Contacts of the helix formed by residues 170 - 181 (chain Z) in PDB entry 5WTI
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 PRO 170 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Z GLU* 3.7 22.0 - - + +
101Z GLU* 3.6 36.1 - - + +
168Z LYS 3.2 10.3 - - - +
169Z ASP* 1.3 92.2 - - - +
171Z LEU* 1.3 57.0 + - - +
172Z ALA 3.3 1.8 - - - -
173Z LYS* 3.3 16.7 + - + +
174Z ILE* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Z LEU* 5.0 7.6 - - + -
101Z GLU* 5.5 1.3 + - + -
119Z LYS* 4.1 36.8 - - + +
120Z PHE* 3.5 30.5 - - + -
123Z PRO* 4.6 4.0 - - + -
124Z LEU* 5.6 0.7 - - + -
131Z SER* 4.3 20.2 - - - +
132Z GLY* 4.4 9.9 - - - -
169Z ASP* 3.3 18.7 + - - +
170Z PRO* 1.3 78.2 - - - +
172Z ALA* 1.3 58.3 + - - +
174Z ILE* 3.2 7.1 + - + -
175Z LEU* 2.7 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132Z GLY 3.9 21.9 + - - +
133Z LYS* 5.7 5.8 - - + +
169Z ASP 4.5 5.4 + - - +
170Z PRO 3.3 0.4 - - - -
171Z LEU* 1.3 78.8 - - - +
173Z LYS* 1.3 58.0 + - - +
175Z LEU* 3.5 9.3 + - - +
176Z GLY* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Z ILE* 4.8 8.1 - - - -
97Z GLU* 3.2 35.6 + - - +
169Z ASP 5.2 0.8 + - - +
170Z PRO* 3.3 16.7 + - + +
171Z LEU 3.3 0.2 - - - -
172Z ALA* 1.3 80.0 - - - +
174Z ILE* 1.3 62.6 + - - +
176Z GLY* 3.2 1.5 + - - -
177Z LYS* 3.1 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Z ILE* 3.9 24.4 - - + +
97Z GLU* 3.6 47.6 - - + +
98Z LEU* 4.0 31.2 - - + -
101Z GLU* 4.3 8.7 - - + -
120Z PHE* 6.4 0.2 - - + -
170Z PRO* 2.9 28.7 + - + +
171Z LEU* 3.2 6.7 + - + +
173Z LYS* 1.3 73.9 - - + +
175Z LEU* 1.3 63.6 + - + +
177Z LYS* 3.4 1.7 + - - +
178Z LEU* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123Z PRO* 3.7 35.2 - - + +
124Z LEU* 4.1 15.3 - - + -
131Z SER 3.9 12.8 - - - +
132Z GLY* 5.5 0.2 - - - -
133Z LYS* 4.1 19.3 - - - -
171Z LEU* 2.7 44.7 + - + +
172Z ALA* 3.9 7.4 - - - +
174Z ILE* 1.3 73.2 - - + +
176Z GLY* 1.3 62.6 + - - +
178Z LEU* 3.4 5.4 + - + +
179Z ALA* 3.1 23.9 + - - +
184Z ILE* 3.9 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172Z ALA 3.0 15.2 + - - -
173Z LYS* 3.2 3.8 + - - -
174Z ILE 3.2 0.2 - - - -
175Z LEU* 1.3 78.5 - - - +
177Z LYS* 1.3 62.3 + - - +
179Z ALA* 3.5 7.4 + - - +
180Z GLU* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Z ILE* 4.1 21.3 - - + -
173Z LYS* 3.1 25.8 + - + +
174Z ILE 4.1 2.5 - - - +
176Z GLY* 1.3 73.6 - - - +
178Z LEU* 1.3 66.8 + - - +
180Z GLU* 2.7 45.7 + - - +
181Z TYR* 3.1 51.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Z ILE* 4.1 18.2 - - + -
95Z LEU* 3.9 22.4 - - + -
98Z LEU* 4.2 8.1 - - + -
124Z LEU* 4.1 18.6 - - + -
174Z ILE* 2.9 41.4 + - + +
175Z LEU* 3.8 2.5 - - + +
177Z LYS* 1.3 75.8 - - - +
179Z ALA* 1.3 61.3 + - - +
181Z TYR* 3.3 6.6 + - - -
183Z LEU* 2.8 53.8 + - + +
184Z ILE* 3.6 28.9 - - + -
186Z LEU* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Z PHE* 4.7 3.3 - - - -
175Z LEU 3.1 16.8 + - - +
176Z GLY* 3.6 7.9 - - - +
177Z LYS 3.2 0.2 - - - -
178Z LEU* 1.3 77.5 - - - +
180Z GLU* 1.3 62.4 + - + +
182Z GLY* 3.2 12.4 + - - +
184Z ILE* 3.7 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Z PHE* 3.3 18.9 - - - -
86Z VAL* 4.8 0.7 - - - +
176Z GLY 3.3 16.7 - - - +
177Z LYS* 2.7 44.7 + - - +
179Z ALA* 1.3 77.3 - - + +
181Z TYR* 1.3 69.4 + - + +
182Z GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Z GLN* 3.0 24.9 + - - +
82Z PHE* 3.3 11.7 - - - -
86Z VAL* 3.5 31.6 - - + -
90Z VAL* 3.0 30.4 - - + +
91Z VAL* 3.9 13.9 - - + -
94Z ILE* 4.1 24.9 - - + -
177Z LYS* 3.1 53.0 + - + +
178Z LEU* 3.3 5.6 + - - +
179Z ALA 3.1 0.6 - - - -
180Z GLU* 1.3 92.2 - - + +
182Z GLY* 1.3 62.5 + - - +
183Z LEU* 3.3 15.2 + - + +
----------------------------------------------------------
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