Contacts of the helix formed by residues 195 - 210 (chain A) in PDB entry 4H2G
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 ASP 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 4.0 24.6 + - - +
194A GLU* 1.3 75.3 - - - +
196A GLU* 1.4 73.3 + - - +
197A ILE* 3.4 12.8 + - - +
198A THR* 2.6 41.6 + - - +
199A ALA* 3.1 21.7 + - - +
225A MET* 5.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 3.8 21.1 - - - +
176A TYR* 4.1 12.1 - - + -
177A THR 4.3 0.2 - - - -
178A SER* 3.8 0.2 - - - -
179A LYS* 3.6 28.2 + - - +
194A GLU 3.2 2.2 + - - -
195A ASP* 1.4 79.6 - - - +
197A ILE* 1.3 54.2 + - - +
199A ALA* 3.2 2.8 + - - +
200A LEU* 2.8 45.1 + - + +
221A SER* 2.6 35.1 + - - +
225A MET* 3.6 28.2 - - + +
229A ILE* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASP* 3.4 10.4 + - - +
196A GLU* 1.3 75.8 - - - +
198A THR* 1.3 63.0 + - - +
200A LEU* 4.0 0.6 - - - +
201A GLN* 3.1 29.3 + - + +
225A MET* 4.3 11.2 - - - -
228A LEU* 3.9 39.5 - - + +
229A ILE* 3.9 18.4 - - + +
232A LYS* 4.2 27.1 - - + +
233A VAL* 4.0 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 6.0 2.2 - - + -
195A ASP* 2.6 36.9 + - + +
197A ILE* 1.3 77.4 - - - +
199A ALA* 1.3 57.3 + - - +
201A GLN* 4.7 1.1 - - - +
202A PRO* 3.1 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 3.7 17.9 - - + +
143A ASN* 3.4 26.9 - - + -
145A LYS* 4.7 0.2 - - - +
194A GLU* 4.0 12.1 - - + +
195A ASP 3.1 15.2 + - - +
196A GLU 3.6 1.3 - - - +
198A THR* 1.3 79.0 - - - +
200A LEU* 1.3 66.4 + - + +
202A PRO* 3.5 9.6 - - - +
203A GLU* 3.6 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.1 3.8 - - + -
143A ASN* 6.2 0.2 - - + -
174A VAL* 3.2 37.7 - - + +
175A GLY 3.5 19.7 - - - +
176A TYR* 3.9 17.9 - - + -
196A GLU 2.8 26.0 + - - +
197A ILE 4.0 2.2 - - - +
199A ALA* 1.3 75.1 - - + +
201A GLN* 1.3 67.1 - - - +
203A GLU* 3.1 7.1 + - - +
204A VAL* 3.0 26.3 + - + +
217A ALA* 5.1 4.3 - - + -
229A ILE* 3.8 42.4 - - + -
233A VAL* 4.2 14.6 - - + -
236A VAL* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 3.1 18.7 + - + +
198A THR* 4.7 1.1 - - - +
200A LEU* 1.3 77.7 - - - +
202A PRO* 1.4 64.9 - - + +
204A VAL* 3.3 3.1 + - - +
205A ASP* 2.8 56.0 + - - +
232A LYS 3.4 6.2 - - - +
233A VAL* 3.4 16.3 - - + +
234A ARG* 2.8 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A THR 3.1 22.2 - - - +
199A ALA* 3.5 9.9 - - - +
201A GLN* 1.4 95.2 - - + +
203A GLU* 1.3 59.4 + - + +
205A ASP* 3.4 13.5 - - + +
206A LYS* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.2 17.8 - - + +
145A LYS* 5.9 2.8 - - - -
160A PRO* 3.7 17.1 - - + +
161A TYR* 3.4 34.4 - - + -
174A VAL* 4.2 11.4 - - + -
199A ALA 3.6 16.3 - - - +
200A LEU 3.1 5.2 + - - +
202A PRO* 1.3 82.3 - - + +
204A VAL* 1.3 57.4 + - - +
206A LYS* 3.2 15.1 + - - +
207A LEU* 3.0 34.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
174A VAL* 4.1 22.0 - - + -
200A LEU* 3.0 18.6 + - + +
201A GLN* 3.8 9.0 - - - +
203A GLU* 1.3 72.8 - - - +
205A ASP* 1.4 56.6 + - - +
207A LEU* 3.2 9.0 + - - +
208A LYS* 2.7 50.4 + - + +
215A ILE* 4.2 8.5 - - + -
217A ALA* 6.3 0.2 - - + -
233A VAL* 4.0 14.1 - - + -
234A ARG 3.2 25.1 - - - +
235A GLY 4.0 12.6 - - - +
236A VAL* 4.1 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLN* 2.8 54.2 + - - +
202A PRO* 3.4 14.8 - - + +
204A VAL* 1.4 71.3 - - - +
206A LYS* 1.3 63.1 + - - +
208A LYS* 3.3 11.5 + - - +
209A THR* 3.2 27.0 + - + +
234A ARG* 4.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.0 41.9 + - - -
202A PRO 2.9 19.4 + - - +
203A GLU* 3.4 11.9 + - - +
205A ASP* 1.3 76.2 - - - +
207A LEU* 1.3 65.8 + - - +
209A THR* 2.9 28.0 + - - +
210A LEU* 3.1 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.8 32.3 - - + +
163A VAL* 3.7 24.5 - - + -
172A GLY* 4.4 12.8 - - - -
174A VAL* 3.7 29.6 - - + -
203A GLU 3.0 17.7 + - - +
204A VAL* 3.2 7.4 + - - +
206A LYS* 1.3 77.1 - - - +
208A LYS* 1.3 58.3 + - - +
210A LEU* 2.9 27.9 + - + +
211A ASN 3.3 0.2 + - - -
212A VAL* 3.1 27.3 + - + +
215A ILE* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 2.7 45.2 + - + +
205A ASP* 3.5 11.0 - - - +
206A LYS 3.2 0.2 - - - -
207A LEU* 1.3 75.0 - - - +
209A THR* 1.3 63.0 + - + +
211A ASN* 3.2 16.8 + - - +
212A VAL 2.8 27.0 + - - -
213A ASN* 3.5 18.2 + - - +
215A ILE* 3.9 12.6 - - + +
234A ARG 5.5 0.2 - - - +
235A GLY* 4.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ASP* 3.2 17.2 + - + +
206A LYS* 2.9 19.6 + - - +
208A LYS* 1.3 77.0 - - + +
210A LEU* 1.3 67.2 + - - +
211A ASN* 3.2 10.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
161A TYR* 5.2 2.2 - - - +
206A LYS* 3.1 37.2 + - + +
207A LEU* 2.9 19.1 + - + +
209A THR* 1.3 85.4 - - - +
211A ASN* 1.3 68.4 + - - +
212A VAL* 3.3 12.4 + - + +
----------------------------------------------------------
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