Contacts of the helix formed by residues 160 - 171 (chain B) in PDB entry 2F4W
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 PHE 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B CYS* 3.7 40.2 - - + -
35B GLU* 3.9 20.9 - - + -
45B HIS* 3.6 43.7 - - + -
46B TYR* 3.7 4.7 - - - -
47B VAL* 3.5 23.1 - - + -
62B HIS* 4.0 10.8 - + - -
156B PHE* 2.9 29.0 + + + +
157B CYS 3.9 3.6 - - - -
159B LEU* 1.3 90.5 - - + +
161B PRO* 1.3 63.7 - - - +
162B GLU 3.3 2.7 - - - -
163B VAL* 2.9 27.5 + - + -
164B VAL* 3.0 13.5 + - - +
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Residues in contact with PRO 161 (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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157B CYS 3.6 12.1 - - - +
158B GLU 3.9 9.6 - - - +
159B LEU 3.3 9.9 - - - +
160B PHE* 1.3 90.0 - - - +
162B GLU* 1.3 68.6 + - + +
164B VAL* 3.3 7.8 + - + +
165B GLU* 3.2 21.5 + - - +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE 3.3 0.8 - - - -
161B PRO* 1.3 83.6 - - + +
163B VAL* 1.3 62.8 + - + +
165B GLU* 3.6 15.8 + - - +
166B GLU* 3.0 27.7 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B CYS* 4.5 22.9 - - + -
47B VAL* 4.2 10.1 - - + -
60B TYR* 3.8 29.8 - - + -
156B PHE* 3.7 20.0 - - + -
160B PHE* 2.9 27.0 + - + +
162B GLU* 1.3 80.1 - - + +
164B VAL* 1.3 61.6 + - - +
166B GLU* 3.2 12.4 + - - +
167B ILE* 2.8 29.7 + - + +
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Residues in contact with VAL 164 (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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151B LEU* 3.8 19.5 - - + -
156B PHE* 3.7 15.7 - - + -
157B CYS* 3.6 39.7 - - + +
160B PHE 3.0 16.4 + - - +
161B PRO* 3.5 8.7 - - + +
163B VAL* 1.3 75.6 - - - +
165B GLU* 1.3 53.1 + - - +
167B ILE* 3.1 6.5 + - - +
168B LYS* 2.7 54.5 + - + +
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Residues in contact with GLU 165 (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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161B PRO 3.2 9.5 + - - +
162B GLU* 3.6 18.6 - - - +
164B VAL* 1.3 77.3 - - - +
166B GLU* 1.3 68.5 + - - +
168B LYS* 3.8 8.6 - - + +
169B GLN* 3.0 38.3 + - - +
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Residues in contact with GLU 166 (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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49B ARG* 3.4 21.3 + - - -
60B TYR* 2.8 33.2 + - + +
162B GLU* 3.0 15.1 + - - +
163B VAL* 3.3 22.1 - - - +
165B GLU* 1.3 78.7 + - - +
167B ILE* 1.3 61.1 + - - +
169B GLN* 3.6 24.9 + - - +
170B LYS* 3.4 18.4 + - - +
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Residues in contact with ILE 167 (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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60B TYR* 3.8 40.8 - - + -
147B LEU* 4.0 23.3 - - + +
150B ASN* 4.5 9.4 - - + +
151B LEU* 3.8 31.2 - - + -
156B PHE* 3.7 34.3 - - + -
163B VAL* 2.8 16.7 + - + +
164B VAL 3.3 6.7 - - - +
166B GLU* 1.3 71.4 - - - +
168B LYS* 1.3 64.9 + - - +
170B LYS* 3.0 22.2 + - - +
171B GLN* 3.3 10.3 + - - +
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Residues in contact with LYS 168 (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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151B LEU* 3.9 28.9 - - + +
164B VAL* 2.7 42.5 + - + +
165B GLU* 3.8 8.3 - - + +
167B ILE* 1.3 71.6 - - - +
169B GLN* 1.3 64.1 + - - +
170B LYS 3.0 1.3 + - - -
171B GLN* 3.1 28.7 + - - +
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Residues in contact with GLN 169 (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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165B GLU* 3.0 27.2 + - - +
166B GLU* 3.6 31.1 + - - +
168B LYS* 1.3 75.6 - - - +
170B LYS* 1.3 61.8 + - - +
171B GLN 3.7 4.5 + - - +
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Residues in contact with LYS 170 (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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58B GLY* 3.3 42.2 - - - -
60B TYR* 3.8 25.5 + - + +
147B LEU* 3.8 19.2 - - + +
166B GLU 3.4 10.0 + - - +
167B ILE 3.0 12.7 + - - +
169B GLN* 1.3 83.7 - - + +
171B GLN* 1.3 59.0 + - - +
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Residues in contact with GLN 171 (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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147B LEU* 3.9 33.7 - - + +
148B ALA* 4.2 11.9 - - - +
151B LEU* 3.6 28.2 - - - +
167B ILE* 3.7 11.2 - - - +
168B LYS* 3.1 24.9 + - - +
169B GLN 4.2 3.8 - - - +
170B LYS* 1.3 82.2 - - - +
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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