Contacts of the helix formed by residues 153 - 158 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B TRP* 3.8 28.9 - - + -
145B TRP* 3.2 46.0 - - + +
151B ARG 3.9 1.1 - - - +
152B ALA* 1.3 88.7 - - + +
154B GLU* 1.3 65.8 + - - +
155B LYS* 4.3 2.9 - - + +
156B LEU* 2.9 17.9 + - + +
157B ARG* 3.0 10.2 + - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PRO* 1.3 71.2 - - - +
155B LYS* 1.3 64.7 + - - +
157B ARG* 3.1 45.2 + - + +
158B LYS* 3.1 33.9 + - + +
186B GLU* 4.0 22.8 - - + +
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Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 5.3 1.2 - - - +
111B TRP* 3.8 30.3 - - + -
153B PRO* 3.1 2.4 - - + +
154B GLU* 1.3 78.9 - - - +
156B LEU* 1.3 60.0 + - - +
158B LYS* 3.5 21.4 + - - +
159B LEU 4.0 0.7 + - - -
187B HIS* 3.7 37.9 + - + +
188B THR 3.2 17.0 + - - -
189B TRP* 2.9 62.9 + - + +
193B GLU* 3.0 32.6 + - - -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B TRP* 3.5 38.3 - - + +
114B TYR* 3.9 25.4 - - + -
115B ILE* 3.7 30.3 - - + -
118B MET* 3.7 14.3 - - - +
145B TRP* 3.6 32.1 - - + -
149B LEU* 4.8 0.7 - - - -
152B ALA* 4.3 7.0 - - + -
153B PRO* 2.9 19.7 + - + +
155B LYS* 1.3 78.2 - - - +
157B ARG* 1.3 63.6 + - - +
159B LEU* 3.2 27.2 - - + +
189B TRP* 4.2 2.0 - - + -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 3.4 38.5 + - + +
150B HIS* 3.7 23.0 + - - +
152B ALA 3.1 24.1 + - - -
153B PRO* 3.0 7.5 + - - +
154B GLU* 3.1 50.6 + - + +
156B LEU* 1.3 72.5 - - - +
158B LYS* 1.3 59.6 + - - +
159B LEU 3.0 5.2 - - - -
160B SER* 3.1 23.0 + - - -
161B GLU 5.0 0.2 + - - -
317B GLU* 3.9 15.1 - - - +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLU* 3.1 30.0 + - + +
155B LYS* 3.6 28.3 - - - +
156B LEU 3.3 0.6 - - - -
157B ARG* 1.3 74.9 - - + +
159B LEU* 1.3 60.5 + - - +
160B SER 3.2 0.9 + - - -
161B GLU* 4.1 10.9 + - - +
162B ILE* 4.7 1.9 + - - +
180B ALA 4.1 16.9 + - - +
181B LEU* 3.9 30.5 + - + +
183B LYS 4.6 8.1 + - - -
185B GLY 6.1 0.2 - - - -
186B GLU* 5.8 3.2 - - - +
187B HIS 2.8 26.0 + - - +
188B THR* 4.1 8.1 - - - +
189B TRP* 4.5 4.8 - - - -
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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