Contacts of the helix formed by residues 134 - 153 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 4.8 5.9 - - - +
110D LEU* 3.9 38.1 - - + +
111D LEU* 4.6 13.7 - - + -
114D HIS* 4.2 8.3 - - + -
129D LEU* 2.9 20.3 + - + +
130D GLU* 3.9 29.3 + - + +
133D TYR* 1.3 76.1 - - + +
135D GLU* 1.3 60.7 + - - +
137D GLN* 3.5 5.9 + - - +
138D VAL* 3.3 26.7 + - - +
123W PRO* 3.8 30.3 - - + -
124W HIS* 3.5 18.1 - - + +
127W ASP* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLU 4.1 10.8 + - - +
131D SER 5.8 2.5 - - - +
133D TYR 3.5 0.4 - - - -
134D LEU* 1.3 76.1 - - - +
136D GLU* 1.3 66.6 + - - +
138D VAL* 3.3 2.7 + - - +
139D LYS* 3.0 31.5 + - + +
68W TYR* 5.4 0.9 - - - -
71W LYS* 2.8 32.5 + - - -
124W HIS* 3.0 34.3 + - + +
127W ASP* 5.1 6.7 - - - +
128W PHE* 5.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D HIS* 5.1 15.0 - - + +
132D GLU 4.2 12.5 - - - +
133D TYR* 3.3 14.2 + - - +
134D LEU 3.3 0.6 - - - -
135D GLU* 1.3 79.5 - - - +
137D GLN* 1.3 58.4 + - + +
139D LYS* 3.5 7.4 - - - +
140D ASP* 3.1 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D HIS* 5.1 1.2 - - - -
103D GLU* 3.0 48.6 + - - +
106D VAL* 3.9 9.1 - - - +
107D ASN* 3.6 23.2 - - - +
110D LEU* 3.7 20.0 - - + -
133D TYR* 3.0 19.0 + - + +
134D LEU 3.7 3.8 - - - +
135D GLU 3.2 0.2 - - - -
136D GLU* 1.3 74.8 - - + +
138D VAL* 1.3 61.1 + - - +
140D ASP* 3.3 2.8 + - - +
141D ILE* 2.9 33.6 + - - +
176D MG 3.4 16.3 - - - -
177D MG 2.7 20.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ASN* 5.0 11.7 - - - +
134D LEU 3.3 12.5 + - - +
135D GLU* 3.3 15.4 + - - +
137D GLN* 1.3 77.0 - - + +
139D LYS* 1.3 63.6 + - - +
141D ILE* 3.9 8.1 - - + +
142D LYS* 3.0 26.5 + - - +
71W LYS* 4.2 26.4 - - + +
72W ARG* 4.3 13.0 - - - +
124W HIS* 3.3 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 3.0 33.4 + - + +
136D GLU* 3.5 12.6 - - - +
137D GLN 3.2 0.2 - - - -
138D VAL* 1.3 79.4 - - - +
140D ASP* 1.3 61.1 + - - +
142D LYS* 3.5 5.4 + - - +
143D ARG* 3.0 34.2 + - - +
71W LYS* 4.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D HIS* 3.7 20.7 - - + -
57D GLU* 4.1 10.0 - - - +
61D HIS* 5.6 0.5 - - - -
103D GLU* 4.4 12.3 - - - +
136D GLU* 3.1 18.6 + - - +
137D GLN* 3.7 4.3 - - - +
139D LYS* 1.3 80.2 - - - +
141D ILE* 1.3 63.7 + - - +
143D ARG* 3.2 29.8 + - - +
144D ILE* 3.1 31.5 + - + +
177D MG 2.5 29.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LEU* 3.9 18.8 - - + +
103D GLU* 3.9 25.4 - - + +
104D LYS* 4.2 7.9 - - + -
107D ASN* 3.9 24.7 - - + +
137D GLN* 2.9 24.9 + - - +
138D VAL* 3.9 7.6 - - + +
140D ASP* 1.3 75.9 - - - +
142D LYS* 1.3 58.3 + - - +
144D ILE* 3.4 1.4 + - - -
145D GLY* 2.9 25.3 + - - -
4W VAL* 3.5 38.5 - - + +
6W GLN* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D VAL 3.0 18.4 + - - +
139D LYS* 3.7 6.1 - - - +
141D ILE* 1.3 78.9 - - - +
143D ARG* 1.3 55.6 + - - +
145D GLY* 3.5 0.7 + - - -
146D ASP* 2.8 67.0 + - - +
38K ASP* 2.9 29.7 + - - -
40K ASP* 3.9 16.2 - - + +
45K HIS* 4.0 6.1 - - - -
4W VAL* 4.0 8.9 - - + +
67W LYS* 5.9 0.6 - - - +
70W ASN* 3.3 32.8 - - - +
71W LYS* 4.1 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE* 3.9 13.1 - - - -
54D HIS* 3.2 30.3 + - - -
57D GLU* 5.8 1.6 + - - -
139D LYS* 3.0 22.0 + - - +
140D ASP* 3.2 30.8 + - - +
141D ILE 3.2 0.4 - - - -
142D LYS* 1.3 76.1 - - - +
144D ILE* 1.3 60.7 + - + +
146D ASP* 3.4 10.9 + - + +
147D PHE* 3.0 56.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 4.3 4.3 - - + +
50D PHE* 4.5 24.0 - - + -
54D HIS* 4.9 5.4 - - + -
96D MET* 3.4 37.2 - - - +
99D ALA* 4.1 15.0 - - + +
100D LEU* 3.9 17.3 - - + +
103D GLU* 3.9 30.3 - - + +
140D ASP 3.1 17.8 + - - +
141D ILE 4.0 2.9 - - - +
143D ARG* 1.3 75.7 - - + +
145D GLY* 1.3 59.7 + - - +
147D PHE* 3.2 7.5 + - - +
148D ILE* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LEU* 4.5 2.6 - - - +
141D ILE 2.9 17.0 + - - -
142D LYS 3.9 1.3 - - - -
144D ILE* 1.3 76.2 - - - +
146D ASP* 1.3 62.3 + - - +
148D ILE* 3.1 5.8 + - - +
149D THR* 3.0 20.3 + - - -
40K ASP* 4.3 3.6 - - - -
3W GLN* 3.2 29.8 + - - -
4W VAL* 4.0 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 2.8 50.7 + - - +
143D ARG* 3.4 12.5 - - + +
145D GLY* 1.3 75.1 - - - +
147D PHE* 1.3 65.7 + - + +
149D THR* 3.4 1.9 + - - -
150D ASN* 3.0 30.9 + - - +
40K ASP* 3.3 16.9 - - - -
43K ALA* 3.8 15.5 - - + +
45K HIS* 3.0 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PHE* 3.7 32.3 - + - -
96D MET* 3.9 27.8 - - + -
143D ARG* 3.0 39.5 + - + -
144D ILE* 3.2 12.1 + - - +
146D ASP* 1.3 80.6 - - + +
148D ILE* 1.3 52.0 + - - +
150D ASN* 3.2 3.9 + - + +
151D LEU* 2.7 43.0 + - + +
166D PHE* 3.6 22.2 - + + -
170D SER* 3.5 33.0 - - - -
171D VAL* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 3.9 14.8 - - + -
96D MET* 3.7 35.4 - - + +
97D GLN* 4.0 17.7 - - + +
100D LEU* 3.7 32.5 - - + -
144D ILE 2.9 20.4 + - - +
145D GLY* 3.5 5.8 - - - +
147D PHE* 1.3 73.8 - - - +
149D THR* 1.3 57.4 + - - +
151D LEU* 3.5 7.5 - - - +
152D LYS* 2.9 48.9 + - + +
3W GLN* 3.6 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D GLY 3.0 4.8 + - - -
146D ASP 3.6 5.8 - - - -
148D ILE* 1.3 76.0 - - - +
150D ASN* 1.3 59.0 + - - +
152D LYS* 3.4 9.6 + - - +
153D ARG* 3.0 45.3 + - - +
40K ASP 2.9 28.0 + - - +
41K ASP* 3.5 28.6 - - - +
43K ALA* 3.9 6.3 - - + -
3W GLN* 3.6 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ASP* 3.0 26.3 + - - +
147D PHE* 3.7 6.5 - - + +
149D THR* 1.3 74.3 - - - +
151D LEU* 1.3 65.8 + - - +
153D ARG* 3.3 22.6 + - - +
154D LEU* 3.1 30.6 + - - +
166D PHE* 4.6 6.3 - - + -
170D SER* 4.8 3.4 - - - +
43K ALA* 3.1 33.3 + - - +
44K LEU* 3.9 5.2 - - - +
45K HIS* 5.9 0.2 - - - -
164K TYR* 3.1 33.8 - - + -
168K LYS* 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D THR* 4.1 8.5 - - + +
93D LEU* 3.9 17.3 - - + +
96D MET* 3.8 28.7 - - + -
147D PHE 2.7 30.6 + - - +
148D ILE* 3.3 7.8 + - - +
150D ASN* 1.3 72.8 - - - +
152D LYS* 1.3 59.9 + - - +
154D LEU* 3.3 10.5 + - + +
155D GLY 3.3 0.2 + - - -
156D LEU* 3.0 61.8 + - + +
166D PHE* 3.5 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 4.3 17.3 - - + -
97D GLN* 4.1 14.8 + - - -
148D ILE* 2.9 39.5 + - + +
149D THR* 3.6 7.6 - - - +
151D LEU* 1.3 75.4 - - - +
153D ARG* 1.3 59.6 + - - +
155D GLY* 2.9 18.6 + - - +
156D LEU* 4.3 4.9 - - - +
157D PRO* 5.7 1.6 - - + -
3W GLN* 4.9 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D THR* 3.0 29.8 + - - +
150D ASN* 3.3 34.7 + - - +
152D LYS* 1.3 70.8 - - - +
154D LEU* 1.3 59.7 + - + +
155D GLY* 3.0 9.0 + - - -
41K ASP 5.5 0.4 + - - -
42K VAL* 2.5 35.7 + - - +
44K LEU* 3.4 24.7 - - - +
160K GLY* 3.3 52.9 + - - +
161K MET 3.6 0.9 + - - -
163K GLU* 3.4 20.1 + - - +
164K TYR* 4.0 13.2 - - - +
----------------------------------------------------------
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