Contacts of the helix formed by residues 159 - 170 (chain D) in PDB entry 3BDW
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 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D ILE* 3.3 22.7 - - - +
158D ASP* 1.3 80.9 + - + +
160D GLU* 1.3 66.5 + - - +
161D GLU* 3.3 32.7 + - + +
162D GLU* 3.8 14.2 + - + +
163D MET* 3.9 7.3 + - - +
196D HIS* 4.2 7.4 - - - -
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Residues in contact with GLU 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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159D ASN* 1.3 76.8 - - - +
161D GLU* 1.3 58.6 + - - +
163D MET* 3.1 50.4 - - + +
164D LYS* 3.2 10.2 + - - +
196D HIS* 4.5 16.6 + - + -
214D ASN* 3.8 10.2 + - - +
215D ARG* 4.3 18.2 + - - -
216D LEU* 6.3 0.2 - - - -
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Residues in contact with GLU 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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64C LYS* 3.5 32.6 + - - +
126D TYR* 4.8 8.0 + - + +
159D ASN* 3.3 19.9 + - + +
160D GLU* 1.3 76.9 - - - +
162D GLU* 1.3 67.6 + - - +
163D MET 3.1 1.1 - - - -
164D LYS* 3.1 9.0 + - + +
165D PHE* 3.0 20.4 + - - +
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Residues in contact with GLU 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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126D TYR* 5.0 11.7 - - + -
131D TYR* 2.8 27.2 + - + +
156D SER 3.4 8.6 - - - +
157D ILE* 4.2 5.8 - - + -
158D ASP* 2.7 40.6 + - + +
159D ASN* 4.0 14.8 - - + +
161D GLU* 1.3 78.5 - - - +
163D MET* 1.3 58.4 + - - +
165D PHE* 3.1 9.7 + - + +
166D LEU* 2.8 39.7 + - + +
230D LYS* 2.7 27.8 + - - +
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Residues in contact with MET 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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157D ILE* 3.3 35.8 - - + +
159D ASN 3.9 6.1 + - - +
160D GLU* 3.1 34.4 + - - +
162D GLU* 1.3 79.0 - - - +
164D LYS* 1.3 57.9 + - - +
166D LEU* 3.2 8.2 + - - +
167D SER* 3.0 28.8 + - - -
196D HIS* 4.5 9.2 - - + -
211D LEU* 3.2 37.4 - - + +
214D ASN* 3.6 16.6 - - - +
215D ARG* 4.9 1.8 - - - -
216D LEU* 3.6 36.8 - - + -
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Residues in contact with LYS 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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77C SER* 4.8 17.7 - - - +
160D GLU 3.2 7.9 + - - +
161D GLU* 3.1 11.7 + - + +
163D MET* 1.3 78.8 - - - +
165D PHE* 1.3 63.3 + - - +
167D SER* 2.6 29.1 + - - +
168D ILE* 3.6 17.4 + - + +
214D ASN* 3.4 24.7 + - - +
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Residues in contact with PHE 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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66C VAL* 3.8 27.8 - - + -
75C ILE* 5.7 3.4 - - + -
124D ILE* 4.8 9.2 - - + -
126D TYR* 3.5 66.2 - + + +
131D TYR* 4.9 5.6 - + - -
161D GLU 3.0 11.7 + - - +
162D GLU* 3.4 11.4 - - + +
164D LYS* 1.3 75.2 - - - +
166D LEU* 1.3 85.9 + - + +
168D ILE* 3.1 30.1 + - + +
169D ILE* 3.6 28.7 + - + +
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Residues in contact with LEU 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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131D TYR* 3.9 23.1 - - + -
133D ILE* 5.9 3.6 - - + -
155D LEU* 3.6 42.0 - - + -
157D ILE* 3.9 17.5 - - + -
162D GLU* 2.8 28.8 + - + +
163D MET 3.2 5.1 + - - +
165D PHE* 1.3 89.3 - - + +
167D SER* 1.3 58.1 + - - +
168D ILE 3.3 0.2 - - - -
169D ILE* 3.4 11.4 + - + +
170D SER* 3.1 31.1 + - - +
211D LEU* 4.1 11.6 - - + +
228D HIS* 4.9 12.1 - - + +
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Residues in contact with SER 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 MET 3.0 12.7 + - - -
164D LYS* 2.6 36.0 + - - +
166D LEU* 1.3 76.9 - - - +
168D ILE* 1.3 60.8 + - - +
170D SER 4.0 12.4 + - - +
171D PRO* 5.1 0.7 - - - +
211D LEU* 5.8 2.0 - - - -
213D VAL* 4.3 15.2 - - - +
214D ASN* 3.5 31.5 - - - +
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Residues in contact with ILE 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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75C ILE* 3.9 27.6 - - + +
76C SER 4.6 5.4 - - - +
77C SER* 3.8 22.4 - - - +
108C MET* 4.3 2.7 - - - +
111C SER* 4.0 21.8 - - - -
113C GLN* 5.1 14.9 - - - +
115C TYR* 3.3 24.5 - - - +
171C ARG* 6.4 0.4 - - - -
164D LYS* 3.7 24.5 - - + +
165D PHE* 3.1 17.0 + - + +
167D SER* 1.3 81.9 - - - +
169D ILE* 1.3 70.4 + - + +
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Residues in contact with ILE 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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75C ILE* 4.7 5.2 - - + -
107C PHE* 3.1 46.6 - - + +
108C MET* 3.7 34.2 - - + -
110C SER* 2.9 12.5 + - - -
124D ILE* 4.8 1.8 - - + -
133D ILE* 3.6 24.6 - - + +
165D PHE* 3.8 38.4 - - + +
166D LEU* 3.4 14.5 + - + +
168D ILE* 1.3 85.5 - - + +
170D SER* 1.3 64.9 + - - +
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Residues in contact with SER 170 (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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110C SER* 3.2 5.9 + - - -
133D ILE* 3.1 26.7 - - - +
166D LEU 3.1 17.4 + - - +
167D SER* 4.0 9.3 - - - -
168D ILE 3.6 1.4 - - - -
169D ILE* 1.3 84.5 + - - +
171D PRO* 1.3 75.0 - - - +
172D SER 3.5 4.1 + - - -
211D LEU* 5.9 2.4 - - - +
226D ILE* 5.8 0.9 - - - -
228D HIS* 3.2 30.3 + - - -
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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