Contacts of the strand formed by residues 173 - 178 (chain B) in PDB entry 1YQZ
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 HIS 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ASP* 2.8 45.5 + - - +
150B LYS* 3.4 12.2 - - + +
151B VAL 3.1 19.5 + - - +
168B TYR* 6.0 4.9 - + - -
171B GLY 4.2 13.2 + - - -
172B LEU* 1.3 77.5 + - - +
174B PRO* 1.3 64.5 - - + +
175B THR* 5.0 1.4 + - - -
230B TYR* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 3.1 11.9 - - + +
153B VAL* 4.0 19.5 - - + -
164B LEU* 3.9 32.8 - - + +
167B LEU* 4.5 11.0 - - + -
168B TYR* 4.2 19.5 - - + +
172B LEU 3.3 11.9 - - - +
173B HIS* 1.3 87.7 - - + +
175B THR* 1.3 64.7 + - - +
204B ILE* 3.4 22.3 - - + +
205B PRO* 3.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LYS* 5.4 2.6 - - - -
151B VAL 2.9 4.9 + - - -
152B LEU* 3.6 8.1 - - + +
153B VAL* 2.8 30.5 + - - +
164B LEU* 4.6 2.7 - - - -
173B HIS 5.0 0.9 + - - -
174B PRO* 1.3 75.8 + - - +
176B LEU* 1.3 65.7 + - - +
177B ILE* 4.5 2.0 - - + -
204B ILE* 4.9 0.2 - - - -
205B PRO* 3.3 36.3 - - + +
206B TYR* 4.5 1.1 - - - +
207B ARG* 4.2 15.5 - - - +
228B GLU* 4.9 2.5 + - - +
230B TYR* 3.3 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.4 22.4 - - + +
155B GLY 3.1 28.3 - - - +
156B ALA* 4.6 10.8 - - + -
160B SER* 4.9 1.6 - - - -
161B LEU* 4.3 20.6 - - + -
164B LEU* 3.5 21.0 - - + +
175B THR* 1.3 73.2 - - - +
177B ILE* 1.3 68.6 + - - +
178B HIS* 5.6 0.4 - - + -
183B ILE* 5.7 1.8 - - + -
195B ILE* 5.4 2.0 - - + -
196B LEU* 5.7 1.6 - - + -
199B LEU* 4.0 24.5 - - + -
205B PRO 3.0 8.0 + - - +
206B TYR* 3.0 16.6 - - + +
207B ARG 2.9 24.6 + - - -
208B LEU* 5.5 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.8 18.8 - - + -
153B VAL 3.0 16.1 + - - +
154B VAL* 4.1 25.1 - - + -
155B GLY* 2.9 28.2 + - - +
175B THR* 4.5 2.7 - - + -
176B LEU* 1.3 82.7 - - - +
178B HIS* 1.3 62.6 + - - +
207B ARG* 3.2 26.5 - - + +
208B LEU* 5.4 0.4 - - - -
210B GLU* 3.8 20.2 - - + +
211B GLU* 4.1 10.8 - - - -
212B ILE* 4.1 20.0 - - + +
222B PHE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 5.7 1.8 - - - -
155B GLY* 3.6 9.5 + - - +
156B ALA* 3.5 39.6 + - + -
176B LEU* 5.6 0.4 - - + -
177B ILE* 1.3 77.6 - - - +
179B ARG* 1.3 94.8 + - + +
180B SER* 3.1 40.6 + - - +
182B LYS 3.6 22.7 + - - -
183B ILE* 4.5 1.3 - - + -
207B ARG 3.2 5.3 + - - -
208B LEU* 3.4 10.2 - - + +
209B ASN 2.8 25.5 + - - -
210B GLU 3.0 9.6 + - - -
----------------------------------------------------------
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