Contacts of the helix formed by residues 138 - 153 (chain U) in PDB entry 5IYB
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 ASP 138 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136U THR* 3.4 2.0 + - - -
137U SER* 1.3 79.0 + - - +
139U SER* 1.3 72.0 + - - +
140U VAL* 3.4 25.1 + - - +
141U ARG* 3.4 34.6 - - + +
142U LEU* 3.1 27.9 + - - +
183U THR* 4.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137U SER 3.6 4.0 + - - -
138U ASP* 1.3 74.1 + - - +
140U VAL* 1.3 63.1 + - - +
142U LEU* 3.6 9.0 + - - +
143U LYS* 3.0 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138U ASP* 3.3 17.7 - - - +
139U SER* 1.3 77.8 - - - +
141U ARG* 1.3 61.1 + - + +
143U LYS* 3.3 6.1 + - - +
144U CYS* 3.0 40.5 + - - -
183U THR* 5.0 12.1 - - + -
187U TYR* 6.2 2.5 - - + -
188U LYS* 4.7 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136U THR* 3.2 38.3 - - - +
138U ASP* 3.4 28.1 + - - +
139U SER 3.5 0.4 - - - -
140U VAL* 1.3 77.0 - - + +
142U LEU* 1.3 56.8 + - - +
144U CYS* 3.3 8.0 + - - +
145U ARG* 3.0 34.4 + - - +
173U GLU* 2.7 41.7 + - - +
174U GLU* 3.2 17.0 + - - -
177U TYR* 3.1 57.7 + - - +
183U THR* 4.8 10.5 - - + -
187U TYR* 4.7 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135U SER* 5.7 2.5 - - - -
136U THR* 3.5 36.3 - - - +
137U SER* 4.6 4.0 - - - +
138U ASP 3.1 25.3 + - - +
139U SER* 3.8 8.3 - - - +
141U ARG* 1.3 77.6 - - - +
143U LYS* 1.3 61.0 + - + +
145U ARG* 3.4 19.4 - - - +
146U GLU* 3.3 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197A TYR* 4.4 22.5 + - - -
139U SER* 3.0 25.0 + - - +
140U VAL* 3.7 6.1 - - - +
142U LEU* 1.3 72.6 - - + +
144U CYS* 1.3 66.6 + - - +
146U GLU* 3.1 52.4 + - - +
147U MET* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 144 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198A GLU* 5.8 4.9 - - - -
140U VAL* 3.0 37.1 + - - +
141U ARG* 3.3 7.4 + - - +
143U LYS* 1.3 77.8 - - - +
145U ARG* 1.3 56.5 + - - +
147U MET* 3.4 21.6 + - - +
148U LEU* 3.0 34.5 + - - +
173U GLU* 5.0 3.1 - - + -
187U TYR* 4.7 23.3 - - - +
188U LYS* 5.5 8.3 - - - -
191U VAL* 4.9 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133U ALA 5.2 0.8 + - - -
134U PRO 2.8 30.3 + - - -
135U SER* 3.8 11.7 - - - +
136U THR* 3.6 27.4 + - - +
141U ARG 3.0 17.5 + - - +
142U LEU* 3.4 24.1 - - + +
144U CYS* 1.3 74.7 - - - +
146U GLU* 1.3 60.2 + - - +
148U LEU* 3.2 9.9 + - - +
149U ALA* 2.8 28.5 + - - +
166U GLU 5.6 0.9 - - - +
169U GLY 5.2 3.9 - - - -
170U SER* 3.6 43.2 + - - +
173U GLU* 3.2 40.7 + - + -
174U GLU* 4.1 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142U LEU 3.3 6.4 + - - +
143U LYS* 3.1 56.8 + - - +
145U ARG* 1.3 75.8 - - - +
147U MET* 1.3 59.3 + - + +
149U ALA* 3.6 8.4 - - - +
150U ALA* 2.6 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195A VAL 5.5 1.1 - - - +
1197A TYR* 3.2 32.3 - - + +
1198A GLU* 3.9 35.7 - - + +
143U LYS* 3.1 27.4 + - - +
144U CYS* 3.5 23.8 - - - +
145U ARG 3.2 0.2 - - - -
146U GLU* 1.3 78.6 - - + +
148U LEU* 1.3 59.0 - - - +
150U ALA* 3.4 7.6 + - - +
151U ALA* 2.9 27.9 + - - +
191U VAL* 5.9 0.4 - - + -
192U ARG* 6.1 0.4 - - + -
195U ILE* 4.1 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144U CYS 3.0 19.4 + - - +
145U ARG* 3.2 7.4 + - - +
147U MET* 1.3 73.4 - - - +
149U ALA* 1.3 58.5 + - - +
151U ALA* 3.3 5.4 + - - +
152U LEU* 2.9 35.7 + - + +
169U GLY* 3.8 28.0 - - - +
172U ILE* 4.3 18.6 - - + -
173U GLU* 4.0 22.4 - - + +
176U ILE* 5.1 1.3 - - + -
191U VAL* 4.2 22.9 - - + +
194U ARG* 4.8 4.5 - - + -
195U ILE* 3.6 22.7 - - + +
198U LEU* 4.7 15.7 - - + -
220U PHE* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145U ARG 2.8 20.1 + - - +
146U GLU* 3.6 10.1 - - - +
148U LEU* 1.3 72.7 - - - +
150U ALA* 1.3 56.4 + - - +
152U LEU* 3.3 8.7 + - - +
153U ARG* 3.0 38.9 + - - +
165U GLU* 4.0 9.4 + - + +
166U GLU* 3.8 37.5 - - + +
169U GLY* 5.1 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146U GLU 2.6 22.1 + - - +
147U MET* 3.5 9.9 - - - +
149U ALA* 1.3 71.8 - - - +
151U ALA* 1.3 61.0 + - - +
153U ARG* 3.2 26.7 + - - +
154U THR* 3.6 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147U MET 2.9 17.2 + - - +
148U LEU* 3.5 8.5 - - - +
150U ALA* 1.3 76.8 - - - +
152U LEU* 1.3 58.9 + - - +
154U THR* 2.9 25.4 + - - -
195U ILE* 4.1 35.2 - - + +
198U LEU* 4.4 16.0 - - + +
199U LYS* 4.3 8.1 - - + -
207U ARG* 4.3 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148U LEU* 2.9 21.6 + - + +
149U ALA 3.6 4.9 - - - +
151U ALA* 1.3 75.1 - - - +
153U ARG* 1.3 61.4 + - - +
154U THR 3.2 2.9 + - - +
158U TYR* 4.0 10.7 + - - +
165U GLU* 3.4 41.3 - - + +
168U LEU* 4.8 5.8 - - + -
169U GLY* 4.2 15.5 - - - +
172U ILE* 4.5 10.1 - - + -
198U LEU* 3.9 32.3 - - + -
207U ARG* 3.9 20.2 - - + +
210U VAL* 4.7 11.2 - - + -
211U LEU* 4.3 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149U ALA* 3.0 22.8 + - - +
150U ALA* 3.5 17.9 - - - +
151U ALA 3.2 0.8 - - - -
152U LEU* 1.3 75.0 - - - +
154U THR* 1.3 65.6 + - - +
155U GLY 3.4 0.7 + - - -
156U ASP* 3.1 23.8 + - - +
158U TYR* 3.8 28.0 + - + +
165U GLU* 3.2 19.4 + - + +
166U GLU* 2.3 34.6 + - - +
----------------------------------------------------------
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