Contacts of the helix formed by residues 134 - 153 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PRO* 3.7 30.7 - - + -
124B HIS* 3.5 18.3 - - + +
127B ASP* 6.0 1.1 - - + +
107V ASN* 4.8 5.2 - - - +
110V LEU* 3.9 37.7 - - + +
111V LEU* 4.6 13.9 - - + -
114V HIS* 4.2 7.2 - - + -
129V LEU* 2.9 21.1 + - + +
130V GLU* 3.9 30.4 + - + +
133V TYR* 1.3 75.5 - - + +
135V GLU* 1.3 62.3 + - - +
137V GLN* 3.5 5.6 + - - +
138V VAL* 3.3 27.4 + - - +
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Residues in contact with GLU 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 5.4 0.7 - - - -
71B LYS* 2.8 32.5 + - - -
124B HIS* 3.0 33.3 + - + +
127B ASP* 5.1 7.2 - - - +
128B PHE* 5.7 3.6 - - - -
130V GLU 4.1 10.8 + - - +
131V SER 5.8 2.2 - - - +
133V TYR 3.5 0.4 - - - -
134V LEU* 1.3 75.9 - - - +
136V GLU* 1.3 68.5 + - - +
138V VAL* 3.3 3.4 + - - +
139V LYS* 3.0 31.0 + - + +
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Residues in contact with GLU 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61V HIS* 5.1 15.5 - - + +
132V GLU 4.2 11.9 - - - +
133V TYR* 3.3 13.8 + - - +
134V LEU 3.3 0.2 - - - -
135V GLU* 1.3 79.6 - - - +
137V GLN* 1.3 57.2 + - + +
139V LYS* 3.5 7.7 - - - +
140V ASP* 3.1 35.4 + - - +
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Residues in contact with GLN 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61V HIS* 5.1 1.7 - - - -
103V GLU* 3.0 47.5 + - - +
106V VAL* 3.9 10.1 - - - +
107V ASN* 3.6 21.7 - - - +
110V LEU* 3.7 20.4 - - + -
133V TYR 3.0 19.7 + - - +
134V LEU 3.7 3.8 - - - +
135V GLU 3.2 0.2 - - - -
136V GLU* 1.3 75.6 - - + +
138V VAL* 1.3 61.1 + - - +
140V ASP* 3.3 2.5 + - - +
141V ILE* 2.9 34.5 + - - +
176V MG 3.4 16.3 - - - -
177V MG 2.7 20.9 - - - -
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Residues in contact with VAL 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 4.3 22.0 - - + +
72B ARG* 4.4 15.7 - - - +
124B HIS* 3.3 43.7 - - + +
107V ASN* 5.0 10.8 - - - +
134V LEU 3.3 13.4 + - - +
135V GLU* 3.3 15.6 + - - +
137V GLN* 1.3 78.1 - - + +
139V LYS* 1.3 63.8 + - - +
141V ILE* 3.9 7.9 - - + +
142V LYS* 3.0 26.3 + - - +
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Residues in contact with LYS 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 4.6 12.1 - - - +
135V GLU* 3.0 33.2 + - + +
136V GLU* 3.5 12.8 - - - +
138V VAL* 1.3 79.1 - - - +
140V ASP* 1.3 60.6 + - - +
142V LYS* 3.5 4.7 + - - +
143V ARG* 3.0 33.8 + - - +
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Residues in contact with ASP 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V HIS* 3.7 20.1 - - + -
57V GLU* 4.1 9.8 - - - +
61V HIS* 5.6 0.7 - - - -
103V GLU* 4.4 12.3 - - + +
136V GLU* 3.1 18.1 + - - +
137V GLN 3.7 3.8 - - - +
139V LYS* 1.3 79.7 - - - +
141V ILE* 1.3 64.4 + - - +
143V ARG* 3.2 29.9 + - - +
144V ILE* 3.1 30.9 + - - +
177V MG 2.5 29.6 - - - -
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Residues in contact with ILE 141 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.5 36.1 - - + +
6B GLN* 3.8 22.7 - - + +
100V LEU* 3.9 22.0 - - + +
103V GLU* 3.9 26.9 - - + +
104V LYS* 4.2 7.0 - - + -
107V ASN* 3.9 24.2 - - + +
137V GLN* 2.9 23.9 + - - +
138V VAL* 3.9 7.6 - - + +
140V ASP* 1.3 74.2 - - - +
142V LYS* 1.3 58.9 + - - +
144V ILE* 3.4 1.6 + - - -
145V GLY* 2.9 24.8 + - - -
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Residues in contact with LYS 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.0 8.5 - - + +
67B LYS* 6.0 0.6 - - - +
70B ASN* 3.3 33.0 - - - +
71B LYS* 4.1 23.6 - - + +
38F ASP* 2.9 30.5 + - - -
40F ASP* 3.9 16.6 - - + +
45F HIS* 4.0 6.1 - - - -
138V VAL 3.0 18.2 + - - +
139V LYS* 3.7 5.8 - - - +
141V ILE* 1.3 78.7 - - - +
143V ARG* 1.3 56.5 + - - +
145V GLY* 3.9 0.3 - - - -
146V ASP* 2.8 67.3 + - - +
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Residues in contact with ARG 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50V PHE* 3.9 13.4 - - - -
54V HIS* 3.1 30.7 + - - -
57V GLU* 5.8 1.4 + - - -
139V LYS* 3.0 22.4 + - - +
140V ASP* 3.2 30.8 + - - +
141V ILE 3.2 0.2 - - - -
142V LYS* 1.3 75.7 - - - +
144V ILE* 1.3 60.5 + - - +
146V ASP* 3.4 11.6 + - + +
147V PHE* 3.0 56.1 + - + -
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Residues in contact with ILE 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V TYR* 4.3 4.5 - - + +
50V PHE* 4.5 23.6 - - + -
54V HIS* 4.9 5.6 - - + -
96V MET* 3.4 37.9 - - - +
99V ALA* 4.1 15.0 - - + +
100V LEU* 3.9 17.0 - - + +
103V GLU* 3.9 28.7 - - + +
140V ASP 3.1 18.2 + - - +
141V ILE* 4.0 2.9 - - - +
143V ARG* 1.3 75.7 - - + +
145V GLY* 1.3 61.1 + - - +
147V PHE* 3.2 7.8 + - - +
148V ILE* 2.9 29.6 + - + +
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Residues in contact with GLY 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 3.2 29.4 + - - -
4B VAL* 4.0 10.8 - - - -
40F ASP* 4.3 2.9 - - - -
100V LEU* 4.5 2.6 - - - +
141V ILE 2.9 17.8 + - - -
142V LYS 3.9 1.6 - - - -
144V ILE* 1.3 76.0 - - - +
146V ASP* 1.3 63.6 + - - +
148V ILE* 3.1 6.2 + - - +
149V THR* 3.0 19.9 + - - -
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Residues in contact with ASP 146 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ARG 4.1 0.2 - - - +
40F ASP* 3.3 17.7 - - - +
43F ALA* 3.8 15.8 - - + +
45F HIS* 3.0 27.0 + - + +
142V LYS* 2.8 51.0 + - - +
143V ARG* 3.4 12.7 - - + +
145V GLY* 1.3 75.5 - - - +
147V PHE* 1.3 65.0 + - + +
149V THR* 3.4 1.9 + - - -
150V ASN* 3.0 30.8 + - - +
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Residues in contact with PHE 147 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V PHE* 3.7 33.4 - + - -
96V MET* 3.9 27.4 - - + -
143V ARG* 3.0 38.9 + - + -
144V ILE* 3.2 11.6 + - - +
146V ASP* 1.3 81.0 - - + +
148V ILE* 1.3 52.0 - - - +
150V ASN* 3.2 3.6 + - + +
151V LEU* 2.7 43.7 + - + +
166V PHE* 3.6 23.2 - + + -
170V SER* 3.5 33.0 - - - -
171V VAL* 4.3 8.7 - - + -
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Residues in contact with ILE 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLN* 3.5 16.6 - - - +
93V LEU* 3.9 15.0 - - + -
96V MET* 3.7 35.2 - - + +
97V GLN* 4.0 17.7 - - + +
100V LEU* 3.7 32.5 - - + -
144V ILE* 2.9 19.8 + - + +
145V GLY 3.1 6.5 + - - +
147V PHE* 1.3 74.6 - - - +
149V THR* 1.3 58.1 + - - +
151V LEU* 3.3 7.9 + - - +
152V LYS* 2.9 47.6 + - - +
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Residues in contact with THR 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 3.5 13.0 + - - -
40F ASP 2.8 28.3 + - - +
41F ASP* 3.5 28.4 - - - +
43F ALA* 3.9 5.4 - - + -
145V GLY 3.0 4.4 + - - -
146V ASP 3.6 5.8 - - - -
147V PHE 3.2 0.2 - - - -
148V ILE* 1.3 76.0 - - - +
150V ASN* 1.3 58.1 + - - +
152V LYS* 3.4 9.2 + - - +
153V ARG* 3.0 45.6 + - - +
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Residues in contact with ASN 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ALA* 3.2 33.7 + - - +
44F LEU* 4.0 5.0 - - - +
164F TYR* 3.2 34.3 - - + -
168F LYS* 4.9 0.9 + - - -
146V ASP* 3.0 26.1 + - - +
147V PHE* 3.2 6.9 + - + +
149V THR* 1.3 74.7 - - - +
151V LEU* 1.3 65.5 + - - +
153V ARG* 3.3 22.3 + - - +
154V LEU* 3.1 29.9 + - - +
166V PHE* 4.6 7.2 - - + -
170V SER* 4.8 2.5 - - - +
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Residues in contact with LEU 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92V THR* 4.1 9.2 - - + +
93V LEU* 3.9 17.5 - - + +
96V MET* 3.8 28.9 - - + -
147V PHE 2.7 29.3 + - - +
148V ILE* 3.3 7.6 + - - +
150V ASN* 1.3 75.3 - - - +
152V LYS* 1.3 59.8 + - - +
154V LEU* 3.3 9.8 + - - +
155V GLY 3.3 0.2 + - - -
156V LEU* 3.0 62.9 + - + +
166V PHE* 3.5 42.6 - - + -
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Residues in contact with LYS 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 4.9 4.6 + - - -
93V LEU* 4.3 17.5 - - + -
97V GLN* 4.1 15.1 + - - -
148V ILE* 2.9 38.6 + - + +
149V THR* 3.7 7.9 - - - +
151V LEU* 1.3 75.0 - - - +
153V ARG* 1.3 59.7 + - - +
155V GLY* 2.9 18.1 + - - +
156V LEU* 4.3 4.7 - - - +
157V PRO* 5.7 1.3 - - + -
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Residues in contact with ARG 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F VAL* 2.5 36.5 + - - +
44F LEU* 3.4 24.3 - - - +
160F GLY* 3.3 52.2 - - - +
161F MET 3.7 0.9 + - - -
163F GLU* 3.5 20.3 + - - +
164F TYR* 4.1 13.5 - - - +
149V THR* 3.0 29.5 + - - +
150V ASN* 3.3 33.4 + - - +
152V LYS* 1.3 71.2 - - - +
154V LEU* 1.3 58.9 + - + +
155V GLY* 3.0 9.0 + - - -
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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