Contacts of the helix formed by residues 145 - 163 (chain A) in PDB entry 1MRJ
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 ASN 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA 5.6 2.1 - - - +
118A ALA* 5.9 2.4 - - - -
143A ASN* 2.9 17.9 + - - +
144A ALA* 1.3 84.9 + - - +
146A SER* 1.3 57.1 + - - +
148A ALA* 5.3 1.1 - - - -
149A SER* 5.3 1.9 + - - -
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A THR* 3.3 22.6 - - - +
143A ASN* 2.8 35.8 + - - +
145A ASN* 1.3 77.4 - - - +
147A ALA* 1.3 65.9 + - - +
148A ALA 3.3 3.0 + - - -
149A SER* 3.4 11.4 + - - -
150A ALA* 3.2 19.4 + - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 3.6 13.7 - - - +
138A THR* 4.5 2.5 - - - +
139A LEU* 4.2 15.3 - - + -
142A TYR* 3.6 34.1 - - + -
143A ASN 3.1 9.6 + - - +
144A ALA 3.4 5.3 + - - +
146A SER* 1.3 76.7 - - - +
148A ALA* 1.3 57.3 - - - +
150A ALA* 3.2 3.1 + - - +
151A LEU* 2.7 37.7 + - + +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.6 13.5 + - + +
114A LEU* 3.7 33.8 - - + +
117A ALA* 3.7 20.9 - - + -
118A ALA* 3.7 9.0 - - + +
144A ALA 4.5 2.5 + - - +
145A ASN 5.3 1.5 - - - -
146A SER 3.3 1.0 - - - -
147A ALA* 1.3 78.1 - - - +
149A SER* 1.3 63.1 + - - +
151A LEU* 3.3 4.4 + - - +
152A MET* 3.0 28.6 + - - +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA* 3.3 22.0 + - - +
120A LYS* 5.2 6.4 - - - +
125A ILE* 4.5 16.1 - - - +
145A ASN 5.3 1.4 + - - -
146A SER* 3.4 11.2 + - - -
147A ALA 3.4 0.4 - - - -
148A ALA* 1.3 75.9 - - - +
150A ALA* 1.3 63.2 + - - +
152A MET* 3.1 16.3 + - - +
153A VAL* 3.1 26.1 + - - +
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA* 3.5 35.7 - - - +
138A THR* 3.8 20.4 - - + -
139A LEU* 3.9 9.5 - - + +
146A SER 3.2 11.1 + - - +
147A ALA 3.2 7.5 + - - +
149A SER* 1.3 79.8 - - - +
151A LEU* 1.3 57.6 + - - +
153A VAL* 3.3 3.5 + - - -
154A LEU* 3.0 27.2 + - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 5.5 4.3 - - + -
73A GLY* 6.5 0.2 - - - -
74A TYR* 4.4 13.7 - - + -
83A PHE* 3.8 39.5 - - + -
105A LEU* 4.2 10.3 - - + -
107A TYR* 3.7 23.3 - - + +
114A LEU* 4.5 6.1 - - + -
139A LEU* 4.0 25.1 - - + -
147A ALA* 2.7 29.2 + - + +
148A ALA* 3.3 5.6 + - - +
150A ALA* 1.3 72.0 - - - +
152A MET* 1.3 56.3 + - - +
154A LEU* 3.2 15.2 + - + +
155A ILE* 2.8 37.9 + - + +
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Residues in contact with MET 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TYR* 4.2 11.9 - - + -
114A LEU* 3.5 35.0 - - + +
115A GLN* 3.7 26.7 - - + -
118A ALA* 3.5 32.5 - - + -
122A ARG* 4.2 14.1 - - - -
125A ILE* 3.5 23.3 - - + -
148A ALA 3.0 15.6 + - - +
149A SER* 3.1 5.6 + - - +
151A LEU* 1.3 72.5 - - - +
153A VAL* 1.3 65.7 + - - +
155A ILE* 3.5 4.8 + - - +
156A GLN* 3.1 40.2 + - - +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 3.7 15.7 - - + -
126A PRO 3.7 19.1 - - - +
127A LEU* 4.0 14.4 - - + -
131A ALA* 3.7 34.3 - - + +
132A LEU* 4.0 4.0 - - + +
135A ALA* 4.0 8.7 - - + -
149A SER 3.1 15.4 + - - +
150A ALA* 3.7 8.5 - - - +
152A MET* 1.3 75.5 - - - +
154A LEU* 1.3 62.4 + - - +
156A GLN* 3.3 1.9 + - - +
157A SER* 2.7 42.3 + - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.5 33.0 - - + -
60A ILE* 4.6 5.4 - - + -
62A VAL* 4.0 25.1 - - + -
71A ILE* 3.8 18.4 - - + -
74A TYR* 5.4 3.4 - - + -
132A LEU* 4.3 14.1 - - + -
135A ALA* 4.6 2.9 - - + +
136A ILE* 5.6 1.3 - - + -
139A LEU* 3.9 23.6 - - + -
150A ALA 3.0 14.1 + - - +
151A LEU* 3.4 19.5 - - + +
153A VAL* 1.3 78.0 - - - +
155A ILE* 1.3 61.3 + - - +
157A SER* 3.3 0.9 + - - -
158A THR* 2.8 35.5 + - + +
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.7 24.2 - - + -
83A PHE* 4.6 7.4 - - + -
111A TYR* 3.5 24.5 - - + +
114A LEU* 3.7 27.4 - - + -
151A LEU* 2.8 27.0 + - + +
152A MET* 3.9 5.4 - - - +
154A LEU* 1.3 72.6 - - + +
156A GLN* 1.3 59.7 + - - +
159A SER* 2.9 27.3 + - - -
160A GLU* 3.2 9.2 + - + -
300A ADN 3.5 56.5 - - + +
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Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TYR* 3.6 16.2 - - + +
122A ARG* 4.2 23.5 - - - +
125A ILE* 5.3 4.5 - - - +
127A LEU* 3.8 37.4 - - + +
152A MET* 3.1 30.7 + - - +
153A VAL 3.9 2.7 - - - +
155A ILE* 1.3 77.2 - - - +
157A SER* 1.3 57.0 + - - +
160A GLU* 3.5 10.0 - - + +
161A ALA 3.2 23.6 + - - -
167A ILE* 4.1 1.4 - - + +
171A ILE* 3.5 12.6 - - + +
181A PRO* 4.6 6.9 - - - +
185A ILE* 4.7 1.4 - - - +
186A ILE* 4.9 0.6 - - - +
189A GLU* 2.7 36.5 + - - +
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 2.7 34.3 + - - -
17A PHE* 4.5 0.7 - - - -
18A ILE* 3.7 2.6 - - - +
127A LEU* 4.7 3.6 - - - +
128A GLY 5.2 1.6 + - - -
132A LEU* 4.0 30.1 - - - +
153A VAL* 2.7 33.0 + - - +
154A LEU 3.8 3.8 - - - -
156A GLN* 1.3 78.7 - - - +
158A THR* 1.3 61.8 + - - +
161A ALA* 3.7 2.8 - - - +
171A ILE* 3.8 17.8 - - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.2 9.2 - - + -
18A ILE* 4.3 1.9 - - - +
21A LEU* 4.0 20.9 - - - +
50A ILE* 3.7 27.1 - - + -
52A LEU* 4.3 4.7 - - + -
62A VAL* 6.4 0.7 - - + -
64A ILE* 6.1 3.6 - - - -
71A ILE* 3.4 18.7 - - - +
132A LEU* 5.5 1.6 - - + -
154A LEU* 2.8 33.2 + - + +
156A GLN 3.3 0.6 - - - -
157A SER* 1.3 85.7 - - - +
159A SER* 1.3 75.0 + - - +
161A ALA* 3.3 3.3 + - - +
162A ALA* 2.9 22.5 + - - +
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 5.0 2.1 - - - +
69A VAL* 2.7 40.6 + - - +
71A ILE* 3.7 16.3 - - - +
155A ILE 2.9 9.3 + - - -
158A THR* 1.3 79.5 + - - +
160A GLU* 1.3 62.9 + - - +
162A ALA* 3.2 5.2 + - - +
163A ARG* 3.1 35.0 + - - +
300A ADN 3.4 21.7 - - - -
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TYR* 2.7 35.9 + - - +
155A ILE* 3.2 6.0 + - + +
156A GLN* 3.5 22.0 - - - +
159A SER* 1.3 71.9 - - - +
161A ALA* 1.3 65.2 + - - +
163A ARG* 2.9 45.5 + - - +
164A TYR* 3.2 13.7 + - - -
167A ILE* 3.9 20.6 - - + +
189A GLU* 3.7 36.4 - - - +
192A TRP* 5.4 0.7 - - - +
300A ADN 2.9 14.8 - - - -
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.2 26.7 - - - +
18A ILE* 3.8 11.0 - - + -
22A ARG* 2.9 22.9 + - - -
156A GLN 3.2 11.3 + - - +
157A SER 3.7 6.1 - - - +
158A THR 3.3 7.2 + - - +
160A GLU* 1.3 76.8 - - - +
162A ALA* 1.3 59.2 + - - +
164A TYR 3.1 9.2 - - - +
167A ILE* 4.0 3.6 - - + +
168A GLU* 3.7 24.6 - - - +
171A ILE* 4.7 0.4 - - + -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.1 6.4 - - + +
21A LEU* 4.4 17.9 - - + -
22A ARG* 2.9 30.7 + - + +
25A LEU* 5.3 0.9 - - + -
69A VAL* 4.2 11.7 - - + -
158A THR 2.9 13.0 + - - +
159A SER 3.3 11.0 - - - +
161A ALA* 1.3 77.8 - - - +
163A ARG* 1.3 59.2 + - - +
238A ALA* 3.6 5.9 - - - +
239A LEU* 3.6 22.6 - - + +
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN 2.8 23.8 + - - -
69A VAL* 3.6 12.1 + - + +
70A TYR* 4.0 1.2 - - - +
159A SER* 3.1 18.9 + - - +
160A GLU* 2.9 37.5 + - - +
162A ALA* 1.3 77.0 - - - +
164A TYR* 1.3 75.8 + - + +
192A TRP* 3.4 54.5 - - + +
237A ILE* 3.5 5.4 - - - +
238A ALA 2.7 28.1 + - - -
239A LEU* 3.7 15.6 + - + -
300A ADN 3.0 38.3 + - - -
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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