Contacts of the helix formed by residues 179 - 184 (chain D) in PDB entry 1Y67
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 TYR 179 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASP* 5.9 0.4 - - - -
23D THR* 5.4 1.8 - - - -
174D VAL* 3.5 22.9 - - - -
175D TRP 3.5 12.3 - - - -
176D GLU* 3.1 27.7 + - + +
177D HIS 3.2 0.2 - - - -
178D ALA* 1.3 80.3 - - - +
180D TYR* 1.3 62.6 + + - +
181D LEU 3.4 2.2 - - - -
182D ASN* 3.4 3.9 + - - -
183D TYR* 2.8 39.8 + - + +
184D GLN 3.3 24.0 - - - -
185D ASN* 4.7 2.6 + - - -
187D ARG* 2.9 60.6 + - + +
190D TYR* 3.4 44.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 5.7 0.6 - - - -
26C ILE* 3.4 15.3 - - + +
27C HIS* 5.2 0.5 + - - -
31C HIS* 2.7 31.2 + + - -
177C HIS* 3.3 38.7 + - + +
180C TYR* 4.2 25.6 - - + -
181C LEU* 3.9 31.9 - - + +
176D GLU* 2.8 37.8 + - + +
177D HIS 4.4 1.8 + - - -
179D TYR* 1.3 74.3 - + - +
181D LEU* 1.3 60.6 + - - +
184D GLN* 2.8 64.4 + - + +
185D ASN* 3.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 5.0 2.4 + - - -
180C TYR* 3.7 47.7 - - + +
181C LEU* 4.2 19.4 - - + +
184C GLN* 4.2 11.7 - - + +
20D ASP* 3.8 9.2 - - - +
22D ARG* 4.1 31.6 - - + +
23D THR* 3.6 24.5 + - - +
26D ILE* 4.2 14.8 - - + -
179D TYR 3.4 0.6 - - - -
180D TYR* 1.3 76.6 - - - +
182D ASN* 1.3 57.8 + - - +
184D GLN* 2.9 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLU* 5.5 1.1 + - - +
17D PRO 3.2 25.5 + - - +
18D HIS 3.5 5.1 + - - -
20D ASP* 3.2 36.7 + - - +
179D TYR* 3.4 3.4 + - - +
181D LEU* 1.3 78.4 - - - +
183D TYR* 1.3 93.2 + - + +
184D GLN* 3.6 4.9 + - - -
186D ARG* 3.5 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PRO 3.9 1.7 + - - -
18D HIS* 2.6 33.6 + - - -
19D ILE* 5.3 1.1 - - - -
179D TYR* 2.8 31.1 + - + +
182D ASN* 1.3 97.7 + - + +
184D GLN* 1.3 69.9 + - - +
185D ASN 3.2 0.5 + - - -
186D ARG* 2.8 51.2 + - + +
189D ASP* 3.7 31.9 - - + -
190D TYR* 3.6 32.3 - + + -
193D ALA* 3.2 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 3.3 28.7 + - - +
26C ILE* 3.8 24.4 - - + +
181C LEU* 4.2 6.3 - - + -
179D TYR* 3.3 23.0 + - - -
180D TYR* 2.8 52.9 + - + +
181D LEU* 2.9 29.1 + - - +
182D ASN 3.6 7.5 + - - -
183D TYR* 1.3 74.7 - - - +
185D ASN* 1.3 72.5 + - - +
186D ARG* 3.1 27.6 + - - +
----------------------------------------------------------
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