Contacts of the helix formed by residues 134 - 153 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I PRO* 3.9 29.6 - - + -
124I HIS* 3.5 20.0 - - + +
127I ASP* 6.1 0.7 - - + +
107W ASN* 4.8 6.0 - - - +
110W LEU* 3.9 37.5 - - + +
111W LEU* 4.6 14.1 - - + -
114W HIS* 4.2 8.1 - - + -
129W LEU* 2.9 21.1 + - + +
130W GLU* 3.9 29.8 + - + +
133W TYR* 1.3 74.6 - - + +
135W GLU* 1.3 62.3 + - - +
137W GLN* 3.5 5.6 + - - +
138W VAL* 3.3 26.7 + - - +
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Residues in contact with GLU 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I TYR* 5.4 0.3 - - - -
71I LYS* 2.8 33.3 + - - -
124I HIS* 3.1 30.7 + - + +
127I ASP* 5.2 5.8 - - - +
128I PHE* 5.8 3.3 - - - -
130W GLU 4.1 11.8 + - - +
131W SER 5.8 2.5 - - - +
133W TYR 3.5 0.4 - - - +
134W LEU* 1.3 75.3 - - - +
136W GLU* 1.3 67.6 + - - +
138W VAL* 3.3 2.9 + - - +
139W LYS* 3.0 31.4 + - + +
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Residues in contact with GLU 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61W HIS* 5.1 15.3 - - + +
132W GLU 4.2 13.2 - - - +
133W TYR* 3.3 13.3 + - - +
135W GLU* 1.3 79.9 - - - +
137W GLN* 1.3 57.4 + - + +
139W LYS* 3.5 7.7 - - - +
140W ASP* 3.1 35.2 + - - +
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Residues in contact with GLN 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61W HIS* 5.1 1.4 - - - -
103W GLU* 3.0 47.2 + - - +
106W VAL* 3.9 9.3 - - - +
107W ASN* 3.6 23.0 - - - +
110W LEU* 3.7 20.6 - - + -
133W TYR* 3.0 19.2 + - + +
134W LEU 3.7 3.8 - - - +
135W GLU 3.2 0.2 - - - -
136W GLU* 1.3 75.8 - - + +
138W VAL* 1.3 62.1 + - - +
140W ASP* 3.3 3.4 + - - +
141W ILE* 2.9 33.4 + - - +
176W MG 3.4 15.9 - - - -
177W MG 2.7 21.6 - - - -
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Residues in contact with VAL 138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I LYS* 4.2 27.4 - - + +
72I ARG* 4.4 12.8 - - - +
124I HIS* 3.4 42.2 - - + +
107W ASN* 5.0 11.4 - - - +
134W LEU 3.3 13.7 + - - +
135W GLU* 3.3 15.6 + - - +
137W GLN* 1.3 77.9 - - + +
139W LYS* 1.3 64.0 + - - +
141W ILE* 3.9 8.2 - - + +
142W LYS* 3.0 25.8 + - - +
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Residues in contact with LYS 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I LYS* 4.6 11.4 - - - +
135W GLU* 3.0 33.8 + - + +
136W GLU* 3.5 12.3 - - - +
138W VAL* 1.3 79.8 - - - +
140W ASP* 1.3 60.4 + - - +
142W LYS* 3.5 4.9 + - - +
143W ARG* 3.0 35.1 + - - +
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Residues in contact with ASP 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54W HIS* 3.7 19.7 - - + -
57W GLU* 4.1 9.0 - - - +
61W HIS* 5.6 0.7 - - - -
103W GLU* 4.4 12.6 - - + +
136W GLU* 3.1 17.4 + - - +
137W GLN 3.3 4.0 + - - +
139W LYS* 1.3 80.2 - - - +
141W ILE* 1.3 64.5 + - - +
143W ARG* 3.2 30.9 + - - +
144W ILE* 3.1 30.7 + - + +
177W MG 2.5 29.1 - - - -
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Residues in contact with ILE 141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 3.5 39.1 - - + +
6I GLN* 3.9 12.1 - - + +
100W LEU* 3.9 19.1 - - + +
103W GLU* 3.9 26.2 - - + +
104W LYS* 4.2 8.3 - - + -
107W ASN* 3.9 34.8 - - + +
137W GLN* 2.9 23.1 + - - +
138W VAL* 3.9 7.6 - - + +
140W ASP* 1.3 73.9 - - - +
142W LYS* 1.3 59.2 + - - +
144W ILE* 3.4 1.5 + - - -
145W GLY 2.9 24.9 + - - -
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Residues in contact with LYS 142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASP* 2.9 28.8 + - - -
40E ASP* 3.9 19.5 - - + +
45E HIS* 4.0 6.9 - - - -
4I VAL* 4.0 8.9 - - + +
67I LYS* 6.0 0.4 - - - +
70I ASN* 3.4 32.1 - - - +
71I LYS* 4.2 22.9 - - + +
138W VAL 3.0 18.2 + - - +
139W LYS* 3.7 6.3 - - - +
141W ILE* 1.3 77.6 - - - +
143W ARG* 1.3 55.5 + - - +
145W GLY* 3.5 0.5 + - - -
146W ASP* 2.8 65.6 + - - +
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Residues in contact with ARG 143 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W PHE* 3.9 13.2 - - - -
54W HIS* 3.1 30.5 + - - -
57W GLU* 5.8 1.6 + - - -
139W LYS* 3.0 22.2 + - - +
140W ASP* 3.2 30.5 + - - +
141W ILE 3.2 0.2 - - - -
142W LYS* 1.3 76.4 - - - +
144W ILE* 1.3 61.5 + - - +
146W ASP* 3.4 11.3 + - + +
147W PHE* 3.0 55.9 + - + -
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Residues in contact with ILE 144 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W TYR* 4.3 4.0 - - - +
50W PHE* 4.5 24.0 - - + -
54W HIS* 4.9 5.6 - - + -
96W MET* 3.4 36.8 - - - +
99W ALA* 4.1 15.0 - - + +
100W LEU* 3.9 17.9 - - + +
103W GLU* 3.9 29.2 - - + +
140W ASP 3.1 17.5 + - - +
141W ILE* 4.0 2.5 - - - +
143W ARG* 1.3 75.7 - - + +
145W GLY* 1.3 60.9 + - - +
147W PHE* 3.2 8.1 + - - +
148W ILE* 2.9 29.7 + - + +
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Residues in contact with GLY 145 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ASP* 4.3 3.1 - - - -
3I GLN* 3.2 29.8 + - - -
4I VAL* 4.1 9.4 - - - -
100W LEU* 4.5 2.8 - - - +
141W ILE 2.9 17.2 + - - -
142W LYS 3.9 1.3 - - - -
144W ILE* 1.3 76.7 - - - +
146W ASP* 1.3 62.2 + - - +
148W ILE* 3.1 7.2 + - - +
149W THR* 3.0 20.3 + - - -
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Residues in contact with ASP 146 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ASP* 3.3 17.1 - - - +
43E ALA* 3.7 16.2 - - + +
45E HIS* 3.0 29.1 + - + +
142W LYS* 2.8 49.8 + - - +
143W ARG* 3.4 12.9 - - + +
145W GLY* 1.3 76.1 - - - +
147W PHE* 1.3 64.1 + - + +
149W THR* 3.4 1.9 + - - -
150W ASN* 3.0 31.0 + - - +
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Residues in contact with PHE 147 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W PHE* 3.7 32.5 - + - -
96W MET* 3.9 27.8 - - + -
143W ARG* 3.0 39.1 + - + -
144W ILE* 3.2 12.1 + - - +
146W ASP* 1.3 80.8 - - + +
148W ILE* 1.3 50.9 + - - +
150W ASN* 3.2 3.9 + - + +
151W LEU* 2.7 43.4 + - + +
166W PHE* 3.6 22.5 - + + -
170W SER* 3.5 32.3 - - - -
171W VAL* 4.3 8.7 - - + -
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Residues in contact with ILE 148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLN* 3.7 16.8 - - - +
93W LEU* 3.9 15.5 - - + -
96W MET* 3.7 34.3 - - + +
97W GLN* 4.0 18.4 - - + +
100W LEU* 3.7 32.8 - - + -
144W ILE 2.9 19.4 + - - +
145W GLY 3.5 5.6 - - - +
147W PHE* 1.3 75.3 - - - +
149W THR* 1.3 58.9 + - - +
151W LEU* 3.3 8.2 + - - +
152W LYS* 2.9 47.8 + - - +
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Residues in contact with THR 149 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ASP 2.9 28.4 + - - +
41E ASP* 3.5 26.4 - - - +
43E ALA* 3.9 5.8 - - + -
3I GLN* 3.6 11.6 + - - -
145W GLY 3.0 4.2 + - - -
146W ASP 3.6 5.8 - - - -
148W ILE* 1.3 77.1 - - - +
150W ASN* 1.3 57.6 + - - +
152W LYS* 3.4 9.8 + - - +
153W ARG* 3.0 46.7 + - - +
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Residues in contact with ASN 150 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ALA* 3.2 33.1 + - - +
44E LEU* 4.0 5.0 - - - +
45E HIS* 5.9 0.2 - - - -
164E TYR* 3.1 34.9 - - + -
168E LYS* 4.8 1.1 + - - -
146W ASP* 3.0 25.7 + - - +
147W PHE* 3.7 5.8 - - + +
149W THR* 1.3 75.3 - - - +
151W LEU* 1.3 65.4 + - - +
153W ARG* 3.3 21.7 + - - +
154W LEU* 3.1 30.2 + - - +
166W PHE* 4.6 7.2 - - + -
170W SER* 4.8 2.2 - - - +
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Residues in contact with LEU 151 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92W THR* 4.1 9.0 - - + +
93W LEU* 3.9 17.3 - - + +
96W MET* 3.8 29.4 - - + -
147W PHE 2.7 31.2 + - - +
148W ILE* 3.5 7.0 - - - +
150W ASN* 1.3 73.9 - - - +
152W LYS* 1.3 59.5 + - - +
154W LEU* 3.3 10.3 + - + +
155W GLY 3.3 0.2 + - - -
156W LEU* 3.0 63.5 + - + +
166W PHE* 3.5 43.1 - - + -
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Residues in contact with LYS 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLN* 5.0 4.0 + - - -
93W LEU* 4.3 18.4 - - + -
97W GLN* 4.1 15.1 + - - -
148W ILE* 2.9 40.2 + - + +
149W THR* 3.6 7.6 - - - +
151W LEU* 1.3 74.9 - - - +
153W ARG* 1.3 60.1 + - - +
155W GLY* 2.9 18.6 + - - +
156W LEU* 4.3 4.9 - - - +
157W PRO* 5.7 1.3 - - + -
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Residues in contact with ARG 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ASP 5.6 0.8 + - - -
42E VAL* 2.6 33.3 + - - +
44E LEU* 3.4 20.4 - - - +
160E GLY* 3.2 53.0 - - - +
161E MET 3.6 0.9 + - - -
163E GLU* 3.4 25.0 + - - +
164E TYR* 4.0 13.9 - - - +
149W THR* 3.0 30.5 + - - +
150W ASN* 3.3 34.8 + - - +
151W LEU 3.3 0.2 - - - -
152W LYS* 1.3 70.4 - - - +
154W LEU* 1.3 58.4 + - + +
155W 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