Contacts of the helix formed by residues 147 - 163 (chain A) in PDB entry 5M7S
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 ASN 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 3.1 17.8 + - + +
146A SER* 1.3 78.0 + - - +
148A PRO* 1.3 65.7 - - - +
149A LYS* 3.0 30.6 + - - +
150A GLU* 3.0 23.0 + - + +
151A VAL* 3.1 13.9 + - - +
538B PHE* 3.8 16.5 - - - -
544B GLU* 2.9 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER 3.4 10.0 - - - +
147A ASN* 1.3 90.7 - - - +
149A LYS* 1.3 53.9 + - - +
151A VAL* 3.7 11.7 - - + +
152A SER* 2.8 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASN* 3.0 19.4 + - - +
148A PRO* 1.3 79.7 - - - +
150A GLU* 1.3 56.5 + - - +
152A SER* 3.4 8.1 + - - -
153A THR* 2.9 34.2 + - - +
156A ARG* 5.3 0.3 + - - -
538B PHE* 4.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.9 5.6 - - + -
108A ARG* 2.8 37.4 + - - +
142A ASP 4.1 2.4 - - - +
143A ILE* 3.4 27.5 - - + +
144A THR* 3.5 26.4 + - - +
147A ASN* 3.0 16.2 + - + +
149A LYS* 1.3 77.3 - - - +
151A VAL* 1.3 65.4 + - - +
153A THR* 3.4 7.1 + - - +
154A LEU* 3.2 21.1 + - - +
538B PHE* 3.0 42.1 - - - -
545B LYS 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 5.3 3.4 - - + -
145A PHE* 3.9 20.0 - - - +
147A ASN 3.1 13.4 + - - +
148A PRO* 3.7 11.4 - - + +
149A LYS 3.4 0.2 - - - -
150A GLU* 1.3 77.0 - - - +
152A SER* 1.3 61.9 + - - +
154A LEU* 3.2 8.5 + - - +
155A LYS* 3.0 35.1 + - - +
198A ILE* 4.0 22.2 - - + -
201A GLU* 3.6 32.3 - - + +
202A ILE* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PRO 2.8 20.1 + - - -
149A LYS* 3.5 8.9 - - - -
150A GLU 3.3 0.4 - - - -
151A VAL* 1.3 77.0 - - - +
153A THR* 1.3 58.0 + - - +
155A LYS* 3.1 17.2 + - - +
156A ARG* 2.8 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 4.4 0.9 - - + -
108A ARG* 3.6 50.4 - - + +
110A MET* 4.3 0.5 - - - +
149A LYS* 2.9 22.3 + - - +
150A GLU* 3.7 12.0 + - - -
151A VAL 3.3 0.2 - - - -
152A SER* 1.3 75.3 - - - +
154A LEU* 1.3 61.4 + - - +
156A ARG* 2.9 33.7 + - - +
157A LYS* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.7 29.1 - - + -
137A ILE* 3.9 32.1 - - + -
139A PRO* 4.4 7.0 - - + -
143A ILE* 4.4 7.0 - - + -
150A GLU 3.2 6.8 + - - +
151A VAL* 3.2 10.8 + - - +
153A THR* 1.3 76.0 - - - +
155A LYS* 1.3 63.4 + - - +
157A LYS* 3.3 4.8 + - + +
158A LEU* 3.1 34.7 + - + +
171A LEU* 3.9 16.8 - - + -
198A ILE* 3.8 28.5 - - + -
202A ILE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 3.0 25.9 + - - +
152A SER* 3.1 18.6 + - - +
154A LEU* 1.3 75.8 - - - +
156A ARG* 1.3 57.1 + - - +
158A LEU* 3.2 5.6 + - - +
159A ASP* 2.9 34.6 + - - +
201A GLU* 3.0 35.1 + - - +
202A ILE* 3.6 17.3 - - + -
205A TYR* 3.8 56.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 4.0 24.1 - - + +
152A SER* 2.8 26.4 + - - +
153A THR* 2.9 48.8 + - - +
155A LYS* 1.3 72.3 - - - +
157A LYS* 1.3 55.7 + - - +
159A ASP* 3.2 11.0 - - - +
160A GLN* 3.0 28.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
102A LYS* 2.9 23.0 + - - +
106A PHE 3.8 1.2 + - - -
107A TRP* 2.8 27.8 + - - +
109A GLU 2.6 29.9 + - - +
110A MET* 3.6 16.0 - - + +
111A TYR* 3.5 29.8 - - + -
135A TYR* 3.6 11.2 - - + +
137A ILE* 3.7 19.7 - - + +
153A THR 3.1 12.9 + - - +
154A LEU* 3.7 10.5 - - + +
156A ARG* 1.3 76.1 - - - +
158A LEU* 1.3 63.4 + - + +
160A GLN* 3.3 14.3 + - - +
161A VAL* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 3.9 29.6 - - + +
137A ILE* 3.9 17.7 - - + -
154A LEU* 3.1 36.5 + - + +
155A LYS* 3.9 4.5 - - - +
157A LYS* 1.3 77.0 - - + +
159A ASP* 1.3 58.5 + - - +
161A VAL* 3.4 2.7 + - - +
162A SER* 2.9 25.5 + - - -
169A PHE* 3.7 23.4 - - + -
170A ALA 5.3 1.1 - - - +
171A LEU* 4.5 7.0 - - + -
202A ILE* 3.5 32.5 - - + -
206A LEU* 4.3 19.5 - - + -
212A PHE* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LYS 2.9 16.6 + - - +
156A ARG* 3.2 18.3 - - - +
158A LEU* 1.3 74.9 - - - +
160A GLN* 1.3 65.7 + - - +
162A SER* 3.2 10.6 + - - -
163A GLN* 3.0 31.4 + - - +
205A TYR* 2.7 40.0 + - + -
206A LEU* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 3.6 21.1 - - - +
111A TYR* 2.9 57.8 + - - +
116A ALA* 4.9 2.4 - - - +
156A ARG 3.0 15.2 + - - +
157A LYS* 3.3 12.0 + - - +
159A ASP* 1.3 77.0 + - - +
161A VAL* 1.3 61.2 + - - +
163A GLN* 3.2 18.0 + - + +
164A PHE* 3.4 35.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TYR* 3.8 19.7 - - + -
119A LEU* 5.1 0.9 - - + -
123A ILE* 5.0 3.6 - - + -
135A TYR* 3.6 56.1 - - + -
157A LYS 3.1 13.2 + - - +
158A LEU 3.8 7.2 - - - +
159A ASP 3.3 0.2 - - - -
160A GLN* 1.3 78.0 - - - +
162A SER* 1.3 64.0 + - - +
164A PHE* 3.0 32.3 + - + +
166A CYS* 3.5 25.9 - - + +
169A PHE* 4.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU 2.9 17.0 + - - -
159A ASP* 3.4 15.9 - - - -
161A VAL* 1.3 78.6 - - - +
163A GLN* 1.3 60.6 + - - +
165A GLY* 3.2 18.5 + - - -
166A CYS 3.6 18.3 + - - +
169A PHE* 4.0 11.5 - - - -
206A LEU* 5.2 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 4.8 5.5 - - - +
159A ASP* 3.0 22.8 + - + +
160A GLN* 3.5 11.9 - - + +
161A VAL 3.2 0.2 - - - -
162A SER* 1.3 79.1 + - - +
164A PHE* 1.3 65.1 + - + +
165A GLY 3.2 3.0 + - - -
----------------------------------------------------------
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