Contacts of the strand formed by residues 172 - 179 (chain Z) in PDB entry 3SDI
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 GLY 172 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Z ASP* 3.0 10.6 - - - +
18Z THR* 2.9 37.6 + - - -
170Z GLY 2.7 10.2 + - - +
171Z ASP* 1.3 76.7 - - - +
173Z LEU* 1.3 61.7 + - - -
188Z PHE* 4.1 9.0 - - - -
189Z TYR 3.4 9.9 - - - -
191Z LEU* 3.7 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15Z ALA* 4.1 13.5 - - + -
16Z GLY 3.6 13.5 - - - +
155Z VAL* 4.2 1.6 - - + -
156Z ARG* 4.0 30.5 - - + -
159Z PHE* 3.5 40.8 - - + -
172Z GLY* 1.3 74.1 - - - +
174Z GLU* 1.3 60.2 + - - +
175Z ILE* 3.9 22.7 - - + -
187Z GLU 3.8 0.7 - - - +
188Z PHE* 3.3 9.0 - - - -
189Z TYR* 2.7 52.2 + - + +
191Z LEU* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Z LEU 4.2 0.7 - - - +
15Z ALA* 3.5 1.7 - - - -
16Z GLY* 2.9 34.2 + - - +
18Z THR* 4.1 12.0 - - + +
30Z TYR* 2.5 37.3 + - - -
32Z PRO* 3.5 24.7 - - + +
33Z LYS 5.4 0.2 + - - -
34Z VAL* 4.6 10.1 + - + +
173Z LEU* 1.3 71.7 - - - +
175Z ILE* 1.3 63.0 + - - +
176Z LEU* 4.2 10.2 + - + +
186Z LYS* 3.8 32.7 + - + +
187Z GLU 3.5 7.2 - - - +
188Z PHE* 4.3 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Z VAL* 4.1 25.8 - - + -
14Z LEU 4.0 2.5 - - - +
15Z ALA* 3.9 16.4 - - + -
152Z ILE* 4.5 15.5 - - + -
155Z VAL* 3.8 19.5 - - + -
156Z ARG* 4.4 5.2 - - + -
173Z LEU* 3.9 24.7 - - + -
174Z GLU* 1.3 76.1 - - - +
176Z LEU* 1.3 68.7 + - - +
177Z ILE* 4.0 12.5 - - + +
185Z ARG 3.8 0.3 - - - +
186Z LYS* 3.4 4.7 - - - -
187Z GLU* 2.9 44.1 + - + +
189Z TYR* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Z ALA 4.0 0.7 - - - +
13Z VAL* 3.4 5.9 - - - +
14Z LEU* 3.1 35.2 + - - +
34Z VAL* 3.6 43.3 - - + +
36Z ASP* 4.0 14.1 - - + +
42Z VAL* 3.8 28.9 - - + -
174Z GLU* 4.4 11.0 - - + +
175Z ILE* 1.3 81.3 - - - +
177Z ILE* 1.3 61.4 + - - +
178Z VAL* 4.2 2.8 + - - +
184Z VAL* 4.3 13.0 - - + -
185Z ARG 3.4 5.4 - - - +
186Z LYS* 4.0 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z PHE* 4.5 9.6 - - + -
12Z ALA 3.6 9.0 - - - +
13Z VAL* 3.8 20.4 - - + -
148Z VAL* 4.2 14.1 - - + -
152Z ILE* 4.6 6.7 - - + -
175Z ILE* 4.0 18.2 - - + +
176Z LEU* 1.3 75.8 - - - +
178Z VAL* 1.3 68.6 + - - +
179Z THR* 4.1 5.4 + - + +
183Z GLY 3.5 1.7 - - - +
184Z VAL* 3.4 4.0 - - - -
185Z ARG* 2.8 87.8 + - - +
187Z GLU* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z PHE* 3.2 8.3 - - - +
12Z ALA 3.0 33.6 + - - +
40Z ASN* 3.4 48.5 - - - +
42Z VAL* 3.8 40.2 - - + -
102Z ALA 4.5 5.6 - - - +
103Z GLY* 4.0 17.9 - - - +
104Z LEU* 4.0 3.9 - - + +
176Z LEU 4.8 0.9 - - - +
177Z ILE* 1.3 76.3 - - - +
179Z THR* 1.3 61.7 + - - +
183Z GLY 3.4 2.5 - - - +
184Z VAL* 4.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z ASP 4.1 11.0 - - - +
11Z PHE* 3.8 17.7 - - + -
40Z ASN* 3.1 13.3 - - - +
104Z LEU* 3.7 8.1 - - - -
148Z VAL* 6.5 0.2 - - + -
177Z ILE* 4.1 10.8 + - + -
178Z VAL* 1.3 77.2 - - - +
180Z LYS* 1.3 60.8 + - - +
182Z ASP* 2.9 24.7 + - - +
183Z GLY 2.9 24.1 + - - +
185Z ARG* 5.2 7.7 + - - +
----------------------------------------------------------
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