Contacts of the helix formed by residues 134 - 153 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PRO* 3.7 31.0 - - + -
124C HIS* 3.5 19.1 - - + +
127C ASP* 6.1 0.9 - - + -
107R ASN* 4.8 7.3 - - - +
110R LEU* 3.9 37.2 - - + +
111R LEU* 4.6 13.0 - - + -
114R HIS* 4.2 7.9 - - + -
129R LEU* 2.9 19.2 + - + +
130R GLU* 3.9 29.8 + - + +
133R TYR* 1.3 75.9 - - + +
135R GLU* 1.3 61.7 + - - +
137R GLN* 3.5 5.3 + - - +
138R VAL* 3.3 26.7 + - - +
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Residues in contact with GLU 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 5.3 0.3 - - - -
71C LYS* 2.8 33.4 + - - -
124C HIS* 3.0 35.2 + - + +
127C ASP* 5.1 6.7 - - - +
128C PHE* 5.7 3.5 - - - -
130R GLU 4.1 11.4 + - - +
131R SER 5.8 2.7 - - - +
133R TYR 5.0 0.4 - - - +
134R LEU* 1.3 75.5 - - - +
136R GLU* 1.3 67.1 + - - +
138R VAL* 3.3 2.9 + - - +
139R LYS* 3.0 31.8 + - + +
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Residues in contact with GLU 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R HIS* 5.1 15.5 - - + +
132R GLU 4.2 12.1 - - - +
133R TYR* 3.3 13.7 + - - +
134R LEU 3.3 0.2 - - - -
135R GLU* 1.3 79.4 - - - +
137R GLN* 1.3 58.0 + - + +
139R LYS* 3.5 7.8 - - - +
140R ASP* 3.1 35.4 + - - +
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Residues in contact with GLN 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R HIS* 5.1 1.7 - - - -
103R GLU* 3.0 47.4 + - - +
106R VAL* 3.9 10.2 - - - +
107R ASN* 3.6 22.6 - - - +
110R LEU* 3.7 20.4 - - + -
133R TYR* 3.0 19.5 + - + +
134R LEU 3.7 3.6 - - - +
135R GLU 3.2 0.4 - - - -
136R GLU* 1.3 76.0 - - + +
138R VAL* 1.3 61.5 + - - +
140R ASP* 3.3 2.8 + - - +
141R ILE* 2.9 34.1 + - - +
176R MG 3.4 16.1 - - - -
177R MG 2.7 21.3 - - - -
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Residues in contact with VAL 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LYS* 4.3 21.3 - - + +
72C ARG* 4.4 16.2 - - - +
124C HIS* 3.3 42.8 - - + +
107R ASN* 5.0 11.4 - - - +
134R LEU 3.3 13.6 + - - +
135R GLU* 3.3 14.7 + - - +
137R GLN* 1.3 77.8 - - + +
139R LYS* 1.3 65.4 + - - +
141R ILE* 3.9 8.8 - - + +
142R LYS* 3.0 26.0 + - - +
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Residues in contact with LYS 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LYS* 4.6 12.6 - - - +
135R GLU* 3.0 34.2 + - + +
136R GLU* 3.5 12.1 - - - +
138R VAL* 1.3 79.5 - - - +
140R ASP* 1.3 60.8 + - - +
142R LYS* 3.5 5.6 + - - +
143R ARG* 3.0 33.2 + - - +
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Residues in contact with ASP 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R HIS* 3.7 20.5 - - + -
57R GLU* 4.1 9.8 - - - +
61R HIS* 5.6 0.7 - - - -
103R GLU* 4.4 12.1 - - + +
136R GLU* 3.1 17.7 + - - +
137R GLN* 3.3 4.5 + - - +
139R LYS* 1.3 80.0 - - - +
141R ILE* 1.3 64.3 + - - +
143R ARG* 3.2 30.0 + - - +
144R ILE* 3.1 30.7 + - + +
177R MG 2.5 29.9 - - - -
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Residues in contact with ILE 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 3.5 35.5 - - + +
6C GLN* 3.8 22.4 - - + +
100R LEU* 3.9 22.3 - - + +
103R GLU* 3.9 27.6 - - + +
104R LYS* 4.2 7.4 - - + -
107R ASN* 3.9 25.4 - - + +
137R GLN* 2.9 23.3 + - - +
138R VAL* 3.9 6.7 - - - +
140R ASP* 1.3 74.7 - - - +
142R LYS* 1.3 59.6 + - - +
144R ILE* 3.4 1.6 + - - -
145R GLY* 2.9 24.8 + - - -
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Residues in contact with LYS 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 3.9 8.5 - - + +
67C LYS* 6.0 0.4 - - - +
70C ASN* 3.2 32.5 - - - +
71C LYS* 4.1 23.6 - - + +
38O ASP* 2.9 29.2 + - - -
40O ASP* 4.0 16.4 - - + +
45O HIS* 4.0 5.7 - - - -
138R VAL 3.0 18.2 + - - +
139R LYS* 3.7 6.3 - - - +
141R ILE* 1.3 79.5 - - - +
143R ARG* 1.3 57.3 + - - +
145R GLY* 3.9 0.5 - - - -
146R ASP* 2.8 66.9 + - - +
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Residues in contact with ARG 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R PHE* 3.9 11.4 - - - -
54R HIS* 3.1 30.3 + - - -
57R GLU* 5.8 1.6 + - - -
139R LYS* 3.0 22.5 + - - +
140R ASP* 3.2 31.4 + - - +
141R ILE 3.2 0.4 - - - -
142R LYS* 1.3 74.8 - - - +
144R ILE* 1.3 62.4 + - + +
146R ASP* 3.4 10.8 + - + +
147R PHE* 3.0 57.2 + - + -
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Residues in contact with ILE 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 4.3 4.5 - - + +
50R PHE* 4.5 23.1 - - + -
54R HIS* 4.9 5.8 - - + -
96R MET* 3.4 38.4 - - - +
99R ALA* 4.1 16.2 - - + +
100R LEU* 3.9 17.5 - - + +
103R GLU* 3.9 28.3 - - + +
140R ASP 3.1 17.1 + - - +
141R ILE* 4.0 2.9 - - - +
143R ARG* 1.3 75.6 - - + +
145R GLY* 1.3 61.2 + - - +
147R PHE* 3.2 8.1 + - - +
148R ILE* 2.9 29.5 + - + +
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Residues in contact with GLY 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN* 3.1 30.2 + - - -
4C VAL* 4.0 10.8 - - - -
40O ASP* 4.4 3.1 - - - -
100R LEU* 4.5 2.6 - - - +
141R ILE 2.9 17.8 + - - -
142R LYS 3.9 1.3 - - - -
144R ILE* 1.3 75.8 - - - +
146R ASP* 1.3 62.5 + - - +
148R ILE* 3.1 6.8 + - - +
149R THR* 3.0 19.8 + - - -
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Residues in contact with ASP 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O ASP* 3.3 17.1 - - - +
43O ALA* 3.8 15.4 - - + +
45O HIS* 3.1 24.5 + - + +
142R LYS* 2.8 54.0 + - - +
143R ARG* 3.4 12.7 - - + +
144R ILE 3.3 0.2 - - - -
145R GLY* 1.3 75.3 - - - +
147R PHE* 1.3 65.0 + - + +
149R THR* 3.4 1.6 + - - -
150R ASN* 3.0 30.8 + - - +
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Residues in contact with PHE 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R PHE* 3.7 32.5 - + - -
96R MET* 3.9 28.3 - - + -
143R ARG* 3.0 40.0 + - + -
144R ILE* 3.2 11.6 + - - +
146R ASP* 1.3 82.2 - - + +
148R ILE* 1.3 52.3 + - - +
150R ASN* 3.2 3.7 + - + +
151R LEU* 2.7 43.7 + - + +
166R PHE* 3.6 22.1 - + + -
170R SER* 3.5 32.5 - - - -
171R VAL* 4.3 9.0 - - + -
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Residues in contact with ILE 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLN* 3.6 16.2 - - - +
93R LEU* 3.9 15.7 - - + -
96R MET* 3.7 34.3 - - + +
97R GLN* 4.0 17.7 - - + +
100R LEU* 3.7 33.4 - - + -
144R ILE 2.9 19.8 + - - +
145R GLY 3.1 6.7 + - - +
147R PHE* 1.3 74.7 - - - +
149R THR* 1.3 57.6 + - - +
151R LEU* 3.3 8.5 + - - +
152R LYS* 2.9 47.5 + - + +
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Residues in contact with THR 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLN* 3.4 13.2 + - - -
40O ASP 2.8 29.6 + - - +
41O ASP* 3.5 26.5 - - - +
43O ALA* 3.9 5.6 - - + -
145R GLY 3.0 4.7 + - - -
146R ASP 3.6 5.2 - - - -
148R ILE* 1.3 75.6 - - - +
150R ASN* 1.3 59.6 + - - +
152R LYS* 3.4 9.5 + - - +
153R ARG* 3.0 45.8 + - - +
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Residues in contact with ASN 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O ALA* 3.2 34.2 + - - +
44O LEU* 4.0 5.4 - - - +
45O HIS* 5.8 0.2 - - - -
164O TYR* 3.2 34.7 - - + -
168O LYS* 4.9 1.0 + - - -
146R ASP* 3.0 25.6 + - - +
147R PHE* 3.7 6.3 - - + +
149R THR* 1.3 75.0 - - - +
151R LEU* 1.3 65.9 + - - +
153R ARG* 3.3 21.8 + - - +
154R LEU* 3.1 30.0 + - - +
166R PHE* 4.6 6.7 - - + -
170R SER* 4.8 3.1 - - - +
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Residues in contact with LEU 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92R THR* 4.1 8.7 - - + +
93R LEU* 3.9 17.7 - - + +
96R MET* 3.8 29.2 - - + -
147R PHE 2.7 30.1 + - - +
148R ILE* 3.5 7.0 - - - +
150R ASN* 1.3 73.9 - - - +
152R LYS* 1.3 59.6 + - - +
154R LEU* 3.3 10.5 + - + +
155R GLY 3.3 0.2 + - - -
156R LEU* 3.0 63.5 + - + +
163R GLU* 5.3 0.2 - - - -
166R PHE* 3.5 43.1 - - + -
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Residues in contact with LYS 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN* 4.9 4.6 + - - -
93R LEU* 4.3 17.3 - - + -
97R GLN* 4.1 14.8 + - - -
148R ILE* 2.9 38.5 + - + +
149R THR* 3.7 8.1 - - - +
151R LEU* 1.3 75.6 - - - +
153R ARG* 1.3 59.9 + - - +
155R GLY* 2.9 19.9 + - - +
156R LEU 4.3 4.5 - - - +
157R PRO* 5.7 0.9 - - + -
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Residues in contact with ARG 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O ASP 5.5 0.4 + - - -
42O VAL* 2.5 36.9 + - - +
44O LEU* 3.4 22.9 - - - +
160O GLY* 3.3 50.8 - - - +
161O MET 3.7 1.0 + - - -
163O GLU* 3.5 21.1 + - - +
164O TYR* 4.1 13.9 - - - +
149R THR* 3.0 29.8 + - - +
150R ASN* 3.3 35.0 + - - +
151R LEU 3.3 0.4 - - - -
152R LYS* 1.3 70.2 - - - +
154R LEU* 1.3 59.6 + - + +
155R GLY* 3.0 9.1 + - - -
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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