Contacts of the helix formed by residues 134 - 153 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G PRO* 3.7 31.6 - - + -
124G HIS* 3.4 17.4 - - + +
127G ASP* 6.4 0.9 - - + -
107O ASN* 4.8 5.4 - - - +
110O LEU* 3.9 37.9 - - + +
111O LEU* 4.6 14.1 - - + -
114O HIS* 4.2 7.2 - - + -
129O LEU* 2.9 19.8 + - + +
130O GLU* 3.9 30.2 + - + +
133O TYR* 1.3 74.0 - - + +
135O GLU* 1.3 62.7 + - - +
137O GLN* 3.5 6.0 + - - +
138O VAL* 3.3 26.7 + - - +
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Residues in contact with GLU 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G TYR* 5.3 0.9 - - - -
71G LYS* 2.8 32.7 + - - -
124G HIS* 3.0 35.9 + - + +
127G ASP* 5.1 6.3 - - - +
128G PHE* 5.7 3.3 - - - -
130O GLU 4.1 11.0 + - - +
131O SER 5.8 2.9 - - - +
133O TYR 3.5 0.4 - - - +
134O LEU* 1.3 75.0 - - - +
136O GLU* 1.3 67.3 + - - +
138O VAL* 3.3 3.1 + - - +
139O LYS* 3.0 31.3 + - + +
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Residues in contact with GLU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O HIS* 5.1 15.3 - - + +
132O GLU 4.2 12.3 - - - +
133O TYR* 3.3 13.8 + - - +
135O GLU* 1.3 80.8 - - - +
137O GLN* 1.3 57.9 - - + +
139O LYS* 3.5 8.3 - - - +
140O ASP* 3.1 34.6 + - - +
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Residues in contact with GLN 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O HIS* 5.1 1.6 - - - -
103O GLU* 3.0 47.9 + - - +
106O VAL* 3.9 9.7 - - - +
107O ASN* 3.6 23.2 - - - +
110O LEU* 3.7 19.5 - - + -
133O TYR* 3.0 20.3 + - - +
134O LEU 3.7 3.6 - - - +
135O GLU 3.2 0.2 - - - -
136O GLU* 1.3 76.2 - - + +
138O VAL* 1.3 60.4 + - - +
140O ASP* 3.3 2.9 + - - +
141O ILE* 2.9 34.0 + - - +
176O MG 3.4 16.1 - - - -
177O MG 2.7 20.9 - - - -
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Residues in contact with VAL 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LYS* 4.3 22.8 - - + +
72G ARG* 4.3 17.7 - - - +
124G HIS* 3.3 43.5 - - + +
107O ASN* 5.0 11.4 - - - +
134O LEU 3.3 13.4 + - - +
135O GLU* 3.3 15.1 + - - +
137O GLN* 1.3 77.4 - - + +
139O LYS* 1.3 65.2 + - - +
141O ILE* 3.9 7.3 - - + +
142O LYS* 3.0 26.2 + - - +
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Residues in contact with LYS 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LYS* 4.5 12.1 - - - +
135O GLU* 3.0 33.4 + - + +
136O GLU* 3.5 12.1 - - - +
138O VAL* 1.3 79.5 - - - +
140O ASP* 1.3 60.6 + - - +
142O LYS* 3.5 4.6 + - - +
143O ARG* 3.0 34.1 + - - +
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Residues in contact with ASP 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O HIS* 3.7 20.1 - - + -
57O GLU* 4.1 9.9 - - - +
61O HIS* 5.6 0.7 - - - -
103O GLU* 4.4 11.9 - - + +
136O GLU* 3.1 17.5 + - - +
137O GLN* 3.3 4.0 + - - +
139O LYS* 1.3 79.5 - - - +
141O ILE* 1.3 64.6 + - - +
143O ARG* 3.2 29.4 + - - +
144O ILE* 3.1 31.5 + - + +
177O MG 2.5 29.9 - - - -
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Residues in contact with ILE 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 3.4 35.9 - - + +
6G GLN* 3.8 23.1 - - + +
71G LYS 5.9 0.2 - - - +
100O LEU* 3.9 22.4 - - + +
103O GLU* 3.9 26.7 - - + +
104O LYS* 4.2 7.0 - - + -
107O ASN* 3.9 24.5 - - + +
137O GLN* 2.9 23.5 + - - +
138O VAL* 3.9 7.2 - - + +
140O ASP* 1.3 72.6 - - - +
142O LYS* 1.3 61.5 + - - +
144O ILE* 3.4 1.6 + - - +
145O GLY 2.9 24.8 + - - -
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Residues in contact with LYS 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 2.9 29.5 + - - -
40A ASP* 4.0 16.6 - - + +
45A HIS* 4.0 6.3 - - - -
4G VAL* 3.9 8.7 - - + +
67G LYS* 6.0 0.4 - - - +
70G ASN* 3.2 32.5 - - - +
71G LYS* 4.1 22.9 - - + +
138O VAL 3.0 19.0 + - - +
139O LYS* 3.7 5.8 - - - +
141O ILE* 1.3 78.7 - - - +
143O ARG* 1.3 56.1 + - - +
145O GLY* 3.9 0.3 - - - -
146O ASP* 2.8 67.0 + - - +
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Residues in contact with ARG 143 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O PHE* 3.9 12.1 - - - -
54O HIS* 3.2 30.7 + - - -
57O GLU* 5.8 2.2 + - - -
139O LYS* 3.0 23.6 + - - +
140O ASP* 3.2 30.6 + - - +
141O ILE 3.2 0.2 - - - -
142O LYS* 1.3 75.9 - - - +
144O ILE* 1.3 61.0 + - - +
146O ASP* 3.4 11.6 + - + +
147O PHE* 3.0 56.1 + - + -
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Residues in contact with ILE 144 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 4.3 4.3 - - + +
50O PHE* 4.5 23.1 - - + -
54O HIS* 4.9 5.8 - - + -
96O MET* 3.4 37.0 - - - +
99O ALA* 4.1 15.5 - - + +
100O LEU* 3.9 16.8 - - + +
103O GLU* 3.9 29.2 - - + +
140O ASP 3.1 17.5 + - - +
141O ILE* 4.0 3.4 - - - +
143O ARG* 1.3 75.6 - - + +
145O GLY* 1.3 60.0 + - - +
147O PHE* 3.2 8.7 + - - +
148O ILE* 2.9 29.1 + - + +
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Residues in contact with GLY 145 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 4.4 3.6 - - - -
3G GLN* 3.1 29.7 + - - -
4G VAL* 4.0 10.3 - - - -
100O LEU* 4.5 2.8 - - - +
141O ILE 2.9 18.4 + - - -
142O LYS 3.9 1.1 - - - -
144O ILE* 1.3 75.0 - - - +
146O ASP* 1.3 61.6 + - - +
148O ILE* 3.1 6.4 + - - +
149O THR* 3.0 19.9 + - - -
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Residues in contact with ASP 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 4.1 0.3 - - - +
40A ASP* 3.3 17.6 - - - +
43A ALA* 3.8 14.9 - - + +
45A HIS* 3.0 27.9 + - + +
142O LYS* 2.8 51.1 + - - +
143O ARG* 3.4 12.5 - - + +
145O GLY* 1.3 76.0 - - - +
147O PHE* 1.3 64.8 + - + +
149O THR* 3.4 1.7 + - - -
150O ASN* 3.0 31.0 + - - +
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Residues in contact with PHE 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O PHE* 3.7 33.2 - + - -
96O MET* 3.9 28.3 - - + -
143O ARG* 3.0 38.1 + - + -
144O ILE* 3.2 12.1 + - - +
146O ASP* 1.3 81.5 - - + +
148O ILE* 1.3 53.0 + - - +
150O ASN* 3.2 3.4 + - + +
151O LEU* 2.8 43.2 + - + +
166O PHE* 3.6 23.4 - + + -
170O SER* 3.5 32.3 - - - -
171O VAL* 4.3 8.7 - - + -
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Residues in contact with ILE 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G GLN* 3.6 17.0 - - - +
93O LEU* 3.9 15.7 - - + -
96O MET* 3.7 35.0 - - + +
97O GLN* 4.0 17.3 - - + +
100O LEU* 3.7 33.0 - - + -
144O ILE 2.9 20.0 + - - +
145O GLY 3.1 6.0 + - - +
147O PHE* 1.3 74.1 - - - +
149O THR* 1.3 57.8 + - - +
151O LEU* 3.3 7.8 + - - +
152O LYS* 2.9 47.1 + - + +
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Residues in contact with THR 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP 2.8 28.1 + - - +
41A ASP* 3.5 27.3 - - - +
43A ALA* 3.9 5.8 - - + -
3G GLN* 3.5 13.3 + - - -
145O GLY 3.0 5.3 + - - -
146O ASP 3.6 5.4 - - - -
148O ILE* 1.3 76.9 - - - +
150O ASN* 1.3 59.2 + - - +
152O LYS* 3.4 9.5 + - - +
153O ARG* 3.0 45.4 + - - +
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Residues in contact with ASN 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 3.1 33.9 + - - +
44A LEU* 4.0 5.2 - - - +
45A HIS* 5.8 0.2 - - - -
164A TYR* 3.2 34.4 - - + -
168A LYS* 4.8 1.7 + - - -
146O ASP* 3.0 26.5 + - - +
147O PHE* 3.2 6.9 + - + +
149O THR* 1.3 75.3 - - - +
151O LEU* 1.3 65.4 + - - +
153O ARG* 3.3 21.3 + - - +
154O LEU* 3.1 29.8 + - - +
166O PHE* 4.6 6.7 - - + -
170O SER* 4.8 2.2 - - - +
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Residues in contact with LEU 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O THR* 4.1 9.4 - - + +
93O LEU* 3.9 16.2 - - + +
96O MET* 3.8 29.2 - - + -
147O PHE 2.8 29.9 + - - +
148O ILE* 3.6 7.2 - - - +
150O ASN* 1.3 73.5 - - - +
152O LYS* 1.3 59.6 + - - +
154O LEU* 3.3 10.3 + - + +
155O GLY 3.3 0.2 + - - -
156O LEU* 3.0 63.3 + - + +
163O GLU* 5.3 0.4 - - - -
166O PHE* 3.5 42.0 - - + -
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Residues in contact with LYS 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G GLN* 4.9 4.6 + - - -
93O LEU* 4.3 17.3 - - + -
97O GLN* 4.1 14.4 + - - -
148O ILE* 2.9 39.9 + - + +
149O THR* 3.7 8.1 - - - +
151O LEU* 1.3 75.5 - - - +
153O ARG* 1.3 59.5 + - - +
155O GLY* 2.9 18.4 + - - +
156O LEU* 4.3 4.9 - - - +
157O PRO* 5.7 1.6 - - + -
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Residues in contact with ARG 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP 5.5 0.6 + - - -
42A VAL* 2.5 36.5 + - - +
44A LEU* 3.4 25.9 - - - +
160A GLY* 3.3 51.2 - - - +
161A MET 3.6 1.2 + - - -
163A GLU* 3.5 20.5 + - - +
164A TYR* 4.1 14.1 - - - +
149O THR* 3.0 29.7 + - - +
150O ASN* 3.3 34.2 + - - +
151O LEU 3.3 0.2 - - - -
152O LYS* 1.3 71.7 - - - +
154O LEU* 1.3 59.1 + - + +
155O 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
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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