Contacts of the helix formed by residues 134 - 153 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 3.7 31.4 - - + -
124D HIS* 3.5 18.3 - - + +
127D ASP* 6.4 0.7 - - + -
107I ASN* 4.8 5.6 - - - +
110I LEU* 3.9 37.7 - - + +
111I LEU* 4.6 13.7 - - + -
114I HIS* 4.2 7.9 - - + -
129I LEU* 2.9 21.7 + - + +
130I GLU* 3.9 29.7 + - + +
133I TYR* 1.3 74.5 - - + +
135I GLU* 1.3 62.1 + - - +
137I GLN* 3.5 6.2 + - - +
138I VAL* 3.3 26.5 + - - +
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Residues in contact with GLU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 5.3 0.7 - - - -
71D LYS* 2.8 33.8 + - - -
124D HIS* 2.9 36.0 + - + +
127D ASP* 5.0 6.9 + - - +
128D PHE* 5.7 3.6 - - - +
130I GLU 4.1 10.6 + - - +
131I SER 5.8 2.9 - - - +
133I TYR 3.5 0.2 - - - -
134I LEU* 1.3 75.1 - - - +
136I GLU* 1.3 68.1 + - - +
138I VAL* 3.3 3.0 + - - +
139I LYS* 3.0 31.4 + - + +
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Residues in contact with GLU 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I HIS* 5.1 15.3 - - + +
132I GLU 4.2 12.1 - - - +
133I TYR* 3.3 14.0 + - - +
134I LEU 3.3 0.2 - - - -
135I GLU* 1.3 80.2 - - - +
137I GLN* 1.3 57.9 + - + +
139I LYS* 3.5 7.5 - - - +
140I ASP* 3.1 35.1 + - - +
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Residues in contact with GLN 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I HIS* 5.1 1.4 - - - -
103I GLU* 3.0 48.0 + - - +
106I VAL* 3.9 9.5 - - - +
107I ASN* 3.6 22.6 - - - +
110I LEU* 3.7 20.2 - - + -
133I TYR* 3.0 19.6 + - + +
134I LEU 3.7 3.6 - - - +
135I GLU 3.2 0.4 - - - -
136I GLU* 1.3 75.3 - - + +
138I VAL* 1.3 60.9 + - - +
140I ASP* 3.3 2.2 + - - +
141I ILE* 2.9 34.4 + - - +
176I MG 3.4 15.9 - - - -
177I MG 2.7 21.4 - - - -
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Residues in contact with VAL 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LYS* 4.3 22.5 - - + +
72D ARG* 4.3 16.8 - - - +
124D HIS* 3.3 43.3 - - + +
107I ASN* 5.0 11.0 - - - +
134I LEU 3.3 12.8 + - - +
135I GLU* 3.3 15.0 + - - +
137I GLN* 1.3 78.1 - - + +
139I LYS* 1.3 64.6 + - - +
141I ILE* 3.9 8.0 - - + +
142I LYS* 3.0 25.6 + - - +
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Residues in contact with LYS 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LYS* 4.5 12.8 - - - +
135I GLU* 3.0 33.4 + - + +
136I GLU* 3.5 11.9 - - - +
138I VAL* 1.3 78.8 - - - +
140I ASP* 1.3 60.8 + - - +
142I LYS* 3.5 4.8 + - - +
143I ARG* 3.0 33.3 + - - +
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Residues in contact with ASP 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I HIS* 3.7 20.1 - - + -
57I GLU* 4.1 9.8 - - - +
61I HIS* 5.6 0.7 - - - -
103I GLU* 4.4 12.6 - - + +
136I GLU* 3.1 18.5 + - - +
137I GLN* 3.3 4.2 + - - +
139I LYS* 1.3 80.2 - - - +
141I ILE* 1.3 63.8 + - - +
143I ARG* 3.2 30.0 + - - +
144I ILE* 3.1 30.1 + - - +
177I MG 2.5 29.5 - - - -
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Residues in contact with ILE 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 3.5 35.9 - - + +
6D GLN* 3.8 23.1 - - + +
100I LEU* 3.9 21.8 - - + +
103I GLU* 3.9 26.5 - - + +
104I LYS* 4.2 8.3 - - + -
107I ASN* 3.9 24.5 - - + +
137I GLN* 2.9 23.3 + - - +
138I VAL* 3.9 7.0 - - + +
140I ASP* 1.3 74.8 - - - +
142I LYS* 1.3 59.0 + - - +
144I ILE* 3.4 1.4 + - - -
145I GLY* 2.9 24.9 + - - -
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Residues in contact with LYS 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.9 8.7 - - + +
67D LYS* 6.0 0.4 - - - +
70D ASN* 3.2 32.1 - - - +
71D LYS* 4.1 24.0 - - + +
38H ASP* 2.9 29.6 + - - -
40H ASP* 3.9 19.3 - - + +
45H HIS* 4.0 5.9 - - - -
138I VAL 3.0 19.0 + - - +
139I LYS* 3.7 5.6 - - - +
141I ILE* 1.3 78.7 - - - +
143I ARG* 1.3 57.2 + - - +
145I GLY* 3.5 0.3 + - - -
146I ASP* 2.8 65.5 + - - +
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Residues in contact with ARG 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I PHE* 3.9 13.0 - - - -
54I HIS* 3.1 31.1 + - - -
57I GLU* 5.8 1.4 + - - -
139I LYS* 3.0 22.2 + - - +
140I ASP* 3.2 30.5 + - - +
141I ILE 3.2 0.2 - - - -
142I LYS* 1.3 75.9 - - - +
144I ILE* 1.3 60.9 + - - +
146I ASP* 3.4 11.2 + - + +
147I PHE* 3.0 57.1 + - + -
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Residues in contact with ILE 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I TYR* 4.3 4.3 - - + +
50I PHE* 4.5 24.2 - - + -
54I HIS* 4.9 5.4 - - + -
96I MET* 3.4 37.5 - - - +
99I ALA* 4.1 15.7 - - + +
100I LEU* 3.9 17.7 - - + +
103I GLU* 3.9 29.2 - - + +
140I ASP 3.1 17.8 + - - +
141I ILE 4.0 3.1 - - - +
143I ARG* 1.3 75.0 - - + +
145I GLY* 1.3 60.7 + - - +
147I PHE* 3.2 7.9 + - - +
148I ILE* 2.9 30.0 + - + +
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Residues in contact with GLY 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.2 30.6 + - - -
4D VAL* 4.0 9.6 - - - -
40H ASP* 4.4 3.4 - - - -
100I LEU* 4.5 2.6 - - - +
141I ILE 2.9 18.0 + - - -
142I LYS 3.9 1.6 - - - -
144I ILE* 1.3 76.4 - - - +
146I ASP* 1.3 62.0 + - - +
148I ILE* 3.1 6.8 + - - +
149I THR* 3.0 20.1 + - - -
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Residues in contact with ASP 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ARG 4.1 0.2 - - - +
40H ASP* 3.3 18.6 - - - +
43H ALA* 3.8 15.9 - - + +
45H HIS* 3.1 23.9 + - + +
142I LYS* 2.8 55.1 + - - +
143I ARG* 3.4 12.7 - - + +
144I ILE 3.3 0.2 - - - -
145I GLY* 1.3 76.8 - - - +
147I PHE* 1.3 64.4 + - + +
149I THR* 3.4 2.1 + - - -
150I ASN* 3.0 30.7 + - - +
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Residues in contact with PHE 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I PHE* 3.7 32.1 - + - -
96I MET* 3.9 27.8 - - + -
143I ARG* 3.0 39.3 + - + -
144I ILE* 3.2 11.4 + - - +
146I ASP* 1.3 81.2 - - + +
148I ILE* 1.3 51.7 + - - +
150I ASN* 3.2 3.3 + - + +
151I LEU* 2.7 43.8 + - + +
166I PHE* 3.6 24.7 - + + -
170I SER* 3.5 33.2 - - - -
171I VAL* 4.3 8.7 - - + -
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Residues in contact with ILE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.6 16.6 - - - +
93I LEU* 3.9 15.3 - - + -
96I MET* 3.7 35.4 - - + +
97I GLN* 4.0 17.3 - - + +
100I LEU* 3.7 33.2 - - + -
144I ILE 2.9 19.6 + - - +
145I GLY* 3.1 6.0 + - - +
147I PHE* 1.3 73.5 - - - +
149I THR* 1.3 57.8 + - - +
151I LEU* 3.6 7.7 - - - +
152I LYS* 2.9 48.1 + - + +
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Residues in contact with THR 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.5 13.7 + - - -
40H ASP 2.9 28.4 + - - +
41H ASP* 3.5 26.4 - - - +
43H ALA* 4.0 4.7 - - + -
145I GLY 3.0 4.7 + - - -
146I ASP 3.6 5.4 - - - -
148I ILE* 1.3 78.0 - - - +
150I ASN* 1.3 58.4 + - - +
152I LYS* 3.4 9.7 + - - +
153I ARG* 3.0 45.8 + - - +
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Residues in contact with ASN 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ALA* 3.2 33.3 + - - +
44H LEU* 4.0 5.4 - - - +
45H HIS* 5.9 0.2 - - - -
164H TYR* 3.2 34.1 - - + -
168H LYS* 4.9 1.0 + - - -
146I ASP* 3.0 25.9 + - - +
147I PHE* 3.7 6.5 - - + +
149I THR* 1.3 75.3 - - - +
151I LEU* 1.3 66.9 + - - +
153I ARG* 3.3 22.8 + - - +
154I LEU* 3.1 30.3 + - - +
166I PHE* 4.6 6.7 - - + -
170I SER* 4.8 2.2 - - - +
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Residues in contact with LEU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I THR* 4.1 9.0 - - + +
93I LEU* 3.9 17.3 - - + +
96I MET* 3.8 28.9 - - + -
147I PHE 2.7 30.6 + - - +
148I ILE* 3.6 7.0 - - - +
150I ASN* 1.3 73.9 - - - +
152I LYS* 1.3 59.4 + - - +
154I LEU* 3.3 9.8 + - + +
155I GLY 3.3 0.2 + - - -
156I LEU* 3.0 62.6 + - + +
163I GLU* 5.3 0.2 - - - -
166I PHE* 3.5 42.0 - - + -
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Residues in contact with LYS 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLN* 4.9 4.6 + - - -
93I LEU* 4.3 17.5 - - + -
97I GLN* 4.1 14.8 + - - -
148I ILE* 2.9 38.3 + - + +
149I THR* 3.6 7.6 - - - +
151I LEU* 1.3 74.6 - - - +
153I ARG* 1.3 59.6 + - - +
155I GLY* 2.9 19.2 + - - +
156I LEU* 4.3 4.5 - - - +
157I PRO* 5.7 1.6 - - + -
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Residues in contact with ARG 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ASP 5.5 0.4 + - - -
42H VAL* 2.5 36.1 + - - +
44H LEU* 3.5 18.4 - - - +
160H GLY* 3.3 51.5 + - - +
161H MET 3.6 0.7 + - - -
163H GLU* 3.4 25.7 + - - +
164H TYR* 4.1 13.2 - - - +
149I THR* 3.0 29.9 + - - +
150I ASN* 3.3 34.8 + - - +
151I LEU 3.3 0.2 - - - -
152I LYS* 1.3 72.1 - - - +
154I LEU* 1.3 59.5 + - + +
155I GLY* 3.0 8.6 + - - -
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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
------------------------------------------------------------
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