Contacts of the helix formed by residues 134 - 153 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107E ASN* 4.8 5.5 - - - +
110E LEU* 3.9 37.7 - - + +
111E LEU* 4.6 14.1 - - + -
114E HIS* 4.2 7.6 - - + -
129E LEU* 2.9 21.1 + - + +
130E GLU* 3.9 30.7 + - + +
133E TYR* 1.3 75.0 - - + +
135E GLU* 1.3 61.4 + - - +
137E GLN* 3.5 5.6 + - - +
138E VAL* 3.3 26.7 + - - +
123V PRO* 3.7 31.6 - - + -
124V HIS* 3.7 17.7 - - + +
127V ASP* 6.4 0.7 - - + -
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E GLU 4.1 10.6 + - - +
131E SER 5.8 2.7 - - - +
133E TYR 3.5 0.2 - - - -
134E LEU* 1.3 76.3 - - - +
136E GLU* 1.3 67.3 + - - +
138E VAL* 3.3 3.4 + - - +
139E LYS* 3.0 31.7 + - + +
68V TYR* 5.4 0.9 - - - -
71V LYS* 2.8 32.1 + - - -
124V HIS* 3.0 34.4 + - + +
127V ASP* 5.1 7.0 - - - +
128V PHE* 5.7 3.3 - - - -
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Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E HIS* 5.1 15.0 - - + +
132E GLU 4.2 12.1 - - - +
133E TYR* 3.3 13.7 + - - +
134E LEU 3.3 0.2 - - - -
135E GLU* 1.3 79.4 - - - +
137E GLN* 1.3 58.5 + - + +
139E LYS* 3.5 7.8 - - - +
140E ASP* 3.1 34.6 + - - +
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Residues in contact with GLN 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E HIS* 5.1 1.4 - - - -
103E GLU* 3.0 47.6 + - - +
106E VAL* 3.9 10.1 - - - +
107E ASN* 3.6 22.8 - - - +
110E LEU* 3.7 20.0 - - + -
133E TYR* 3.0 20.7 + - + +
134E LEU 3.7 4.0 - - - +
135E GLU 3.2 0.4 - - - -
136E GLU* 1.3 75.0 - - + +
138E VAL* 1.3 59.7 + - - +
140E ASP* 3.3 2.6 + - - +
141E ILE* 2.9 34.7 + - - +
176E MG 3.4 16.5 - - - -
177E MG 2.7 20.9 - - - -
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ASN* 5.0 11.7 - - - +
134E LEU 3.3 13.0 + - - +
135E GLU* 3.3 15.8 + - - +
137E GLN* 1.3 78.7 - - + +
139E LYS* 1.3 64.4 + - - +
141E ILE* 3.9 8.1 - - + +
142E LYS* 3.0 26.3 + - - +
71V LYS* 4.3 22.4 - - + +
72V ARG* 4.3 16.6 - - - +
124V HIS* 3.3 42.6 - - + +
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Residues in contact with LYS 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLU* 3.0 32.5 + - + +
136E GLU* 3.5 12.8 - - - +
138E VAL* 1.3 79.7 - - - +
140E ASP* 1.3 60.4 + - - +
142E LYS* 3.5 4.9 + - - +
143E ARG* 3.0 33.6 + - - +
71V LYS* 4.6 11.7 - - - +
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Residues in contact with ASP 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E HIS* 3.7 20.4 - - + -
57E GLU* 4.1 9.4 - - - +
61E HIS* 5.6 0.7 - - - -
103E GLU* 4.4 12.6 - - - +
136E GLU* 3.1 19.1 + - - +
137E GLN 3.3 4.0 + - - +
139E LYS* 1.3 79.0 - - - +
141E ILE* 1.3 64.8 + - - +
143E ARG* 3.2 30.3 + - - +
144E ILE* 3.1 31.0 + - + +
177E MG 2.5 29.1 - - - -
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Residues in contact with ILE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LEU* 3.9 21.6 - - + +
103E GLU* 3.9 26.2 - - + +
104E LYS* 4.2 7.4 - - + -
107E ASN* 3.9 24.0 - - + +
137E GLN* 2.9 23.7 + - - +
138E VAL* 3.9 7.0 - - + +
140E ASP* 1.3 73.8 - - - +
142E LYS* 1.3 59.3 + - - +
144E ILE* 3.4 1.8 + - - -
145E GLY 2.9 24.8 + - - -
4V VAL* 3.5 35.7 - - + +
6V GLN* 3.8 22.7 - - + +
71V LYS 5.9 0.2 - - - +
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Residues in contact with LYS 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E VAL 3.0 18.4 + - - +
139E LYS* 3.7 6.5 - - - +
141E ILE* 1.3 78.2 - - - +
143E ARG* 1.3 56.9 + - - +
145E GLY* 3.5 0.5 + - - -
146E ASP* 2.8 65.4 + - - +
38L ASP* 2.9 29.4 + - - -
40L ASP* 3.9 18.6 - - + +
45L HIS* 4.0 6.7 - - - -
4V VAL* 4.0 8.7 - - + +
67V LYS* 6.0 0.4 - - - +
70V ASN* 3.3 32.5 - - - +
71V LYS* 4.1 24.2 - - + +
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Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E PHE* 3.9 12.8 - - - -
54E HIS* 3.1 31.1 + - - -
57E GLU* 5.8 1.6 + - - -
139E LYS* 3.0 21.0 + - - +
140E ASP* 3.2 31.2 + - - +
141E ILE 3.2 0.4 - - - -
142E LYS* 1.3 76.9 - - - +
144E ILE* 1.3 61.8 + - - +
146E ASP* 3.4 10.8 + - + +
147E PHE* 3.0 56.7 + - + -
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Residues in contact with ILE 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 4.3 4.3 - - + +
50E PHE* 4.5 23.3 - - + -
54E HIS* 4.9 5.6 - - + -
96E MET* 3.4 37.9 - - - +
99E ALA* 4.1 15.0 - - + +
100E LEU* 3.9 17.3 - - + +
103E GLU* 3.9 28.5 - - + +
140E ASP 3.1 17.8 + - - +
141E ILE* 4.0 2.9 - - - +
143E ARG* 1.3 76.0 - - + +
145E GLY* 1.3 60.7 + - - +
147E PHE* 3.2 7.9 + - - +
148E ILE* 2.9 29.3 + - + +
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Residues in contact with GLY 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LEU* 4.5 2.6 - - - +
141E ILE 2.9 17.6 + - - -
142E LYS 3.9 1.1 - - - -
144E ILE* 1.3 75.8 - - - +
146E ASP* 1.3 62.4 + - - +
148E ILE* 3.1 6.8 + - - +
149E THR* 3.0 19.9 + - - -
40L ASP* 4.3 3.1 - - - -
3V GLN* 3.2 29.0 + - - -
4V VAL* 4.0 11.4 - - - -
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Residues in contact with ASP 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 2.8 50.0 + - - +
143E ARG* 3.4 12.7 - - + +
145E GLY* 1.3 75.9 - - - +
147E PHE* 1.3 64.5 + - + +
149E THR* 3.4 1.7 + - - -
150E ASN* 3.0 31.1 + - - +
39L ARG 4.1 0.2 - - - +
40L ASP* 3.3 17.1 - - - +
43L ALA* 3.7 15.7 - - + +
45L HIS* 3.0 27.7 + - + +
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Residues in contact with PHE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E PHE* 3.7 32.8 - + - -
96E MET* 3.9 27.6 - - + -
143E ARG* 3.0 39.9 + - + -
144E ILE* 3.2 12.1 + - - +
146E ASP* 1.3 79.8 - - + +
148E ILE* 1.3 52.5 + - - +
150E ASN* 3.2 4.1 + - + +
151E LEU* 2.7 43.6 + - + +
166E PHE* 3.6 24.2 - + + -
170E SER* 3.5 32.1 - - - -
171E VAL* 4.3 9.0 - - + -
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Residues in contact with ILE 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LEU* 3.9 15.5 - - + -
96E MET* 3.7 36.3 - - + +
97E GLN* 4.0 18.2 - - + +
100E LEU* 3.7 32.1 - - + -
144E ILE 2.9 19.4 + - - +
145E GLY 3.1 6.7 + - - +
147E PHE* 1.3 73.5 - - - +
149E THR* 1.3 57.7 + - - +
151E LEU* 3.3 8.2 + - - +
152E LYS* 2.9 47.6 + - + +
3V GLN* 3.6 16.8 - - - +
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Residues in contact with THR 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLY 3.0 4.8 + - - -
146E ASP 3.6 6.1 - - - -
148E ILE* 1.3 77.5 - - - +
150E ASN* 1.3 59.3 + - - +
152E LYS* 3.4 9.2 + - - +
153E ARG* 3.0 45.0 + - - +
40L ASP 2.9 27.6 + - - +
41L ASP* 3.5 28.7 - - - +
42L VAL 3.9 2.5 - - - +
43L ALA* 3.9 3.4 - - + -
3V GLN* 3.5 11.8 + - - -
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Residues in contact with ASN 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ASP* 3.0 27.9 + - - +
147E PHE* 3.7 6.5 - - + +
149E THR* 1.3 74.1 - - - +
151E LEU* 1.3 65.2 + - - +
153E ARG* 3.3 22.3 + - - +
154E LEU* 3.1 30.6 + - - +
166E PHE* 4.6 6.7 - - + -
170E SER* 4.8 2.0 - - - +
43L ALA* 3.2 33.3 + - - +
44L LEU* 3.9 5.5 - - - +
164L TYR* 3.2 34.6 - - + -
168L LYS* 4.9 1.3 + - - -
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E THR* 4.1 8.3 - - + +
93E LEU* 3.9 16.8 - - + +
96E MET* 3.8 29.6 - - + -
147E PHE 2.7 31.0 + - - +
148E ILE* 3.3 7.2 + - - +
150E ASN* 1.3 72.9 - - - +
152E LYS* 1.3 59.6 + - - +
154E LEU* 3.3 10.6 + - + +
155E GLY 3.3 0.2 + - - -
156E LEU* 3.0 62.5 + - + +
163E GLU* 5.3 0.2 - - - -
166E PHE* 3.5 42.0 - - + -
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Residues in contact with LYS 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LEU* 4.3 17.0 - - + -
97E GLN* 4.1 14.8 + - - -
148E ILE* 2.9 39.6 + - + +
149E THR* 3.6 7.6 - - - +
151E LEU* 1.3 74.3 - - - +
153E ARG* 1.3 60.0 + - - +
155E GLY* 2.9 18.4 + - - +
156E LEU* 4.3 4.9 - - - +
157E PRO* 5.7 1.3 - - + -
3V GLN* 4.9 4.6 + - - -
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Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E THR* 3.0 29.5 + - - +
150E ASN* 3.3 34.2 + - - +
152E LYS* 1.3 71.2 - - - +
154E LEU* 1.3 58.5 + - + +
155E GLY* 3.0 9.4 + - - -
41L ASP 5.5 0.4 + - - -
42L VAL* 2.5 36.1 + - - +
44L LEU* 3.4 19.8 - - - +
160L GLY* 3.2 52.3 + - - +
161L MET 3.6 0.7 + - - -
163L GLU* 3.4 25.6 + - - +
164L TYR* 4.1 13.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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