Contacts of the strand formed by residues 160 - 166 (chain Z) in PDB entry 1O19
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 160 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Z LEU* 4.4 6.5 - - + -
154Z ASP 3.2 9.4 - - - +
155Z SER* 2.6 26.3 + - - +
159Z VAL* 1.4 71.2 - - - +
161Z HIS* 1.3 73.5 + - - +
162Z ASN* 5.0 2.7 - - - +
177Z ARG* 3.3 6.6 - - - +
178Z LEU* 2.9 45.9 + - + -
180Z LEU 3.1 17.0 + - - -
181Z ALA* 4.3 0.2 - - - +
261Z LEU* 5.1 0.2 - - - +
274Z ILE* 3.6 31.1 - - + +
277Z THR* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Z HIS 5.2 0.9 - - - -
108Z ALA* 4.9 7.4 - - + -
109Z PRO* 3.6 41.2 - - + +
110Z LEU* 5.2 3.2 + - - +
152Z VAL 4.1 0.2 - - - -
153Z LEU* 3.4 4.9 - - - -
154Z ASP* 2.7 41.7 + - + +
159Z VAL* 4.0 32.4 - - + +
160Z THR* 1.3 79.6 + - - +
162Z ASN* 1.3 65.9 + - - +
163Z VAL* 4.2 10.5 - - + -
175Z ILE* 4.0 8.7 - - + +
176Z MET 3.0 16.4 - - - -
177Z ARG* 3.7 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151Z ILE* 4.5 6.1 - - + +
152Z VAL 3.2 7.4 + - - +
153Z LEU* 3.6 20.8 - - - +
160Z THR* 5.0 2.3 - - - +
161Z HIS* 1.3 74.8 + - - +
163Z VAL* 1.3 63.9 + - - +
164Z PRO* 3.5 2.0 - - - +
175Z ILE* 3.2 24.3 - - - +
176Z MET* 2.9 12.9 + - - +
178Z LEU 5.8 0.3 + - - -
277Z THR* 2.9 31.8 - - - +
278Z THR* 3.4 34.8 + - - +
281Z SER* 3.6 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109Z PRO* 3.5 33.9 - - + -
136Z ILE* 5.1 2.2 - - + -
138Z ALA* 3.4 21.5 - - + -
139Z VAL* 5.0 0.9 - - + -
151Z ILE* 3.7 1.7 - - - +
152Z VAL 2.9 28.8 + - - +
154Z ASP* 5.8 0.2 - - + -
161Z HIS* 4.2 9.6 - - + -
162Z ASN* 1.3 78.1 - - - +
164Z PRO* 1.3 63.7 - - - +
165Z ILE* 3.5 17.8 + - + +
170Z ALA* 3.6 31.0 - - + -
175Z ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 164 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150Z GLY 3.7 7.0 - - - +
151Z ILE* 3.9 16.4 - - + -
162Z ASN 3.5 7.0 - - - +
163Z VAL* 1.3 83.7 - - - +
165Z ILE* 1.3 59.1 + - - +
170Z ALA* 3.6 0.2 - - - -
171Z LEU* 2.8 36.4 + - + +
174Z ALA* 3.7 15.0 - - + -
175Z ILE* 4.0 17.5 - - + +
281Z SER* 3.4 21.5 - - - +
285Z CYS* 3.8 21.3 - - - -
293Z LEU* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138Z ALA* 3.7 9.4 - - + +
139Z VAL* 3.5 40.6 - - + +
142Z LEU* 3.9 18.4 - - + -
148Z THR 3.4 16.8 - - - +
149Z THR* 3.1 24.4 - - - +
150Z GLY 2.9 12.9 + - - +
152Z VAL* 4.5 3.1 - - + -
163Z VAL* 3.5 21.1 + - + +
164Z PRO* 1.3 76.2 - - - +
166Z TYR* 1.3 60.6 + - - +
168Z GLY* 3.6 26.0 - - - +
169Z TYR 3.7 2.9 - - - +
170Z ALA* 3.6 16.2 - - + -
171Z LEU* 4.7 1.3 - - - -
293Z LEU* 4.3 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 MET* 5.9 1.3 - - + -
602 SER 4.8 9.2 + - - -
612 LYS* 6.1 2.1 - - + +
149Z THR* 3.6 18.8 - - + -
165Z ILE* 1.3 73.0 - - - +
167Z GLU* 1.3 90.1 + - + +
168Z GLY 2.9 5.2 + - - -
169Z TYR* 3.1 26.2 + - + +
171Z LEU* 4.3 21.5 - - + +
289Z ILE* 3.7 35.7 - - + -
292Z ASP* 4.0 17.0 + - - -
----------------------------------------------------------
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