Contacts of the helix formed by residues 153 - 159 (chain D) in PDB entry 6N0M
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 PRO 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D TRP* 4.1 25.1 - - + -
145D TRP* 3.4 40.6 - - + +
151D ARG 4.0 0.6 - - - +
152D ALA* 1.3 92.4 - - + +
154D GLU* 1.3 65.6 + - - +
155D LYS* 4.3 4.5 - - + +
156D LEU* 3.1 9.8 + - + +
157D ARG* 3.1 15.9 + - - +
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Residues in contact with GLU 154 (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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153D PRO* 1.3 72.4 - - - +
155D LYS* 1.3 53.8 + - - +
157D ARG* 2.9 36.3 + - + +
158D LYS* 2.8 61.1 + - + +
184D THR* 4.7 3.6 - - - +
185D GLY* 3.4 27.2 + - - -
186D GLU* 3.9 7.9 + - + +
187D HIS* 6.0 2.9 - - + +
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Residues in contact with LYS 155 (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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107D LEU* 5.3 2.8 - - - +
111D TRP* 3.6 33.1 - - + -
153D PRO* 4.8 2.0 - - + -
154D GLU* 1.3 78.6 - - - +
156D LEU* 1.3 59.7 + - - +
158D LYS* 3.7 11.9 + - - +
159D LEU 4.0 1.2 + - - -
187D HIS* 3.8 38.0 + - + +
188D THR 3.3 19.6 + - - +
189D TRP* 2.8 56.6 + - + +
193D GLU* 2.7 31.4 + - - -
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Residues in contact with LEU 156 (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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111D TRP* 3.3 49.4 - - + +
114D TYR* 4.0 23.8 - - + -
115D ILE* 3.9 27.8 - - + -
118D MET* 3.4 24.6 - - - +
145D TRP* 3.8 24.5 - - + -
152D ALA* 4.3 8.5 - - + -
153D PRO* 3.1 18.1 + - + +
155D LYS* 1.3 77.2 - - - +
157D ARG* 1.3 64.7 + - - +
159D LEU* 3.3 13.7 + - + +
189D TRP* 4.1 8.7 - - + -
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Residues in contact with ARG 157 (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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149D LEU* 3.8 32.3 - - + +
150D HIS* 3.0 34.3 + - - +
152D ALA 3.2 21.1 + - - +
153D PRO* 3.1 5.0 + - - +
154D GLU* 2.9 46.6 + - + +
156D LEU* 1.3 72.5 - - - +
158D LYS* 1.3 56.3 + - - +
160D SER* 2.9 34.8 + - - -
161D GLU 4.8 0.2 + - - -
317D GLU* 4.2 12.9 - - - +
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Residues in contact with LYS 158 (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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154D GLU* 2.8 37.0 + - + +
155D LYS* 3.7 16.2 - - - +
157D ARG* 1.3 77.6 - - - +
159D LEU* 1.3 60.2 + - - +
160D SER 3.1 1.3 + - - -
161D GLU* 3.6 12.6 + - - +
162D ILE 4.7 0.7 + - - -
180D ALA* 3.9 17.5 - - + +
181D LEU* 3.5 37.7 + - + +
183D LYS 3.3 10.3 + - - -
184D THR* 3.0 36.5 + - + -
187D HIS 3.3 20.2 + - - -
188D THR* 4.2 1.0 - - - +
189D TRP* 4.3 3.9 - - - +
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Residues in contact with LEU 159 (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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115D ILE* 3.8 26.5 - - + -
118D MET* 4.2 8.7 - - + -
155D LYS 4.0 0.2 + - - -
156D LEU* 3.3 16.8 + - + +
157D ARG 3.1 0.6 - - - -
158D LYS* 1.3 76.5 - - - +
160D SER* 1.3 57.5 + - - +
161D GLU 3.2 0.8 + - - -
162D ILE* 3.5 8.7 - - + +
163D ASN* 2.8 30.6 + - + +
181D LEU* 3.9 20.9 - - + -
189D TRP* 3.4 50.5 - - + +
194D LEU* 4.3 9.4 - - + -
197D ALA* 4.1 7.6 - - + -
201D LEU* 4.1 19.7 - - + -
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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