Contacts of the helix formed by residues 147 - 169 (chain A) in PDB entry 2XFR
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 SER 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 3.2 16.7 + - - -
139A ASN* 3.8 7.9 + - - -
140A GLN 3.2 27.1 - - - -
141A PRO* 3.9 4.0 - - - +
143A PHE* 4.3 2.9 - - - -
146A ARG* 1.3 75.4 - - - +
148A ALA* 1.3 65.0 + - - +
149A VAL* 4.1 1.6 - - - +
150A GLN* 2.9 36.6 + - - +
151A MET* 3.0 22.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
133A LEU* 4.0 17.3 - - + -
137A VAL* 3.4 27.2 + - + +
138A ASP* 4.1 9.4 - - - +
143A PHE* 4.2 3.6 - - + -
147A SER* 1.3 73.2 - - - +
149A VAL* 1.3 63.2 + - - +
151A MET* 3.1 14.5 + - - +
152A TYR* 3.0 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 3.0 46.0 + - + +
139A ASN* 4.2 6.7 - - - +
147A SER* 4.2 1.6 - - - +
148A ALA* 1.3 74.4 - - - +
150A GLN* 1.3 60.0 + - + +
152A TYR* 3.2 9.0 + - + +
153A ALA* 2.9 27.0 + - - +
274A ARG* 3.9 17.0 - - + +
275A ILE* 3.9 20.9 - - + -
278A GLU* 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO* 5.2 2.1 - - - +
145A GLY 3.9 5.0 - - - +
146A ARG* 3.3 21.6 - - + +
147A SER* 2.9 44.4 + - - +
149A VAL* 1.3 77.8 - - + +
151A MET* 1.3 59.0 + - - +
153A ALA* 3.4 5.4 + - - +
154A ASP* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TRP* 3.9 25.3 + - + -
58A GLU* 4.8 3.8 - - - +
65A TYR* 4.7 0.5 + - - -
90A PHE* 4.7 0.4 - - - -
108A TRP* 3.6 29.6 - - - -
109A VAL* 4.2 1.6 - - + -
133A LEU* 3.7 27.4 - - + -
143A PHE* 3.6 37.7 - - + -
146A ARG* 3.7 32.8 + - + +
147A SER 3.0 14.3 + - - +
148A ALA* 3.5 11.0 - - - +
150A GLN* 1.3 77.7 - - - +
152A TYR* 1.3 64.2 + - + +
154A ASP* 3.9 1.0 - - - +
155A TYR* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TRP* 4.2 17.2 - + - -
90A PHE* 3.5 54.9 - + + -
132A TYR* 3.9 24.6 - - - -
133A LEU* 3.8 26.5 + - - +
138A ASP* 4.5 5.2 + - - -
148A ALA* 3.0 38.1 + - + +
149A VAL* 3.2 8.2 + - - +
151A MET* 1.3 77.4 - - + +
153A ALA* 1.3 61.4 + - - +
155A TYR* 3.3 2.6 + - - +
156A MET* 3.0 37.0 + - + +
275A ILE* 3.8 37.9 - - + -
278A GLU* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL 2.9 16.8 + - - +
150A GLN* 3.8 7.2 - - - +
152A TYR* 1.3 76.6 - - - +
154A ASP* 1.3 60.2 + - - +
156A MET* 3.3 13.9 + - - +
157A THR* 2.9 33.6 + - - +
278A GLU* 3.8 30.7 - - + +
282A VAL* 4.0 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.6 13.2 + - + -
65A TYR* 3.2 22.7 + - + +
146A ARG* 2.9 36.8 + - - +
150A GLN* 2.9 20.7 + - - +
151A MET 3.9 0.2 - - - +
153A ALA* 1.3 79.4 - - - +
155A TYR* 1.3 62.5 + - - +
157A THR* 3.4 7.4 + - - -
158A SER* 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 2.9 37.6 + - + +
53A TRP 3.3 13.5 + - - -
54A TRP* 3.7 33.0 - + + -
57A VAL* 3.8 22.5 - - + +
58A GLU* 4.7 2.0 - - - +
65A TYR* 3.5 25.7 + + + -
67A TRP* 3.8 15.2 - + - -
88A MET* 4.2 21.5 - - - -
89A SER 5.0 0.4 - - - -
90A PHE* 3.5 27.6 - + + -
151A MET 3.0 18.4 + - - +
152A TYR 3.6 3.8 - - - +
153A ALA 3.3 0.2 - - - -
154A ASP* 1.3 76.9 - - - +
156A MET* 1.3 58.1 - - - +
158A SER* 3.3 3.3 + - - -
159A PHE* 2.9 28.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
88A MET* 3.9 33.0 - - + -
90A PHE* 4.3 5.6 - - + -
152A TYR* 3.0 35.6 + - + +
153A ALA* 3.3 10.5 + - - +
155A TYR* 1.3 77.5 - - - +
157A THR* 1.3 56.5 + - - +
159A PHE* 3.3 8.5 + - - +
160A ARG* 2.9 23.9 + - - +
177A VAL* 4.4 10.3 - - + -
275A ILE* 4.4 12.6 - - + +
278A GLU* 4.5 3.1 - - + +
279A ALA* 3.7 42.4 - - + +
282A VAL* 3.6 21.2 - - + +
283A PHE* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 2.9 21.8 + - - +
154A ASP* 3.6 9.7 + - - -
155A TYR 3.3 0.2 - - - -
156A MET* 1.3 75.7 - - - +
158A SER* 1.3 61.9 + - - +
160A ARG* 3.2 18.4 + - - +
161A GLU* 3.0 45.1 + - - +
282A VAL* 3.5 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.2 33.0 - - - +
67A TRP* 2.9 25.7 + - - -
154A ASP 3.0 15.1 + - - -
155A TYR 3.3 4.2 + - - -
157A THR* 1.3 77.3 - - - +
159A PHE* 1.3 63.2 + - - +
161A GLU* 3.4 11.2 + - - +
162A ASN* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.3 8.1 - - + -
67A TRP* 3.5 33.5 - + + -
74A PHE* 3.8 25.4 - + - -
86A ALA* 3.8 21.3 - - + -
88A MET* 3.8 21.5 - - + -
155A TYR 2.9 14.5 + - - +
156A MET* 3.4 11.2 - - - +
158A SER* 1.3 76.9 - - - +
160A ARG* 1.3 60.5 + - - +
162A ASN* 4.8 0.2 - - - -
163A MET* 2.8 56.8 + - + +
167A LEU* 5.4 2.0 - - + -
172A ILE* 4.0 11.0 - - + -
175A ILE* 3.9 21.8 - - + -
283A PHE* 4.0 18.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A MET 2.9 16.4 + - - +
157A THR* 3.2 28.1 + - - +
159A PHE* 1.3 80.9 - - - +
161A GLU* 1.3 82.3 + - - +
163A MET 3.7 0.2 - - - -
164A LYS* 3.0 26.2 + - - +
167A LEU* 4.1 14.3 - - + +
281A LYS 4.4 3.2 + - - -
282A VAL* 2.9 48.2 + - + +
283A PHE* 4.0 8.3 - - + -
286A TYR* 3.8 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 3.0 37.7 + - - +
158A SER* 3.8 11.3 + - - +
160A ARG* 1.3 97.0 + - - +
162A ASN* 1.3 66.6 + - - +
163A MET 3.5 0.2 + - - -
164A LYS* 3.7 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 3.2 41.9 - - + +
71A LYS* 3.3 35.9 + - + +
158A SER* 2.9 35.3 + - - +
159A PHE 4.1 2.0 - - - +
161A GLU* 1.3 82.7 + - - +
163A MET* 1.3 63.5 + - - +
164A LYS 3.4 1.5 + - - -
165A GLU* 4.3 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 3.7 33.0 - - + -
70A TYR* 4.0 12.1 - - + -
71A LYS* 3.7 33.4 - - + -
74A PHE* 3.7 27.1 - - + -
159A PHE* 2.8 42.3 + - + +
160A ARG 3.7 2.0 - - - -
162A ASN* 1.3 76.7 - - + +
164A LYS* 1.3 64.3 + - - +
165A GLU 3.2 3.1 - - - -
166A PHE* 2.9 24.1 + - + +
167A LEU* 3.1 14.5 + - + +
172A ILE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG 3.0 15.9 + - - +
161A GLU* 3.7 12.8 - - - +
162A ASN 3.4 2.4 + - - -
163A MET* 1.3 77.2 - - - +
165A GLU* 1.3 57.9 + - - +
167A LEU* 3.2 8.7 + - - +
168A ASP* 2.9 59.8 + - - +
286A TYR* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.0 28.3 + - - -
78A GLN* 5.1 1.9 - - - +
162A ASN 4.3 1.8 + - - +
163A MET 3.2 1.9 - - - -
164A LYS* 1.3 78.8 - - - +
166A PHE* 1.3 95.5 + - + +
168A ASP* 3.5 6.3 + - - +
169A ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.8 21.1 - - + -
74A PHE* 3.7 22.7 - + + -
75A GLU* 3.7 33.4 - - + -
78A GLN* 3.4 31.2 - - + -
163A MET* 2.9 35.7 + - - +
165A GLU* 1.3 100.1 - - + +
167A LEU* 1.3 62.6 + - - +
169A ALA* 3.7 2.6 + - - -
170A GLY 3.5 1.7 + - - -
171A VAL* 3.0 37.8 + - + +
172A ILE* 3.2 22.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 5.4 1.6 - - + -
160A ARG* 4.1 31.2 - - + +
163A MET* 3.1 20.0 + - + +
164A LYS* 3.6 6.5 - - - +
166A PHE* 1.3 77.2 - - - +
168A ASP* 1.3 63.8 + - - +
170A GLY* 3.0 14.7 + - - -
172A ILE* 3.8 28.8 - - + +
175A ILE* 5.0 0.9 - - + -
283A PHE* 4.5 13.7 - - + -
286A TYR* 3.7 35.2 - - + -
287A LYS* 5.9 3.5 + - - +
288A VAL* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LYS* 2.9 52.8 + - - +
165A GLU* 4.0 6.5 - - - +
167A LEU* 1.3 74.0 - - - +
169A ALA* 1.3 58.9 + - - +
170A GLY* 3.2 0.9 + - - -
286A TYR* 3.5 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN* 3.7 26.0 - - - +
165A GLU 3.0 19.5 + - - +
166A PHE 4.2 0.4 - - - +
167A LEU 3.2 0.4 - - - -
168A ASP* 1.3 75.0 - - - +
170A GLY* 1.3 61.1 + - - +
171A VAL* 3.5 9.7 + - + +
----------------------------------------------------------
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