Contacts of the helix formed by residues 174 - 188 (chain A) in PDB entry 1YNU
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 THR 174 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 3.5 31.6 - - + +
172A GLN 3.7 3.3 + - - +
173A ILE* 1.3 76.9 - - - +
175A GLU* 1.3 65.4 + - - +
176A THR* 3.7 11.0 + - - +
177A ALA* 3.1 34.6 + - - +
178A LEU* 3.1 14.9 + - - +
215A LEU* 3.8 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 1.3 71.5 - - - +
176A THR* 1.3 62.6 + - - +
178A LEU* 3.4 5.2 + - - +
179A GLU* 3.2 26.0 + - - +
215A LEU* 3.5 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.7 10.5 + - - +
175A GLU* 1.3 79.8 - - - +
177A ALA* 1.3 63.5 + - - +
179A GLU* 3.5 3.7 + - - +
180A GLU* 3.0 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 3.7 16.3 - - + +
164A HIS 3.3 27.9 + - - +
165A CYS* 5.4 0.9 - - - -
172A GLN 5.9 0.2 - - - +
174A THR* 3.1 24.1 + - - +
176A THR* 1.3 78.7 - - - +
178A LEU* 1.3 58.2 + - - +
180A GLU* 3.5 13.3 - - - +
181A ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.7 0.3 - - - +
163A ILE* 3.6 29.6 - - + -
173A ILE* 3.9 16.2 - - + -
174A THR 3.1 13.2 + - - +
175A GLU* 3.6 7.2 - - - +
176A THR 3.3 0.2 - - - -
177A ALA* 1.3 74.7 - - - +
179A GLU* 1.3 64.6 + - - +
181A ALA* 3.3 3.8 + - - +
182A TYR* 3.0 24.6 + - - +
195A VAL* 5.3 0.9 - - + -
215A LEU* 3.5 39.9 - - + +
216A LEU* 4.2 13.0 - - + -
219A PHE* 3.6 48.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLU 3.2 14.4 + - - +
176A THR* 4.0 3.8 - - - +
178A LEU* 1.3 77.9 - - - +
180A GLU* 1.3 52.8 + - - +
182A TYR* 3.2 4.5 + - - +
183A GLN* 2.8 54.7 + - - +
219A PHE* 3.3 21.5 - - - -
223A LYS* 3.3 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 4.7 20.7 + - + +
176A THR* 3.0 28.0 + - + +
177A ALA* 3.5 12.7 - - - +
179A GLU* 1.3 77.3 - - - +
181A ALA* 1.3 63.0 + - - +
183A GLN* 3.2 8.2 + - - +
184A GLU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.2 7.1 - - + +
161A VAL* 3.4 14.3 - - + +
162A PRO 3.5 25.4 - - - +
163A ILE* 3.7 21.3 - - + -
164A HIS 5.4 0.2 - - - +
177A ALA 2.9 18.3 + - - +
178A LEU 3.7 3.1 - - - +
180A GLU* 1.3 76.7 - - - +
182A TYR* 1.3 61.5 + - - +
184A GLU* 3.2 10.2 + - - +
185A ALA* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.4 8.7 - - + +
178A LEU 3.0 17.1 + - - +
179A GLU* 3.6 4.5 - - - +
181A ALA* 1.3 77.3 - - - +
183A GLN* 1.3 68.7 + - - +
185A ALA* 3.3 4.5 + - + +
186A GLU* 3.1 52.0 + - + +
192A VAL* 3.7 41.3 - - + -
219A PHE* 3.8 12.6 - + + -
223A LYS* 3.2 53.6 + - + +
225A ILE* 5.7 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 2.8 43.6 + - - +
180A GLU* 3.2 9.4 + - - +
182A TYR* 1.3 90.1 - - - +
184A GLU* 1.3 59.0 + - - +
186A GLU* 3.7 9.0 + - + +
187A LYS* 3.0 38.7 + - - +
223A LYS* 5.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 4.4 12.8 - - + -
162A PRO* 6.3 0.7 - - + -
180A GLU 3.0 11.8 + - - +
181A ALA* 3.3 13.5 - - - +
183A GLN* 1.3 75.3 - - - +
185A ALA* 1.3 63.9 + - - +
187A LYS* 3.3 13.2 - - - +
188A ARG* 3.1 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.8 0.7 - - + -
161A VAL* 4.6 10.0 - - + +
181A ALA 3.2 11.7 + - - +
182A TYR* 3.4 8.7 - - + +
183A GLN 3.3 0.2 - - - -
184A GLU* 1.3 74.4 - - - +
186A GLU* 1.3 58.3 + - - +
188A ARG* 2.8 22.5 + - - -
189A ASN 3.0 9.0 + - - -
190A LEU* 3.0 28.9 + - + +
192A VAL* 3.3 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 3.1 47.1 + - + +
183A GLN* 3.9 9.4 - - + +
185A ALA* 1.3 78.2 - - - +
187A LYS* 1.3 64.6 + - - +
189A ASN* 3.0 19.4 + - - +
190A LEU 4.4 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 3.0 26.6 + - + +
184A GLU* 3.3 22.7 - - - +
185A ALA 3.0 0.4 - - - -
186A GLU* 1.3 79.5 - - - +
188A ARG* 1.3 58.2 + - + +
189A ASN* 3.3 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 3.7 25.7 + - - +
160A ILE 5.2 4.6 + - - -
161A VAL* 4.7 9.9 - - - +
162A PRO* 5.9 3.0 - - - +
184A GLU* 3.1 40.6 + - - +
185A ALA 2.8 8.0 + - - +
187A LYS* 1.3 73.0 - - + +
189A ASN* 1.3 72.4 + - - +
190A LEU* 2.9 44.1 + - + +
----------------------------------------------------------
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