - +
213A GLU* 1.3 68.8 + - - +
214A ILE 3.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG 3.6 15.1 - - - +
210A LEU 2.9 8.4 + - - +
212A ASN* 1.3 88.0 - - - +
214A ILE* 1.3 61.8 + - - +
215A PRO* 3.7 7.9 - - - +
527B ILE* 5.5 5.6 - - + -
530B LEU* 3.8 21.6 - - + +
531B ASN* 3.7 24.6 + - - +
534B ALA* 4.5 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 4.4 8.7 - - - +
143A ILE* 4.2 6.5 - - + -
164A ARG* 4.0 22.2 - - - +
166A ILE* 3.6 29.6 - - + -
210A LEU* 3.5 17.0 - - + +
211A LYS 3.1 7.0 + - - +
212A ASN 3.5 0.6 - - - -
213A GLU* 1.3 80.6 - - - +
215A PRO* 1.3 75.8 - - + +
217A SER* 2.6 41.0 + - - +
1554A EDO 4.5 4.0 - - - -
530B LEU* 3.9 28.5 - - + -
----------------------------------------------------------
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