Contacts of the helix formed by residues 134 - 153 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K ASN* 4.8 6.2 - - - +
110K LEU* 3.9 37.0 - - + +
111K LEU* 4.6 13.7 - - + -
114K HIS* 4.2 8.1 - - + -
129K LEU* 2.9 20.4 + - + +
130K GLU* 3.9 30.4 + - + +
133K TYR* 1.3 75.9 - - + +
135K GLU* 1.3 61.7 + - - +
137K GLN* 3.5 5.4 + - - +
138K VAL* 3.3 27.2 + - - +
123U PRO* 3.8 31.0 - - + -
124U HIS* 3.5 17.4 - - + +
127U ASP* 6.4 0.7 - - + -
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Residues in contact with GLU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K GLU 4.1 11.0 + - - +
131K SER 5.8 2.2 - - - +
133K TYR 3.5 0.6 - - - +
134K LEU* 1.3 75.0 - - - +
136K GLU* 1.3 66.4 + - - +
138K VAL* 3.3 3.2 + - - +
139K LYS* 3.0 31.2 + - + +
68U TYR* 5.4 0.7 - - - -
71U LYS* 2.8 32.8 + - - -
124U HIS* 3.0 34.6 + - + +
127U ASP* 5.1 6.1 - - - +
128U PHE* 5.8 2.9 - - - -
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Residues in contact with GLU 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K HIS* 5.1 15.3 - - + +
132K GLU 4.2 12.7 - - - +
133K TYR* 3.3 13.8 + - - +
135K GLU* 1.3 80.0 - - - +
137K GLN* 1.3 57.8 + - + +
139K LYS* 3.5 7.7 - - - +
140K ASP* 3.1 34.7 + - - +
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Residues in contact with GLN 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K HIS* 5.1 1.0 - - - -
103K GLU* 3.0 48.0 + - - +
106K VAL* 3.9 9.7 - - - +
107K ASN* 3.6 23.0 - - - +
110K LEU* 3.7 20.4 - - + -
133K TYR* 3.0 19.2 + - + +
134K LEU 3.7 3.6 - - - +
135K GLU 3.2 0.4 - - - -
136K GLU* 1.3 74.5 - - + +
138K VAL* 1.3 61.4 + - - +
140K ASP* 3.3 3.1 + - - +
141K ILE* 2.9 34.0 + - - +
176K MG 3.4 16.1 - - - -
177K MG 2.7 21.4 - - - -
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Residues in contact with VAL 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K ASN* 5.0 11.7 - - - +
134K LEU 3.3 13.2 + - - +
135K GLU* 3.3 15.6 + - - +
137K GLN* 1.3 77.8 - - + +
139K LYS* 1.3 65.5 + - - +
141K ILE* 3.9 8.4 - - + +
142K LYS* 3.0 26.2 + - - +
71U LYS* 4.3 26.5 - - + +
72U ARG* 4.4 13.0 - - - +
124U HIS* 3.4 41.7 - - + +
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Residues in contact with LYS 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135K GLU* 3.0 33.4 + - + +
136K GLU* 3.5 12.3 - - - +
138K VAL* 1.3 79.3 - - - +
140K ASP* 1.3 61.6 + - - +
142K LYS* 3.5 5.5 + - - +
143K ARG* 3.0 33.7 + - - +
71U LYS* 4.6 11.9 - - - +
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Residues in contact with ASP 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K HIS* 3.7 20.2 - - + -
57K GLU* 4.1 9.6 - - - +
61K HIS* 5.6 0.5 - - - -
103K GLU* 4.4 12.3 - - - +
136K GLU* 3.1 17.7 + - - +
137K GLN 3.3 4.0 + - - +
139K LYS* 1.3 79.9 - - - +
141K ILE* 1.3 65.1 + - - +
143K ARG* 3.2 30.3 + - - +
144K ILE* 3.1 30.4 + - - +
177K MG 2.5 29.6 - - - -
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Residues in contact with ILE 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K LEU* 3.9 21.5 - - + +
103K GLU* 3.9 26.9 - - + +
104K LYS* 4.2 8.3 - - + -
107K ASN* 3.9 24.9 - - + +
137K GLN* 2.9 24.4 + - - +
138K VAL* 3.9 7.0 - - - +
140K ASP* 1.3 72.6 - - - +
142K LYS* 1.3 62.0 + - - +
144K ILE* 3.4 1.4 + - - -
145K GLY 2.9 24.9 + - - -
4U VAL* 3.5 36.1 - - + +
6U GLN* 3.9 21.8 - - + +
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Residues in contact with LYS 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K VAL 3.0 18.8 + - - +
139K LYS* 3.7 5.2 - - - +
141K ILE* 1.3 78.2 - - - +
143K ARG* 1.3 57.4 + - - +
145K GLY* 3.5 0.5 + - - -
146K ASP* 2.8 66.0 + - - +
38Q ASP* 2.9 29.4 + - - -
40Q ASP* 3.8 19.7 - - + +
45Q HIS* 4.0 6.3 - - - -
4U VAL* 4.0 8.7 - - + +
67U LYS* 6.0 0.2 - - - +
70U ASN* 3.3 31.2 - - - +
71U LYS* 4.2 22.4 - - + +
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Residues in contact with ARG 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K PHE* 3.9 12.1 - - - -
54K HIS* 3.1 30.5 + - - -
57K GLU* 5.8 1.6 + - - -
139K LYS* 3.0 23.0 + - - +
140K ASP* 3.2 30.7 + - - +
141K ILE 3.2 0.4 - - - -
142K LYS* 1.3 76.5 - - - +
144K ILE* 1.3 60.9 + - - +
146K ASP* 3.4 10.9 + - + +
147K PHE* 3.0 56.7 + - + -
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Residues in contact with ILE 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 4.3 4.0 - - - +
50K PHE* 4.5 24.2 - - + -
54K HIS* 4.9 5.8 - - + -
96K MET* 3.4 37.7 - - - +
99K ALA* 4.1 15.3 - - + +
100K LEU* 3.9 17.7 - - + +
103K GLU* 3.9 28.7 - - + +
140K ASP 3.1 17.5 + - - +
141K ILE* 4.0 2.7 - - - +
143K ARG* 1.3 75.5 - - + +
145K GLY* 1.3 61.1 + - - +
147K PHE* 3.2 8.4 + - - +
148K ILE* 2.9 29.1 + - + +
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Residues in contact with GLY 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K LEU* 4.5 3.1 - - - +
141K ILE 2.9 17.4 + - - -
142K LYS 3.9 1.3 - - - -
144K ILE* 1.3 75.4 - - - +
146K ASP* 1.3 62.1 + - - +
148K ILE* 3.1 6.8 + - - +
149K THR* 3.0 19.9 + - - -
40Q ASP* 4.3 2.7 - - - -
3U GLN* 3.2 30.5 + - - -
4U VAL* 4.0 9.2 - - - -
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Residues in contact with ASP 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K LYS* 2.8 53.2 + - - +
143K ARG* 3.4 12.8 - - + +
145K GLY* 1.3 75.1 - - - +
147K PHE* 1.3 66.3 + - + +
149K THR* 3.4 1.7 + - - -
150K ASN* 3.0 30.6 + - - +
39Q ARG 4.1 0.2 - - - +
40Q ASP* 3.3 18.0 - - - +
43Q ALA* 3.7 16.4 - - + +
45Q HIS* 3.1 24.8 + - + +
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Residues in contact with PHE 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K PHE* 3.7 33.4 - + - -
96K MET* 3.9 28.0 - - + -
143K ARG* 3.0 40.6 + - + -
144K ILE* 3.2 11.4 + - - +
146K ASP* 1.3 81.3 - - + +
148K ILE* 1.3 52.6 + - - +
150K ASN* 3.2 4.1 + - + +
151K LEU* 2.7 42.9 + - + +
166K PHE* 3.6 23.6 - + + -
170K SER* 3.5 32.5 - - - -
171K VAL* 4.3 9.6 - - + -
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Residues in contact with ILE 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K LEU* 3.9 14.8 - - + -
96K MET* 3.7 34.5 - - + +
97K GLN* 4.0 18.2 - - + +
100K LEU* 3.7 32.5 - - + -
144K ILE 2.9 20.0 + - - +
145K GLY 3.5 6.1 - - - +
147K PHE* 1.3 74.8 - - - +
149K THR* 1.3 58.2 + - - +
151K LEU* 3.3 8.9 + - - +
152K LYS* 2.9 48.4 + - + +
3U GLN* 3.6 16.2 - - - +
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Residues in contact with THR 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K GLY 3.0 4.0 + - - -
146K ASP 3.6 5.6 - - - -
148K ILE* 1.3 76.9 - - - +
150K ASN* 1.3 59.2 + - - +
152K LYS* 3.4 10.0 + - - +
153K ARG* 3.0 45.3 + - - +
40Q ASP 2.9 27.2 + - - +
41Q ASP* 3.5 28.3 - - - +
42Q VAL 4.0 2.2 - - - +
43Q ALA* 4.0 3.8 - - + -
3U GLN* 3.5 11.6 + - - -
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Residues in contact with ASN 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ASP* 3.0 26.1 + - - +
147K PHE* 3.7 6.7 - - + +
149K THR* 1.3 75.3 - - - +
151K LEU* 1.3 66.2 + - - +
153K ARG* 3.3 22.7 + - - +
154K LEU* 3.1 30.0 + - - +
166K PHE* 4.6 6.7 - - + -
170K SER* 4.8 2.5 - - - +
43Q ALA* 3.2 33.1 + - - +
44Q LEU* 4.0 5.4 - - - +
164Q TYR* 3.1 35.1 - - + -
168Q LYS* 4.9 1.2 + - - -
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Residues in contact with LEU 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K THR* 4.1 8.1 - - + +
93K LEU* 3.9 17.0 - - + +
96K MET* 3.8 29.6 - - + -
147K PHE 2.7 30.9 + - - +
148K ILE* 3.5 7.0 - - - +
150K ASN* 1.3 72.8 - - - +
152K LYS* 1.3 59.3 + - - +
154K LEU* 3.3 9.7 + - + +
155K GLY 3.3 0.2 + - - -
156K LEU* 3.0 64.6 + - + +
166K PHE* 3.5 42.6 - - + -
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Residues in contact with LYS 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K LEU* 4.3 18.4 - - + -
97K GLN* 4.1 15.3 + - - -
148K ILE* 2.9 38.7 + - + +
149K THR* 3.7 7.6 - - - +
151K LEU* 1.3 75.6 - - - +
153K ARG* 1.3 60.8 + - - +
155K GLY* 2.9 18.9 + - - +
156K LEU* 4.3 4.5 - - - +
157K PRO* 5.7 1.3 - - + -
3U GLN* 5.0 4.4 + - - -
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Residues in contact with ARG 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K THR* 3.0 31.6 + - - +
150K ASN* 3.3 34.8 + - - +
151K LEU 3.3 0.4 - - - -
152K LYS* 1.3 70.6 - - - +
154K LEU* 1.3 60.1 + - + +
155K GLY* 3.0 9.4 + - - -
41Q ASP 5.5 0.8 + - - -
42Q VAL* 2.6 33.1 + - - +
44Q LEU* 3.5 18.8 - - - +
160Q GLY* 3.2 52.2 - - - +
161Q MET 3.6 0.9 + - - -
163Q GLU* 3.4 25.4 + - - +
164Q TYR* 4.1 13.0 - - - +
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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
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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