Contacts of the helix formed by residues 134 - 153 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ASN* 4.8 5.5 - - - +
110J LEU* 3.9 38.4 - - + +
111J LEU* 4.6 14.1 - - + -
114J HIS* 4.2 7.2 - - + -
129J LEU* 2.9 21.1 + - + +
130J GLU* 3.9 30.2 + - + +
133J TYR* 1.3 74.2 - - + +
135J GLU* 1.3 61.9 + - - +
137J GLN* 3.5 5.3 + - - +
138J VAL* 3.3 27.5 + - - +
123N PRO* 3.8 30.7 - - + -
124N HIS* 3.7 18.2 - - + +
127N ASP* 6.1 0.7 - - + +
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Residues in contact with GLU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J GLU 4.1 11.2 + - - +
131J SER 5.8 2.7 - - - +
133J TYR 3.5 0.4 - - - -
134J LEU* 1.3 75.9 - - - +
136J GLU* 1.3 67.4 + - - +
137J GLN 3.3 0.2 + - - -
138J VAL* 3.3 2.9 + - - +
139J LYS* 3.0 31.6 + - + +
68N TYR* 5.4 0.7 - - - -
71N LYS* 2.8 32.3 + - - -
124N HIS* 3.0 35.7 + - + +
127N ASP* 5.1 6.3 - - - +
128N PHE* 5.8 3.1 - - - -
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Residues in contact with GLU 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J HIS* 5.1 15.0 - - + +
132J GLU 4.2 12.1 - - - +
133J TYR* 3.5 13.8 - - - +
134J LEU 3.3 0.2 - - - -
135J GLU* 1.3 80.7 - - - +
137J GLN* 1.3 57.6 + - - +
139J LYS* 3.5 8.2 - - - +
140J ASP* 3.1 34.5 + - - +
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Residues in contact with GLN 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J HIS* 5.1 1.4 - - - -
103J GLU* 3.0 47.8 + - - +
106J VAL* 3.9 9.9 - - - +
107J ASN* 3.6 22.4 - - - +
110J LEU* 3.7 20.2 - - + -
133J TYR* 3.0 19.2 + - + +
134J LEU 3.7 3.6 - - - +
135J GLU 3.2 0.2 - - - -
136J GLU* 1.3 75.4 - - + +
138J VAL* 1.3 60.3 + - - +
140J ASP* 3.3 3.2 + - - +
141J ILE* 2.9 34.5 + - - +
176J MG 3.4 16.1 - - - -
177J MG 2.7 21.6 - - - -
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Residues in contact with VAL 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ASN* 5.0 11.7 - - - +
134J LEU 3.3 13.2 + - - +
135J GLU* 3.3 15.4 + - - +
137J GLN* 1.3 77.8 - - + +
139J LYS* 1.3 63.9 + - - +
141J ILE* 3.9 7.7 - - + +
142J LYS* 3.0 26.0 + - - +
71N LYS* 4.3 22.9 - - + +
72N ARG* 4.4 16.4 - - - +
124N HIS* 3.3 42.2 - - + +
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Residues in contact with LYS 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135J GLU* 3.0 32.5 + - + +
136J GLU* 3.5 13.0 - - - +
138J VAL* 1.3 79.5 - - - +
140J ASP* 1.3 59.7 + - - +
142J LYS* 3.5 5.1 + - - +
143J ARG* 3.0 34.9 + - - +
71N LYS* 4.6 11.9 - - - +
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Residues in contact with ASP 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J HIS* 3.7 20.7 - - + -
57J GLU* 4.1 9.2 - - - +
61J HIS* 5.6 0.7 - - - -
103J GLU* 4.4 12.3 - - + +
136J GLU* 3.1 18.4 + - - +
137J GLN* 3.7 4.3 - - - +
139J LYS* 1.3 79.8 - - - +
141J ILE* 1.3 63.8 + - - +
143J ARG* 3.2 29.9 + - - +
144J ILE* 3.1 30.4 + - + +
177J MG 2.5 29.4 - - - -
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Residues in contact with ILE 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J LEU* 3.9 21.8 - - + +
103J GLU* 3.9 27.4 - - + +
104J LYS* 4.2 8.1 - - + -
107J ASN* 3.9 24.0 - - + +
137J GLN* 2.9 23.1 + - - +
138J VAL* 3.9 6.7 - - + +
140J ASP* 1.3 75.4 - - - +
142J LYS* 1.3 59.7 + - - +
144J ILE* 3.4 1.2 + - - -
145J GLY* 2.9 24.8 + - - -
4N VAL* 3.5 35.6 - - + +
6N GLN* 3.8 22.9 - - + +
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Residues in contact with LYS 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J VAL 3.0 18.6 + - - +
139J LYS* 3.7 5.8 - - - +
141J ILE* 1.3 78.9 - - - +
143J ARG* 1.3 56.9 + - - +
145J GLY* 3.9 0.3 - - - -
146J ASP* 2.8 66.1 + - - +
4N VAL* 3.9 8.7 - - + +
70N ASN* 3.3 31.9 - - - +
71N LYS* 4.1 22.9 - - + +
38R ASP* 2.9 30.3 + - - -
40R ASP* 3.9 18.4 - - + +
45R HIS* 4.0 6.3 - - - -
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Residues in contact with ARG 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J PHE* 3.9 12.2 - - - -
54J HIS* 3.1 31.1 + - - -
57J GLU* 5.8 1.4 + - - -
139J LYS* 3.0 22.1 + - - +
140J ASP* 3.2 29.9 + - - +
141J ILE 3.2 0.2 - - - -
142J LYS* 1.3 75.6 - - - +
144J ILE* 1.3 61.3 + - + +
146J ASP* 3.4 11.8 + - + +
147J PHE* 3.0 55.8 + - + -
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Residues in contact with ILE 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 4.3 4.3 - - + +
50J PHE* 4.5 23.3 - - + -
54J HIS* 4.9 5.6 - - + -
96J MET* 3.4 38.1 - - - +
99J ALA* 4.1 15.3 - - + +
100J LEU* 3.9 17.7 - - + +
103J GLU* 3.9 28.7 - - + +
140J ASP 3.1 17.7 + - - +
141J ILE* 4.0 3.4 - - - +
143J ARG* 1.3 75.5 - - + +
145J GLY* 1.3 61.2 + - - +
147J PHE* 3.2 8.2 + - - +
148J ILE* 2.9 29.3 + - + +
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Residues in contact with GLY 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J LEU* 4.5 2.6 - - - +
141J ILE 2.9 18.0 + - - -
142J LYS 3.9 1.6 - - - -
144J ILE* 1.3 75.2 - - - +
146J ASP* 1.3 61.7 + - - +
148J ILE* 3.1 7.0 + - - +
149J THR* 3.0 19.2 + - - -
3N GLN* 3.1 30.2 + - - -
4N VAL* 4.0 10.8 - - - -
40R ASP* 4.3 2.9 - - - -
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Residues in contact with ASP 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 2.8 50.4 + - - +
143J ARG* 3.4 13.1 - - + +
145J GLY* 1.3 75.5 - - - +
147J PHE* 1.3 65.8 + - + +
149J THR* 3.4 1.9 + - - -
150J ASN* 3.0 31.4 + - - +
40R ASP* 3.3 18.2 - - - +
43R ALA* 3.7 16.1 - - + +
45R HIS* 3.0 29.0 + - + +
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Residues in contact with PHE 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J PHE* 3.7 33.4 - + - -
96J MET* 3.9 27.8 - - + -
143J ARG* 3.0 39.1 + - + -
144J ILE* 3.2 11.8 + - - +
146J ASP* 1.3 80.8 - - + +
148J ILE* 1.3 52.5 + - - +
150J ASN* 3.2 3.9 + - + +
151J LEU* 2.7 44.1 + - + +
166J PHE* 3.6 24.1 - + + -
170J SER* 3.5 33.2 - - - -
171J VAL* 4.3 9.0 - - + -
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Residues in contact with ILE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J LEU* 3.9 15.0 - - + -
96J MET* 3.7 35.7 - - + +
97J GLN* 4.0 17.5 - - + +
100J LEU* 3.7 32.8 - - + -
144J ILE 2.9 19.1 + - - +
145J GLY* 3.1 6.3 + - - +
147J PHE* 1.3 75.1 - - - +
149J THR* 1.3 57.3 + - - +
151J LEU* 3.3 8.2 + - - +
152J LYS* 2.9 48.1 + - + +
3N GLN* 3.6 15.9 - - - +
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Residues in contact with THR 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J GLY 3.0 4.6 + - - -
146J ASP 3.6 5.6 - - - -
148J ILE* 1.3 76.6 - - - +
150J ASN* 1.3 58.6 + - - +
152J LYS* 3.4 9.5 + - - +
153J ARG* 3.0 46.0 + - - +
3N GLN* 3.5 13.0 + - - -
40R ASP 2.9 27.9 + - - +
41R ASP* 3.5 26.7 - - - +
42R VAL 3.9 2.5 - - - +
43R ALA* 4.0 3.1 - - + -
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Residues in contact with ASN 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J ASP* 3.0 26.3 + - - +
147J PHE* 3.7 6.9 - - + +
149J THR* 1.3 74.5 - - - +
151J LEU* 1.3 65.9 + - - +
153J ARG* 3.3 23.6 + - - +
154J LEU* 3.1 30.2 + - - +
166J PHE* 4.6 7.2 - - + -
170J SER* 4.8 2.2 - - - +
43R ALA* 3.2 32.9 + - - +
44R LEU* 4.0 5.0 - - - +
164R TYR* 3.1 34.9 - - + -
168R LYS* 4.9 1.1 + - - -
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J THR* 4.1 9.4 - - + +
93J LEU* 3.9 17.0 - - + +
96J MET* 3.8 28.9 - - + -
147J PHE 2.7 29.3 + - - +
148J ILE* 3.3 7.6 + - - +
150J ASN* 1.3 73.4 - - - +
152J LYS* 1.3 58.5 + - - +
154J LEU* 3.3 9.9 + - - +
155J GLY 3.3 0.2 + - - -
156J LEU* 3.0 63.0 + - + +
163J GLU* 5.3 0.2 - - - -
166J PHE* 3.5 42.6 - - + -
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Residues in contact with LYS 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J LEU* 4.3 16.8 - - + -
97J GLN* 4.1 15.0 + - - -
148J ILE* 2.9 38.8 + - + +
149J THR* 3.7 8.1 - - - +
151J LEU* 1.3 75.5 - - - +
153J ARG* 1.3 59.5 + - - +
155J GLY* 2.9 18.6 + - - +
156J LEU* 4.3 4.7 - - - +
157J PRO* 5.7 1.6 - - + -
3N GLN* 4.9 4.2 + - - -
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Residues in contact with ARG 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J THR* 3.0 31.7 + - - +
150J ASN* 3.3 35.0 + - - +
152J LYS* 1.3 71.7 - - - +
154J LEU* 1.3 59.0 + - + +
155J GLY* 3.0 9.1 + - - -
42R VAL* 2.6 33.5 + - - +
44R LEU* 3.5 18.0 - - - +
160R GLY* 3.2 52.2 - - - +
161R MET 3.7 1.0 + - - -
163R GLU* 3.4 26.4 + - - +
164R TYR* 4.1 12.8 - - - +
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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) + - + + + + + -
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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