Contacts of the helix formed by residues 159 - 169 (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 THR 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D ASP* 1.3 73.9 + - - +
160D LYS* 1.3 62.0 + - - +
162D LEU* 3.6 6.5 + - + +
163D GLU* 3.3 47.5 + - + +
173D ARG* 6.3 1.1 - - - +
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Residues in contact with LYS 160 (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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158D ASP* 3.3 13.6 + - - +
159D THR* 1.3 77.4 - - - +
161D GLY* 1.3 62.9 + - - +
163D GLU* 3.7 9.4 + - - +
164D ASN* 3.2 32.6 + - - +
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Residues in contact with GLY 161 (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* 4.2 15.6 - - - -
157D LEU* 4.5 4.7 - - - -
158D ASP* 3.1 22.6 + - - -
160D LYS* 1.3 75.2 - - - +
162D LEU* 1.3 63.5 - - - +
164D ASN* 3.4 6.2 + - - +
165D LEU* 3.0 31.5 + - - +
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Residues in contact with LEU 162 (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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157D LEU* 3.8 35.2 - - + +
158D ASP 3.1 16.9 + - - +
159D THR* 3.9 7.4 - - + +
160D LYS 3.5 0.2 - - - -
161D GLY* 1.3 75.0 - - - +
163D GLU* 1.3 59.3 + - + +
165D LEU* 3.3 4.4 + - - +
166D MET* 2.9 42.4 + - + +
173D ARG* 3.5 43.7 - - + +
176D ILE* 4.1 20.9 - - + -
177D LYS* 3.9 18.2 - - + +
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Residues in contact with GLU 163 (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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159D THR* 3.3 37.2 + - + +
160D LYS* 4.0 7.3 - - - +
161D GLY 3.3 0.2 - - - -
162D LEU* 1.3 76.1 - - + +
164D ASN* 1.3 61.5 + - - +
166D MET* 3.3 12.1 + - - +
167D LYS* 2.9 29.3 + - - +
173D ARG* 4.9 16.8 + - - +
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Residues in contact with ASN 164 (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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160D LYS* 3.2 22.7 + - - +
161D GLY* 3.4 5.8 + - - +
163D GLU* 1.3 79.3 - - - +
165D LEU* 1.3 59.8 + - + +
167D LYS* 3.5 26.2 - - - +
168D ASN* 2.9 35.6 + - - +
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Residues in contact with LEU 165 (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* 4.0 26.0 - - + +
144D LEU* 4.2 15.5 - - + -
147D TRP* 3.9 38.8 - - + -
157D LEU* 3.9 17.5 - - + -
161D GLY 3.0 20.5 + - - +
162D LEU 3.6 4.3 - - - +
164D ASN* 1.3 75.8 - - + +
166D MET* 1.3 60.3 + - - +
167D LYS 3.0 1.6 - - - -
168D ASN* 3.1 1.9 + - - -
169D THR* 2.8 35.0 + - + +
176D ILE* 3.7 32.5 - - + -
180D VAL* 5.2 1.8 - - + -
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Residues in contact with MET 166 (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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162D LEU* 2.9 30.6 + - + +
163D GLU* 3.6 13.0 - - - +
165D LEU* 1.3 74.5 - - - +
167D LYS* 1.3 57.4 + - - +
169D THR* 4.2 0.2 - - - -
170D SER* 2.8 31.5 + - - -
171D LEU 3.9 9.0 - - - +
172D SER* 4.4 2.0 - - - -
173D ARG* 3.5 61.7 - - + +
176D ILE* 3.5 20.8 - - + +
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Residues in contact with LYS 167 (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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163D GLU 2.9 16.6 + - - +
164D ASN* 3.5 24.8 - - - +
166D MET* 1.3 79.8 - - - +
168D ASN* 1.3 71.4 + - - +
170D SER* 3.8 9.9 + - - -
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Residues in contact with ASN 168 (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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140D ASN* 4.2 1.2 - - - +
143D ILE* 3.4 40.4 - - + +
164D ASN* 2.9 20.6 + - - +
165D LEU 3.1 2.7 + - - +
167D LYS* 1.3 95.7 + - - +
169D THR* 1.3 60.4 + - - +
170D SER* 4.9 0.2 - - - -
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Residues in contact with THR 169 (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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140D ASN* 3.1 41.5 + - - +
143D ILE* 3.7 27.8 - - + -
144D LEU* 4.2 15.0 - - + -
165D LEU* 2.8 24.3 + - - +
168D ASN* 1.3 76.2 - - - +
170D SER* 1.3 72.1 + - - +
171D LEU* 3.1 29.7 + - - +
176D ILE* 3.7 6.2 - - - +
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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