Contacts of the helix formed by residues 134 - 153 (chain Q) in PDB entry 1MFR
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 LEU 134 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J PRO* 3.7 31.4 - - + -
124J HIS* 3.5 18.6 - - + +
127J ASP* 6.2 0.7 - - + -
107Q ASN* 4.8 5.4 - - - +
110Q LEU* 3.9 37.7 - - + +
111Q LEU* 4.6 13.9 - - + -
114Q HIS* 4.2 7.9 - - + -
129Q LEU* 2.9 20.5 + - + +
130Q GLU* 3.9 29.7 + - + +
133Q TYR* 1.3 74.8 - - + +
135Q GLU* 1.3 61.3 + - - +
137Q GLN* 3.5 5.4 + - - +
138Q VAL* 3.3 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J TYR* 5.3 0.5 - - - -
71J LYS* 2.8 33.8 + - - -
124J HIS* 3.0 35.7 + - + +
127J ASP* 5.1 6.3 - - - +
128J PHE* 5.8 3.3 - - - -
130Q GLU 4.1 11.4 + - - +
131Q SER 5.8 2.5 - - - +
133Q TYR 3.5 0.4 - - - +
134Q LEU* 1.3 75.4 - - - +
136Q GLU* 1.3 67.2 + - - +
137Q GLN 3.3 0.2 + - - -
138Q VAL* 3.3 3.4 + - - +
139Q LYS* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q HIS* 5.1 14.8 - - + +
132Q GLU 4.2 12.3 - - - +
133Q TYR* 3.3 14.0 + - - +
134Q LEU 3.3 0.2 - - - -
135Q GLU* 1.3 80.6 - - - +
137Q GLN* 1.3 57.0 + - + +
139Q LYS* 3.5 7.2 - - - +
140Q ASP* 3.1 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q HIS* 5.1 1.2 - - - -
103Q GLU* 3.0 47.9 + - - +
106Q VAL* 3.9 9.3 - - - +
107Q ASN* 3.6 23.0 - - - +
110Q LEU* 3.7 19.5 - - + -
133Q TYR* 3.0 20.7 + - + +
134Q LEU 3.7 3.4 - - - +
135Q GLU 3.2 0.2 - - - -
136Q GLU* 1.3 75.6 - - + +
138Q VAL* 1.3 62.2 + - - +
140Q ASP* 3.3 2.4 + - - +
141Q ILE* 2.9 34.2 + - - +
176Q MG 3.4 15.9 - - - -
177Q MG 2.7 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J LYS* 4.3 26.4 - - + +
72J ARG* 4.3 13.0 - - - +
124J HIS* 3.3 42.6 - - + +
107Q ASN* 5.0 11.4 - - - +
134Q LEU 3.3 13.2 + - - +
135Q GLU* 3.3 15.2 + - - +
137Q GLN* 1.3 77.7 - - + +
139Q LYS* 1.3 64.5 + - - +
141Q ILE* 3.9 8.0 - - + +
142Q LYS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71J LYS* 4.6 11.9 - - - +
135Q GLU* 3.0 32.7 + - + +
136Q GLU* 3.5 12.6 - - - +
138Q VAL* 1.3 78.3 - - - +
140Q ASP* 1.3 60.5 + - - +
142Q LYS* 3.5 5.4 + - - +
143Q ARG* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q HIS* 3.7 20.4 - - + -
57Q GLU* 4.1 9.6 - - - +
61Q HIS* 5.6 0.5 - - - -
103Q GLU* 4.4 11.9 - - - +
136Q GLU* 3.1 18.6 + - - +
137Q GLN* 3.3 4.9 + - - +
139Q LYS* 1.3 79.3 - - - +
141Q ILE* 1.3 65.0 + - - +
143Q ARG* 3.2 30.1 + - - +
144Q ILE* 3.1 31.0 + - + +
177Q MG 2.5 28.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J VAL* 3.4 41.3 - - + +
6J GLN* 3.8 22.9 - - + +
100Q LEU* 3.9 16.9 - - + +
103Q GLU* 3.9 26.5 - - + +
104Q LYS* 4.2 7.2 - - + -
107Q ASN* 3.9 23.6 - - + +
137Q GLN* 2.9 23.3 + - - +
138Q VAL* 3.9 6.3 - - - +
140Q ASP* 1.3 74.8 - - - +
142Q LYS* 1.3 60.7 + - - +
144Q ILE* 3.4 1.8 + - - -
145Q GLY 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J VAL* 3.9 9.1 - - + +
67J LYS* 6.0 0.4 - - - +
70J ASN* 3.3 32.5 - - - +
71J LYS* 4.1 23.1 - - + +
138Q VAL 3.0 18.9 + - - +
139Q LYS* 3.7 5.2 - - - +
141Q ILE* 1.3 77.8 - - - +
143Q ARG* 1.3 57.1 + - - +
145Q GLY* 3.5 0.3 + - - -
146Q ASP* 2.8 64.6 + - - +
38X ASP* 2.9 30.0 + - - -
40X ASP* 3.9 19.0 - - + +
45X HIS* 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q PHE* 3.9 12.2 - - - -
54Q HIS* 3.1 31.1 + - - -
57Q GLU* 5.8 1.4 + - - -
139Q LYS* 3.0 22.2 + - - +
140Q ASP* 3.2 30.5 + - - +
141Q ILE 3.2 0.2 - - - -
142Q LYS* 1.3 75.4 - - - +
144Q ILE* 1.3 61.5 + - - +
146Q ASP* 3.4 11.8 + - + +
147Q PHE* 3.0 55.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q TYR* 4.3 3.8 - - + +
50Q PHE* 4.5 23.8 - - + -
54Q HIS* 5.0 6.1 - - + -
96Q MET* 3.4 37.7 - - - +
99Q ALA* 4.1 15.5 - - + +
100Q LEU* 3.9 17.7 - - + +
103Q GLU* 3.9 28.3 - - + +
140Q ASP 3.1 18.0 + - - +
141Q ILE* 4.0 2.9 - - - +
143Q ARG* 1.3 76.0 - - + +
145Q GLY* 1.3 60.9 + - - +
147Q PHE* 3.2 7.7 + - - +
148Q ILE* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLN* 3.1 32.7 + - - -
4J VAL* 4.0 9.0 - - - -
100Q LEU* 4.5 2.8 - - - +
141Q ILE 2.9 17.5 + - - -
142Q LYS 3.9 1.3 - - - -
144Q ILE* 1.3 75.8 - - - +
146Q ASP* 1.3 62.2 + - - +
148Q ILE* 3.1 6.0 + - - +
149Q THR* 3.0 20.1 + - - -
40X ASP* 4.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142Q LYS* 2.8 50.3 + - - +
143Q ARG* 3.4 12.7 - - + +
145Q GLY* 1.3 76.4 - - - +
147Q PHE* 1.3 66.5 + - + +
149Q THR* 3.4 1.6 + - - -
150Q ASN* 3.0 31.1 + - - +
39X ARG 4.0 0.3 - - - +
40X ASP* 3.3 18.0 - - - +
43X ALA* 3.7 15.3 - - + +
45X HIS* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q PHE* 3.7 33.0 - + - -
96Q MET* 3.9 28.0 - - + -
143Q ARG* 3.0 41.3 + - + -
144Q ILE* 3.2 11.6 + - - +
146Q ASP* 1.3 81.5 - - + +
148Q ILE* 1.3 52.7 + - - +
150Q ASN* 3.2 3.9 + - + +
151Q LEU* 2.7 43.2 + - + +
166Q PHE* 3.6 23.6 - + + -
170Q SER* 3.5 33.4 - - - -
171Q VAL* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLN* 3.5 15.9 - - - +
93Q LEU* 3.9 15.7 - - + +
96Q MET* 3.7 35.4 - - + +
97Q GLN* 4.0 17.9 - - + +
100Q LEU* 3.7 32.8 - - + -
144Q ILE 2.9 19.6 + - - +
145Q GLY 3.1 6.3 + - - +
147Q PHE* 1.3 73.4 - - - +
149Q THR* 1.3 58.8 + - - +
151Q LEU* 3.3 8.1 + - - +
152Q LYS* 2.9 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLN* 3.6 11.1 + - - -
145Q GLY 3.0 5.2 + - - -
146Q ASP 3.6 5.6 - - - -
148Q ILE* 1.3 77.6 - - - +
150Q ASN* 1.3 58.3 + - - +
152Q LYS* 3.4 9.5 + - - +
153Q ARG* 3.0 45.8 + - - +
40X ASP 2.8 28.6 + - - +
41X ASP* 3.4 28.8 - - - +
42X VAL 3.8 3.4 - - - +
43X ALA* 3.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146Q ASP* 3.0 26.4 + - - +
147Q PHE* 3.7 6.0 - - + +
149Q THR* 1.3 74.5 - - - +
151Q LEU* 1.3 65.7 + - - +
153Q ARG* 3.3 22.5 + - - +
154Q LEU* 3.1 30.4 + - - +
166Q PHE* 4.6 6.7 - - + -
170Q SER* 4.8 2.2 - - - +
43X ALA* 3.1 33.9 + - - +
44X LEU* 3.9 5.7 - - - +
45X HIS* 5.9 0.2 - - - -
164X TYR* 3.2 34.6 - - + -
168X LYS* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q THR* 4.1 8.5 - - + +
93Q LEU* 3.9 17.0 - - + +
96Q MET* 3.8 29.2 - - + -
147Q PHE 2.7 31.4 + - - +
148Q ILE* 3.5 7.6 - - - +
150Q ASN* 1.3 73.5 - - - +
152Q LYS* 1.3 59.4 + - - +
154Q LEU* 3.3 10.3 + - + +
155Q GLY 3.3 0.2 + - - -
156Q LEU* 3.0 61.8 + - + +
163Q GLU* 5.3 0.2 - - - -
166Q PHE* 3.5 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J GLN* 5.0 4.2 + - - -
93Q LEU* 4.3 16.8 - - + -
97Q GLN* 4.1 14.8 + - - -
148Q ILE* 2.9 39.3 + - + +
149Q THR* 3.7 7.9 - - - +
151Q LEU* 1.3 75.2 - - - +
153Q ARG* 1.3 60.5 + - - +
155Q GLY* 2.9 18.4 + - - +
156Q LEU* 4.3 4.9 - - - +
157Q PRO* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149Q THR* 3.0 28.7 + - - +
150Q ASN* 3.3 33.6 + - - +
151Q LEU 3.3 0.2 - - - -
152Q LYS* 1.3 71.5 - - - +
154Q LEU* 1.3 59.5 + - + +
155Q GLY* 3.0 9.2 + - - -
41X ASP 5.5 0.2 + - - -
42X VAL* 2.5 32.9 + - - +
44X LEU* 3.4 29.2 - - - +
160X GLY* 3.2 53.1 - - - +
161X MET 3.5 0.9 + - - -
163X GLU* 3.4 22.2 + - - +
164X TYR* 4.0 14.1 - - - +
----------------------------------------------------------
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