Contacts of the helix formed by residues 152 - 164 (chain A) in PDB entry 1R8E
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 TYR 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 4.1 8.6 - - + +
148A LEU 3.4 20.2 - - - -
149A ASN 3.0 10.2 + - - +
151A SER* 1.3 77.4 - - - +
153A SER* 1.3 64.2 + - - +
154A LYS* 3.0 8.7 - - - +
155A LEU* 3.1 16.7 + - + +
156A LYS* 2.8 33.3 + - + +
167A ASN* 5.8 0.2 - - - -
170A TYR* 3.6 32.8 - + + -
171A GLY 2.6 32.4 + - - -
172A ALA* 4.4 0.2 - - - +
190A ILE* 3.8 22.2 - - + +
191A PHE 3.4 17.5 - - - -
192A THR* 5.0 5.4 - - - -
302A IMD 3.1 19.1 + - - -
307A IMD 3.8 14.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN 3.9 1.6 + - - -
150A ALA* 3.1 23.5 + - - +
151A SER 3.3 1.0 - - - -
152A TYR* 1.3 77.1 - - - +
154A LYS* 1.3 61.8 + - - +
156A LYS* 3.4 7.5 + - - +
157A LYS* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 4.3 10.8 - - + +
140A GLU* 5.7 0.4 - - - +
150A ALA 5.0 0.4 - - - -
151A SER 2.7 30.6 + - - -
152A TYR* 3.0 9.3 - - - +
153A SER* 1.3 74.8 - - - +
155A LEU* 1.3 83.1 + - + +
157A LYS* 3.5 8.9 + - - +
158A PHE* 3.0 34.8 + - + -
206A ASP* 5.4 7.6 - - - +
207A MET* 3.9 20.9 - - + -
306A IMD 3.3 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.4 41.2 - - + +
136A GLN 4.1 7.2 - - - -
137A THR* 4.0 12.8 - - + -
152A TYR* 3.5 17.3 - - + +
154A LYS* 1.3 94.4 - - + +
156A LYS* 1.3 63.1 + - - +
158A PHE* 3.3 5.5 + - - +
159A ILE* 3.1 24.1 + - - +
190A ILE* 3.8 30.1 - - + +
191A PHE* 4.0 5.4 - - - -
192A THR* 3.5 22.9 - - + -
207A MET* 3.7 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN 5.1 3.1 - - - +
152A TYR* 2.8 31.9 + - + +
153A SER* 3.9 5.8 - - - +
155A LEU* 1.3 74.0 - - + +
157A LYS* 1.3 59.8 + - + +
159A ILE* 4.5 1.3 - - - +
160A GLU* 2.7 58.0 + - - +
166A THR* 4.0 7.9 + - - -
167A ASN* 2.9 61.0 + - - +
170A TYR* 3.5 31.3 + - + +
192A THR* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER* 2.9 41.3 + - - +
154A LYS* 3.6 10.4 - - - +
155A LEU 3.2 0.2 - - - -
156A LYS* 1.3 76.9 - - + +
158A PHE* 1.3 69.0 + - + +
160A GLU* 3.6 12.3 - - - +
161A SER* 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 5.6 2.5 - - + -
154A LYS* 3.0 28.0 - - + -
155A LEU 3.3 6.5 + - - +
157A LYS* 1.3 84.0 - - + +
159A ILE* 1.3 63.7 + - + +
161A SER* 3.0 20.8 + - - -
162A ALA* 3.4 6.6 + - - +
200A ILE* 3.4 40.7 - - + +
201A SER* 4.3 5.6 - - - -
202A SER 3.6 9.2 - - - -
203A ILE* 3.4 31.4 - - + -
204A THR* 3.5 25.8 - - + -
207A MET* 3.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.4 18.6 - - + -
155A LEU 3.1 13.4 + - - +
156A LYS* 4.0 4.5 - - - +
158A PHE* 1.3 77.3 - - + +
160A GLU* 1.3 59.9 + - + +
162A ALA* 4.6 2.5 - - - +
163A ASP* 2.8 48.6 + - + +
165A PHE 4.7 0.7 - - - +
167A ASN* 4.4 21.8 - - + +
192A THR* 3.0 44.2 - - + +
193A PRO 3.1 18.6 - - - +
194A VAL* 3.7 13.5 - - + -
195A LEU* 6.1 0.7 - - + -
200A ILE* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LYS* 2.7 49.4 + - + +
157A LYS* 3.6 12.0 - - - +
159A ILE* 1.3 74.0 - - + +
161A SER* 1.3 58.9 + - - +
162A ALA 3.1 0.4 - - - -
164A GLY* 2.9 32.9 + - - +
166A THR* 3.4 47.8 - - + +
167A ASN 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS 2.9 13.6 + - - -
158A PHE* 3.0 14.5 + - - -
160A GLU* 1.3 77.4 - - - +
162A ALA* 1.3 55.9 + - - +
164A GLY 4.9 0.2 - - - -
198A LYS* 4.6 11.1 + - - -
199A GLN 5.4 0.5 - - - +
200A ILE* 5.6 1.6 - - - -
201A SER* 3.3 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE 3.4 10.0 + - - +
159A ILE* 3.3 4.1 + - - +
160A GLU 3.1 0.2 - - - -
161A SER* 1.3 80.5 - - - +
163A ASP* 1.3 67.8 + - - +
164A GLY 3.7 0.2 - - - -
196A THR* 3.1 17.0 + - + +
198A LYS* 3.4 42.4 - - - +
199A GLN 4.2 9.2 - - - +
200A ILE* 4.4 12.6 - - + -
310A IMD 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 6.0 1.9 - - - +
104A THR* 4.6 9.4 + - + +
159A ILE* 2.8 26.0 + - + +
162A ALA* 1.3 80.7 - - - +
164A GLY* 1.3 54.5 + - - +
165A PHE* 2.7 33.8 + - + +
194A VAL* 3.5 9.2 - - - +
195A LEU* 2.6 36.4 + - + +
196A THR* 2.8 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE 4.0 0.2 + - - -
160A GLU* 2.9 24.0 + - - +
162A ALA 3.7 0.4 - - - -
163A ASP* 1.3 73.7 - - - +
165A PHE* 1.3 56.9 + - - -
166A THR* 3.1 16.2 + - - +
----------------------------------------------------------
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