Contacts of the helix formed by residues 138 - 152 (chain D) in PDB entry 1MNM
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 LYS 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D PRO* 4.8 6.3 - - + +
136D PHE 3.7 2.1 + - - -
137D THR* 1.3 75.9 - - + +
139D GLU* 1.3 61.3 + - - +
141D VAL* 3.2 24.9 - - - +
142D ARG* 3.2 11.4 + - - +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D THR* 3.0 14.8 - - + +
138D LYS* 1.3 80.9 - - - +
140D ASN* 1.3 60.8 + - - +
142D ARG* 3.6 13.8 + - - +
143D ILE* 3.2 30.3 + - + +
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Residues in contact with ASN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D PHE* 4.2 8.6 - - + +
137D THR* 2.9 34.2 + - - +
139D GLU* 1.3 76.0 - - - +
141D VAL* 1.3 60.3 + - - +
142D ARG 3.1 2.0 - - - -
143D ILE* 3.2 5.6 + - - +
144D LEU* 3.0 33.0 + - - +
168D ASN 4.2 2.9 - - - +
169D THR* 3.1 47.7 + - - +
171D LEU* 3.7 21.3 - - + +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D PHE* 5.0 8.2 - - + +
137D THR 3.0 13.0 + - - +
138D LYS* 3.2 22.0 - - + +
140D ASN* 1.3 77.1 - - - +
142D ARG* 1.3 61.1 + - - +
144D LEU* 4.4 7.2 - - - -
145D GLU* 3.0 43.5 + - + +
179D TRP* 4.4 19.1 - - + +
50F A 5.2 6.7 - - - +
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Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LYS 3.2 13.9 + - - +
139D GLU* 3.6 11.2 + - - +
140D ASN 3.1 0.2 - - - -
141D VAL* 1.3 84.7 - - + +
143D ILE* 1.3 83.1 + - - +
145D GLU* 3.9 4.2 - - - +
146D SER* 3.1 36.3 + - - -
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D GLU* 3.2 21.5 - - + +
140D ASN* 3.2 8.2 + - - +
142D ARG* 1.3 98.9 - - - +
144D LEU* 1.3 62.6 + - - +
146D SER* 3.4 8.3 + - - -
147D TRP* 3.3 19.6 + - - +
165D LEU* 4.0 13.5 - - + +
168D ASN* 3.4 50.7 - - + +
169D THR* 3.7 17.9 - - + -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D PHE* 4.5 4.0 - - + -
140D ASN 3.0 23.2 + - - +
141D VAL* 4.1 3.6 - - - +
143D ILE* 1.3 75.6 - - - +
145D GLU* 1.3 63.7 + - - +
147D TRP* 3.4 5.2 + - - +
148D PHE 3.2 15.9 + - - -
165D LEU* 4.2 18.2 - - + -
169D THR* 4.2 11.0 - - + -
171D LEU* 3.9 24.0 - - + -
176D ILE* 4.0 30.5 - - + -
179D TRP* 3.4 62.3 - - + +
180D VAL* 5.4 0.4 - - + -
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Residues in contact with GLU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D VAL* 3.0 31.4 + - + +
142D ARG* 3.9 5.2 - - - +
144D LEU* 1.3 73.4 - - - +
146D SER* 1.3 61.3 + - - +
148D PHE* 3.3 6.0 + - - +
149D ALA* 2.9 31.7 + - - +
179D TRP* 3.6 12.2 - - + -
183D ARG* 2.8 45.8 + - - -
186D LYS* 5.0 4.5 + - - -
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Residues in contact with SER 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ARG* 3.1 26.4 + - - -
143D ILE* 3.5 9.2 - - - -
145D GLU* 1.3 73.8 - - - +
147D TRP* 1.3 65.3 + - - +
149D ALA* 3.4 6.0 + - - +
150D LYS* 3.1 23.9 + - - +
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Residues in contact with TRP 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE 3.3 3.6 + - - -
144D LEU 3.7 8.1 - - - +
145D GLU 3.3 0.2 - - - -
146D SER* 1.3 77.1 + - - +
148D PHE* 1.3 91.2 + + + +
150D LYS* 3.2 4.9 + - - -
151D ASN* 3.0 61.9 + - + +
155D PRO 4.0 6.1 - - - -
156D TYR 3.5 40.2 - - - -
157D LEU* 3.8 20.4 - - + -
158D ASP* 5.0 5.8 + - - -
161D GLY* 4.2 18.5 - - - -
165D LEU* 3.9 37.7 - - + -
179D TRP* 5.5 0.9 - + - -
180D VAL* 4.1 27.6 - - + -
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Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU 3.2 10.3 + - - +
145D GLU* 3.5 11.7 - - - +
146D SER 3.3 0.2 - - - -
147D TRP* 1.3 95.7 - + + +
149D ALA* 1.3 52.8 + - - +
151D ASN 3.1 1.7 + - - -
152D ILE* 2.7 63.0 + - + -
155D PRO* 3.5 32.3 - - + -
179D TRP* 4.3 10.5 - + + -
180D VAL* 4.8 3.8 - - + -
183D ARG* 3.5 56.3 - - + -
184D ARG* 4.2 11.7 - - + -
187D GLU* 3.5 21.8 - - + -
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLU* 2.9 17.2 + - - +
146D SER* 3.8 6.7 - - - +
148D PHE* 1.3 78.2 - - - +
150D LYS* 1.3 63.0 + - - +
151D ASN 3.2 0.7 + - - -
152D ILE* 3.3 27.7 - - - +
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D SER 3.1 15.3 + - - +
147D TRP* 3.7 5.6 - - - +
149D ALA* 1.3 77.5 - - - +
151D ASN* 1.3 67.0 + - - +
152D ILE* 5.2 0.7 - - - -
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Residues in contact with ASN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D TRP* 3.0 66.2 + - + +
148D PHE 3.1 4.0 - - - +
150D LYS* 1.3 88.6 + - - +
152D ILE* 1.3 63.1 + - - +
153D GLU* 3.1 3.4 - - - -
154D ASN* 2.9 19.0 + - - +
155D PRO* 2.9 22.2 - - - +
156D TYR 5.1 0.9 - - - +
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE* 2.7 42.5 + - + +
149D ALA* 3.3 21.1 - - - +
150D LYS 3.6 1.1 - - - -
151D ASN* 1.3 74.2 - - - +
153D GLU* 1.3 82.3 + - + +
154D ASN 3.5 0.2 + - - -
155D PRO* 3.6 13.7 - - - +
187D GLU* 3.9 21.8 - - + +
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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