Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 6ABP
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 146 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 5.8 0.8 - - - +
91A GLN* 4.8 14.9 - - + +
107A MET* 5.7 0.3 - - - +
144A GLU 3.9 3.6 + - - -
145A LEU* 1.3 73.1 - - + +
147A THR* 1.4 60.9 + - - +
149A ARG* 2.9 39.6 + - - +
150A ARG* 2.9 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP 4.1 4.9 + - - +
90A ASP* 3.6 14.4 - - - +
91A GLN 5.9 0.9 - - - -
107A MET* 3.3 29.4 - - - +
108A LEU* 4.6 2.1 - - - +
110A ALA* 3.6 12.4 - - - +
145A LEU* 3.8 14.9 - - + +
146A ASP* 1.4 87.7 + - - +
148A ALA* 1.3 61.1 - - - +
150A ARG* 5.0 0.2 - - - +
151A ARG* 3.1 41.5 + - - +
307A ARA 3.3 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 3.6 23.3 - - + +
145A LEU* 3.0 14.9 + - + +
147A THR* 1.3 77.3 - - - +
149A ARG* 1.3 59.8 + - - +
151A ARG* 3.2 6.1 + - - +
152A THR* 3.0 30.1 + - - -
204A MET* 3.7 47.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 4.2 0.6 + - - -
143A ASN* 3.0 56.5 + - - +
144A GLU* 4.9 1.8 + - - +
145A LEU 2.8 14.0 + - - +
146A ASP* 2.9 37.9 + - - +
148A ALA* 1.3 72.9 - - - +
150A ARG* 1.3 64.6 + - - +
152A THR* 3.6 5.3 + - - -
153A THR* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 5.9 1.0 + - - -
107A MET* 3.9 27.9 - - - +
110A ALA* 3.8 21.8 - - + +
111A THR* 3.4 48.6 + - - +
146A ASP* 2.9 55.1 + - - +
147A THR* 5.3 0.2 - - - +
149A ARG* 1.3 76.3 - - - +
151A ARG* 1.3 57.8 + - - +
153A THR* 4.2 4.2 - - - -
154A GLY* 2.8 27.9 + - - -
280A PHE* 5.4 4.2 - - - -
282A GLU* 4.2 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.3 15.4 - - + +
110A ALA* 3.3 24.2 - - - +
113A ILE* 5.1 1.3 - - + -
114A GLY* 3.2 11.6 - - - +
117A GLN* 5.6 0.9 - - - +
147A THR* 3.1 44.5 + - - +
148A ALA 3.2 7.4 + - - +
150A ARG* 1.3 76.8 - - - +
152A THR* 1.3 59.1 - - - +
154A GLY 3.2 0.5 + - - -
155A SER* 2.9 27.0 + - - -
204A MET* 2.9 48.3 + - + +
231A ILE* 3.6 32.1 - - + +
307A ARA 2.8 50.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 5.5 0.4 - - - -
139A ALA* 5.4 0.4 - - - -
140A ILE 3.7 19.5 - - - +
141A THR* 4.1 16.5 - - + +
142A ALA 5.1 0.8 + - - +
143A ASN* 4.1 9.5 + - - -
148A ALA 3.0 18.1 + - - +
149A ARG* 3.6 8.1 + - - -
151A ARG* 1.3 73.3 - - - +
153A THR* 1.3 63.7 + - - +
155A SER* 3.4 6.6 + - - -
156A MET* 3.0 39.1 + - - +
202A VAL* 4.2 9.1 - - + +
203A GLY* 3.8 9.0 - - - -
204A MET* 3.7 28.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
143A ASN* 5.2 0.9 + - - -
149A ARG* 2.9 29.8 + - - +
150A ARG* 4.2 4.0 - - - -
152A THR* 1.3 76.4 + - - +
154A GLY* 1.3 56.2 + - - +
156A MET* 3.3 14.6 + - + +
157A ASP* 2.8 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR* 4.2 6.3 - - - -
115A GLU* 3.4 38.8 - - - +
150A ARG 2.8 20.3 + - - -
151A ARG 3.6 1.6 - - - -
153A THR* 1.3 77.3 - - - +
155A SER* 1.3 56.5 + - - +
157A ASP* 3.7 6.1 - - - +
158A ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLY 3.1 16.2 + - - -
117A GLN* 2.9 28.6 + - - +
118A GLY* 3.4 15.4 + - - +
151A ARG 2.9 15.0 + - - -
152A THR 3.6 5.6 - - - -
154A GLY* 1.3 76.0 - - - +
156A MET* 1.3 56.8 + - - +
158A ALA* 3.3 3.6 + - - +
159A LEU* 3.0 30.7 + - - +
202A VAL* 3.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.9 5.2 - - + -
139A ALA* 3.6 26.2 - - + -
141A THR* 4.9 2.9 - - + -
152A THR* 3.0 32.9 + - - +
153A THR* 3.8 12.8 - - + +
155A SER* 1.3 74.2 - - - +
157A ASP* 1.3 57.4 + - - +
159A LEU* 3.1 8.0 + - - +
160A LYS* 2.8 49.6 + - - +
169A ILE* 3.6 32.0 - - + +
171A GLN* 3.9 31.0 - - - +
202A VAL* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 5.2 7.3 - - - +
153A THR* 2.8 41.8 + - - +
154A GLY* 3.7 7.6 - - - +
156A MET* 1.3 73.1 - - - +
158A ALA* 1.3 58.6 + - - +
160A LYS* 3.4 19.5 + - - +
161A ALA* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 3.4 32.9 - - + +
118A GLY 5.0 1.9 - - - +
119A GLN* 4.0 19.1 - - + +
154A GLY 3.0 16.5 + - - +
155A SER 3.6 5.4 - - - +
157A ASP* 1.3 77.2 - - - +
159A LEU* 1.3 61.0 + - - +
161A ALA* 3.3 7.8 + - - +
162A ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY* 3.5 22.0 - - - +
121A LEU* 4.2 8.5 - - + -
122A TYR* 4.0 20.9 - - + +
137A VAL* 3.9 19.3 - - + -
155A SER* 3.0 22.4 + - - +
156A MET* 3.7 8.1 - - - +
158A ALA* 1.3 76.9 - - - +
160A LYS* 1.3 62.6 - - - +
162A ALA* 3.2 11.0 + - - +
163A GLY 3.2 0.5 + - - -
164A PHE* 2.9 36.2 + - + +
169A ILE* 4.9 4.9 - - + -
200A LEU* 3.8 23.1 - - + -
202A VAL* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A MET* 2.8 34.0 + - - +
157A ASP* 3.6 19.1 + - - +
159A LEU* 1.3 77.7 - - - +
161A ALA* 1.3 63.0 + - - +
163A GLY* 3.1 13.5 + - - -
164A PHE 3.8 11.1 - - - +
166A GLU* 3.0 44.2 + - + +
169A ILE* 3.6 23.1 - - + +
171A GLN* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP 2.8 21.3 + - - +
158A ALA* 3.7 7.6 - - - +
159A LEU 3.2 0.2 - - - -
160A LYS* 1.3 73.4 - - - +
162A ALA* 1.3 60.2 + - - +
163A GLY* 3.3 1.2 + - - -
----------------------------------------------------------
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