Contacts of the helix formed by residues 177 - 193 (chain D) in PDB entry 2Y0N
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 PRO 177 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLU 3.7 8.3 - - - +
176D ILE* 1.3 86.2 - - + +
178D GLU* 1.3 56.0 + - - +
179D VAL* 3.1 4.3 - - + +
180D LEU* 2.8 30.7 + - + -
181D LYS 2.9 9.0 + - - -
488D LEU* 3.8 41.1 - - + +
489D ARG* 4.4 8.5 - - + +
492D ALA* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ILE 3.3 4.2 + - - +
177D PRO* 1.3 70.6 - - - +
179D VAL* 1.3 61.5 + - + +
180D LEU 3.2 0.2 - - - -
181D LYS* 3.5 30.7 + - + +
182D LYS* 3.0 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D PRO* 5.2 2.0 - - + -
178D GLU* 1.3 77.5 - - - +
180D LEU* 1.3 57.5 + - - +
182D LYS* 3.7 19.9 - - + +
183D GLN* 3.2 22.3 + - - +
492D ALA* 4.5 21.8 - - + +
495D HIS* 4.1 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ILE* 3.8 8.7 - - + -
177D PRO* 2.8 24.5 + - + +
179D VAL* 1.3 72.1 - - - +
181D LYS* 1.3 58.3 + - - +
182D LYS 3.3 0.7 - - - -
183D GLN* 3.3 6.2 + - + +
184D LEU* 2.9 33.1 + - - +
457D LEU* 3.8 16.0 - - + +
488D LEU* 3.3 50.3 - - + +
491D LEU* 3.8 25.4 - - + +
492D ALA* 3.9 12.3 - - + +
495D HIS* 4.7 8.1 - - + -
499D PHE* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ILE* 3.5 45.7 - - + +
177D PRO 2.9 5.1 + - - -
178D GLU* 3.5 33.2 + - + +
180D LEU* 1.3 73.4 - - - +
182D LYS* 1.3 63.8 + - + +
184D LEU* 3.2 11.0 + - + +
185D GLU* 3.1 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D GLU* 3.0 32.2 + - + +
179D VAL* 3.7 19.7 - - + +
181D LYS* 1.3 72.9 - - + +
183D GLN* 1.3 57.3 + - - +
185D GLU* 2.7 38.3 + - - +
186D ASP* 2.8 21.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
179D VAL 3.2 12.8 + - - +
180D LEU* 3.3 13.0 + - + +
182D LYS* 1.3 78.5 - - - +
184D LEU* 1.3 57.8 + - - +
186D ASP* 3.3 15.8 + - - +
187D ASP* 2.9 31.5 + - + +
190D TYR* 5.8 1.4 - - - -
454D GLN* 5.1 0.8 - - - +
457D LEU* 4.0 9.0 - - + -
495D HIS* 3.4 25.0 + - + +
499D PHE* 3.5 49.3 - - + +
501D GLU* 5.4 3.8 - - - +
504D TYR* 4.1 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ILE* 4.0 18.4 - - + -
180D LEU 2.9 16.3 + - - +
181D LYS* 3.5 10.8 - - + +
182D LYS 3.1 0.4 - - - -
183D GLN* 1.3 73.1 - - - +
185D GLU* 1.3 61.3 + - + +
187D ASP* 3.4 10.1 - - + +
188D CYS* 3.1 26.5 + - - +
275D TYR* 5.1 1.0 + - - -
454D GLN 5.1 0.7 - - - +
457D LEU* 3.8 30.3 - - + +
458D ARG* 4.1 32.5 - - + +
461D VAL* 3.8 25.1 - - + -
589H PHE* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LYS* 3.1 20.2 + - - +
182D LYS* 2.7 23.3 + - - +
184D LEU* 1.3 70.4 - - + +
186D ASP* 1.3 64.0 + - - +
188D CYS* 3.4 8.1 + - - +
189D TYR* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LYS* 2.8 20.5 + - - +
183D GLN* 3.4 23.3 - - - +
185D GLU* 1.3 74.9 - - - +
187D ASP* 1.3 65.1 + - - +
189D TYR* 3.0 10.0 + - - +
190D TYR* 3.0 45.3 + - + -
501D GLU* 5.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D GLN* 2.9 18.3 + - - +
184D LEU* 3.4 17.5 - - + +
186D ASP* 1.3 75.9 - - - +
188D CYS* 1.3 63.5 + - - +
190D TYR* 3.4 13.6 + - - +
191D ILE* 3.4 20.3 + - - +
198D VAL* 5.0 0.3 - - - +
275D TYR* 5.0 0.5 - - - -
454D GLN* 3.9 14.6 - - - +
458D ARG* 2.6 37.4 + - - +
504D TYR* 2.5 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D LEU 3.1 10.6 + - - +
185D GLU* 3.5 10.8 - - - +
187D ASP* 1.3 78.6 - - - +
189D TYR* 1.3 62.3 + - - +
191D ILE* 3.1 11.1 + - - -
192D ASN* 2.8 40.7 + - - +
193D ARG* 6.2 1.3 - - - -
275D TYR* 3.5 34.3 + - - +
590H GLU 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLU 3.1 9.9 + - - +
186D ASP* 3.0 12.0 + - - +
188D CYS* 1.3 79.1 - - - +
190D TYR* 1.3 64.9 + + - +
192D ASN* 4.6 0.4 - - - -
193D ARG* 3.2 45.4 + - + +
194D ARG* 3.0 68.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D GLN* 5.8 1.8 - - - -
186D ASP* 3.0 43.3 + - + +
187D ASP* 3.5 12.1 - - - +
188D CYS 3.2 0.2 - - - -
189D TYR* 1.3 78.5 - + + +
191D ILE* 1.3 51.5 + - - +
194D ARG* 3.4 33.3 + - - -
195D LYS 3.2 9.7 + - - -
196D ARG* 2.8 59.5 + - + +
501D GLU* 2.8 40.0 + - + +
504D TYR* 3.9 40.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ASP* 3.4 33.2 - - - +
188D CYS 3.1 4.2 + - - +
190D TYR* 1.3 78.5 - - - +
192D ASN* 1.3 63.0 + - - +
193D ARG 3.5 0.2 - - - -
195D LYS* 3.4 18.4 - - - +
196D ARG 3.2 21.5 + - - +
197D LEU* 4.6 3.0 - - + +
198D VAL* 5.1 3.6 - - + -
275D TYR* 4.3 17.7 - - + -
277D TYR* 4.3 19.0 - - + +
278D GLU* 3.4 44.0 - - + +
458D ARG* 3.5 12.8 - - - +
504D TYR* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D CYS* 2.8 33.9 + - - +
189D TYR* 4.6 0.2 - - - -
191D ILE* 1.3 74.6 - - + +
193D ARG* 1.3 69.4 + - - +
195D LYS* 4.7 5.5 - - - +
275D TYR* 3.1 47.3 - - - +
276D PRO* 5.6 0.6 - - + +
277D TYR* 3.9 34.5 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
188D CYS* 6.2 1.2 - - - -
189D TYR* 3.2 49.8 + - + +
191D ILE 3.5 0.8 - - - -
192D ASN* 1.3 89.3 + - - +
194D ARG* 1.3 60.7 + - - +
195D LYS* 3.0 14.3 + - - +
----------------------------------------------------------
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