Contacts of the helix formed by residues 182 - 198 (chain D) in PDB entry 5FLZ
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 VAL 182 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 4.6 15.9 - - - +
180D VAL* 4.1 12.1 - - + -
181D VAL* 1.4 81.4 - - + +
183D GLN* 1.4 63.3 + - - +
184D SER 3.1 0.9 - - - +
185D TYR* 2.9 47.4 + - + +
186D ASN* 3.2 17.1 + - - +
397D VAL* 4.6 2.5 - - + -
400D LYS* 5.7 0.4 - - - -
402D ALA* 4.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 5.5 0.9 + - - -
143D ALA* 4.4 12.9 - - + +
174D PRO* 4.1 25.4 - - + +
175D ALA 5.2 2.6 + - - -
177D SER 4.9 5.2 + - - +
178D SER* 3.1 26.9 + - - -
180D VAL* 3.5 26.4 - - + +
181D VAL 3.1 9.0 - - - +
182D VAL* 1.4 77.5 - - - +
184D SER* 1.4 73.9 + - - +
186D ASN* 3.2 11.0 + - - +
187D THR* 2.8 53.8 + - - +
390D ALA* 5.7 6.1 - - - +
393D THR* 3.5 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D VAL 3.1 14.1 + - - -
183D GLN* 1.4 90.1 + - - +
185D TYR* 1.4 55.6 + - - +
187D THR* 4.0 2.4 - - - -
188D ILE* 3.0 34.5 + - - +
390D ALA* 3.4 9.8 + - - +
393D THR* 3.4 27.2 - - - -
394D PHE* 3.3 26.2 + - - +
397D VAL* 4.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 5.6 0.2 - - - -
182D VAL* 2.9 40.2 + - + +
184D SER* 1.4 75.4 - - - +
186D ASN* 1.3 67.4 + - - +
188D ILE* 3.3 9.3 - - + +
189D LEU* 3.1 30.9 + - - +
397D VAL* 3.2 52.7 + - + -
398D PHE* 4.5 4.6 - - + -
401D GLY 4.4 0.5 - - - -
402D ALA* 2.9 35.8 + - + +
403D PHE* 5.6 3.1 - + + -
404D LEU* 4.5 1.7 - - - +
407D TYR* 3.7 24.9 - + - +
417D GLN* 3.9 21.6 + - - -
420D GLN* 3.6 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 3.3 35.4 + - - +
104D SER* 3.8 0.6 - - - +
105D TRP* 3.2 40.1 - - - +
143D ALA* 3.7 20.4 - - - +
144D GLY 3.5 15.4 + - - -
148D SER* 4.0 6.8 + - - +
182D VAL* 3.2 16.7 + - - +
183D GLN* 3.2 8.0 + - - +
185D TYR* 1.3 78.2 - - - +
187D THR* 1.3 63.2 + - - +
190D ALA* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D VAL* 4.0 24.7 - - + +
143D ALA* 4.3 7.8 - - - +
173D PHE* 4.5 15.3 - - + -
174D PRO* 4.5 7.0 - - + +
183D GLN* 2.8 39.1 + - - +
184D SER* 4.0 5.4 - - - -
186D ASN* 1.3 76.5 - - - +
188D ILE* 1.4 54.5 + - - +
190D ALA* 3.4 2.6 + - - +
191D LEU* 2.9 50.1 + - + +
390D ALA* 5.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D SER* 3.0 34.5 + - - +
185D TYR* 3.3 13.2 - - + +
187D THR* 1.4 67.7 - - - +
189D LEU* 1.3 67.3 + - - +
191D LEU* 3.4 9.2 + - + +
192D ARG* 3.4 17.5 + - - +
390D ALA* 4.3 10.8 - - + +
394D PHE* 3.6 22.9 - - + -
420D GLN* 3.4 41.5 - - + +
423D PHE* 3.7 20.7 - - + -
427D ARG* 3.6 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 3.6 38.0 + - + -
106D ALA 5.8 0.2 - - - +
185D TYR 3.1 15.4 + - - +
188D ILE* 1.3 76.5 - - - +
190D ALA* 1.4 61.4 + - - +
192D ARG* 3.7 6.2 + - - +
193D ARG* 3.4 32.2 + - - +
407D TYR* 3.9 23.3 - - + +
413D PHE* 4.1 11.9 - - + -
419D VAL* 3.9 29.6 - - + -
420D GLN* 3.5 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 3.3 21.9 - - + +
140D HIS* 6.1 0.9 - - + -
142D VAL* 4.3 17.7 - - + -
148D SER* 4.4 6.7 - - - +
152D SER* 3.6 9.1 + - - +
186D ASN 3.2 19.8 + - - +
187D THR 3.6 3.1 - - - +
189D LEU* 1.4 75.8 - - - +
191D LEU* 1.4 64.1 + - - +
193D ARG* 3.1 10.0 + - - +
194D LEU* 3.1 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D VAL* 6.1 0.4 - - + -
173D PHE* 4.1 16.2 - - + -
187D THR* 2.9 36.3 + - + +
188D ILE* 3.8 6.5 - - - +
189D LEU 3.4 0.4 - - - -
190D ALA* 1.4 71.5 - - - +
192D ARG* 1.4 66.0 + - - +
194D LEU* 4.2 14.1 - - + -
195D ILE* 3.0 31.2 + - + +
267D PHE* 3.8 33.4 - - + -
386D VAL* 5.9 2.2 - - + -
387D PHE* 4.0 24.2 - - + -
390D ALA* 5.0 11.7 - - + -
423D PHE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE 3.4 13.6 + - - +
189D LEU* 3.9 7.9 - - - +
190D ALA 3.3 1.4 - - - -
191D LEU* 1.4 77.7 - - - +
193D ARG* 1.4 81.3 - - - +
195D ILE* 3.8 2.8 - - - +
196D GLU* 3.2 39.1 + - - +
419D VAL* 3.1 35.2 + - - +
422D GLU* 3.5 25.3 + - - +
423D PHE* 3.4 54.2 - - + +
426D SER* 4.2 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D TRP* 3.6 32.8 - - - -
109D TYR* 3.7 17.6 + - - -
152D SER* 3.8 31.6 - - - +
155D LEU* 4.4 2.4 - - + +
156D GLU* 4.4 12.9 - - + +
189D LEU* 3.4 24.2 + - - +
190D ALA 3.1 8.1 + - - +
192D ARG* 1.4 99.0 - - - +
194D LEU* 1.4 60.6 + - + +
196D GLU* 4.8 1.6 - - - -
197D ASP* 2.9 49.6 + - + +
412D LEU* 5.4 9.5 - - - +
413D PHE* 6.0 1.8 - - - -
419D VAL* 4.2 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 5.4 1.6 - - + -
140D HIS* 3.8 37.5 - - + +
142D VAL* 4.1 17.5 - - + -
152D SER* 4.2 14.1 - - - +
155D LEU* 4.4 16.6 - - + -
169D THR* 4.9 8.3 - - + +
171D SER* 4.2 8.1 - - - +
173D PHE* 5.2 3.8 - - + -
190D ALA* 3.1 26.0 + - + +
191D LEU* 3.3 22.4 + - + +
193D ARG* 1.4 77.2 - - + +
195D ILE* 1.4 60.0 + - - +
198D SER* 3.2 31.0 + - - +
201D THR* 5.0 8.4 - - + +
266D HIS* 3.7 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LEU* 3.0 22.6 + - + +
192D ARG* 3.8 4.3 - - - +
194D LEU* 1.4 74.1 - - - +
196D GLU* 1.3 68.0 + - + +
198D SER 3.3 12.8 - - - +
263D PRO* 4.8 3.1 - - - +
264D GLU 5.8 3.1 - - - +
266D HIS* 3.6 16.5 + - - +
267D PHE* 3.8 22.7 - - + -
387D PHE* 3.5 31.9 - - + -
423D PHE* 4.2 22.9 - - + -
427D ARG* 5.9 0.9 - - + -
430D VAL* 5.4 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D CYS* 5.1 3.0 - - - -
192D ARG* 3.2 28.8 + - - +
193D ARG* 4.7 0.7 + - - -
195D ILE* 1.3 84.9 - - + +
197D ASP* 1.3 74.2 + - - +
198D SER 3.3 4.4 + - - +
199D ASP* 4.9 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 3.9 24.9 - - + +
156D GLU* 3.4 33.5 - - - +
159D CYS* 3.1 35.5 - - + +
167D LEU* 3.6 25.5 - - - +
193D ARG* 2.9 35.0 + - - +
196D GLU* 1.3 83.3 - - - +
198D SER* 1.4 58.5 + - - +
199D ASP* 4.0 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 3.7 15.3 - - - +
167D LEU* 3.2 12.5 + - - -
168D THR 3.8 1.7 - - - -
169D THR* 3.6 21.5 + - - +
193D ARG 3.8 0.6 + - - -
194D LEU* 3.2 18.7 + - - -
195D ILE 3.3 17.5 - - - +
196D GLU 3.7 4.0 - - - +
197D ASP* 1.4 79.0 - - - +
199D ASP* 1.4 60.9 + - - +
200D ALA 3.0 25.3 + - - -
201D THR* 4.8 0.4 - - - -
263D PRO* 4.7 4.0 - - - +
266D HIS* 3.4 9.8 - - - -
----------------------------------------------------------
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