Contacts of the helix formed by residues 192 - 204 (chain A) in PDB entry 4HYJ
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 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 3.6 25.0 - - + -
188A LEU 3.6 13.5 - - - +
189A ILE* 3.1 19.2 + - - +
191A TRP* 1.3 77.2 - - - +
193A ILE* 1.3 62.2 + - - +
195A PRO* 3.2 4.7 - - - +
196A ILE* 3.1 37.6 + - + +
307A LFA 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE 4.4 1.6 - - - +
190A GLY* 3.4 22.9 - - - +
191A TRP 3.0 0.8 - - - -
192A ALA* 1.3 77.1 - - - +
194A TYR* 1.3 58.8 + - - +
196A ILE* 3.3 10.1 + - - +
197A GLY* 2.9 26.2 + - - -
216A ILE* 3.7 26.5 - - + -
217A TYR* 3.9 10.8 - - + -
220A ALA* 3.7 24.0 - - + -
223A THR* 6.5 0.2 - - - -
307A LFA 4.2 29.2 - - + -
308A LFA 5.1 2.7 - - + +
313A LFA 3.6 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 3.5 27.8 - + + -
190A GLY 4.1 1.8 - - - -
191A TRP* 3.3 19.1 - - - -
193A ILE* 1.3 76.4 - - - +
195A PRO* 1.4 62.5 - - + +
197A GLY 3.1 1.0 + - - -
198A TYR* 2.9 16.8 + - - +
217A TYR* 2.7 41.2 + + - -
220A ALA* 3.3 19.6 - - + -
221A ASP* 2.6 31.1 + - - -
224A ASN* 2.9 32.5 + - - -
301A RET 3.3 59.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 2.6 39.1 + - + +
151A CYS* 4.4 5.2 - - - -
154A TRP* 3.9 18.4 - - + -
191A TRP 3.0 25.8 - - - +
192A ALA 3.2 15.5 - - - +
194A TYR* 1.4 81.9 - - + +
196A ILE* 1.3 54.3 + - + +
198A TYR* 3.3 2.9 + - + -
199A ALA 3.0 17.5 + - - -
301A RET 3.7 40.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR* 4.6 0.4 - - - -
192A ALA* 3.1 30.9 + - + +
193A ILE* 3.5 10.3 - - - +
194A TYR 3.2 0.6 - - - -
195A PRO* 1.3 74.8 - - + +
197A GLY* 1.3 65.2 + - - +
199A ALA* 3.1 18.1 + - + +
200A VAL* 3.1 15.4 + - + +
302A LFA 4.6 21.1 - - + -
303A LFA 5.7 5.4 - - + -
307A LFA 4.6 14.6 - - + -
308A LFA 4.5 14.8 - - + -
313A LFA 5.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ILE 2.9 12.9 + - - -
194A TYR 3.1 3.8 + - - -
196A ILE* 1.3 77.2 - - - +
198A TYR* 1.3 59.9 + - - +
200A VAL* 3.5 3.5 + - - +
201A THR* 2.9 27.0 + - - -
213A ARG* 3.3 17.0 - - - -
217A TYR* 3.5 8.3 - - - -
308A LFA 4.0 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 4.2 0.7 - - - -
126A GLY* 3.7 11.4 - - - -
129A GLY* 3.0 23.7 - - - -
130A GLU* 3.4 36.8 - - + -
133A ILE* 3.5 17.1 - - + +
143A GLY 2.7 29.6 + - - -
146A SER* 4.5 0.2 - - - -
147A TYR* 3.2 33.9 + + + +
194A TYR 2.9 13.1 + - - +
195A PRO* 3.5 9.6 - - + +
196A ILE 3.2 0.2 - - - -
197A GLY* 1.3 74.1 - - - +
199A ALA* 1.3 56.0 + - - +
201A THR* 2.9 5.4 + - + -
202A LEU* 2.7 40.4 + - + -
213A ARG* 3.7 10.8 - - - +
217A TYR* 3.5 0.8 + - - -
301A RET 3.7 22.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
147A TYR* 3.7 17.0 - - + +
195A PRO 3.0 13.9 + - - +
196A ILE* 3.1 12.1 + - - +
198A TYR* 1.3 78.6 - - - +
200A VAL* 1.3 63.0 + - - +
202A LEU* 3.1 6.4 + - - +
203A PHE* 3.1 37.9 + - + -
303A LFA 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 3.1 17.2 + - + +
197A GLY 3.6 6.7 - - - +
199A ALA* 1.3 76.2 - - - +
201A THR* 1.3 54.5 + - - +
203A PHE 3.2 0.2 + - - -
204A ALA* 2.7 44.1 + - + +
209A ILE* 4.0 23.3 - - + -
213A ARG* 6.4 0.4 - - + -
302A LFA 4.2 34.5 - - + -
303A LFA 4.2 16.8 - - + +
308A LFA 4.1 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 5.0 4.9 - - + +
133A ILE* 4.2 27.3 - - + +
134A ASN* 5.2 1.8 - - - +
138A GLY* 5.8 1.6 - - - -
197A GLY 2.9 7.3 + - - -
198A TYR* 2.9 10.9 + - - -
200A VAL* 1.3 77.2 - - - +
202A LEU* 1.3 63.3 + - - +
203A PHE 3.3 0.5 + - - -
204A ALA 3.8 15.1 + - - +
205A PRO* 4.4 4.9 - - - +
209A ILE* 5.4 2.0 - - - +
210A GLN* 3.1 31.7 + - - +
213A ARG* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 3.5 35.6 - - + +
138A GLY* 4.7 0.3 - - - -
139A PHE* 3.6 50.2 + - + +
140A THR 4.0 9.4 - - - +
143A GLY 4.0 8.1 - - - +
144A LEU* 4.1 24.5 - - + -
147A TYR* 4.8 7.2 - - + -
198A TYR* 2.7 24.5 + - + +
199A ALA* 3.1 8.9 + - - +
201A THR* 1.3 75.3 - - - +
203A PHE* 1.3 83.8 + - + +
205A PRO* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 3.8 26.5 - + + -
144A LEU* 4.7 9.6 - - + -
147A TYR* 6.2 1.6 - + - -
199A ALA* 3.1 32.3 + - + +
202A LEU* 1.3 105.0 - - + +
204A ALA* 1.3 60.6 + - - +
205A PRO* 3.9 7.2 - - - +
303A LFA 3.8 58.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 2.7 32.6 + - + +
201A THR* 4.1 5.1 - - - +
202A LEU 3.7 0.6 - - - -
203A PHE* 1.3 77.0 - - - +
205A PRO* 1.3 69.7 - - - +
209A ILE* 3.7 20.3 - - + +
210A GLN* 6.1 0.5 - - - -
302A LFA 4.5 19.3 - - + -
303A LFA 4.8 9.2 - - + -
----------------------------------------------------------
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