Contacts of the helix formed by residues 167 - 174 (chain F) in PDB entry 3PRJ
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 167 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F PRO* 5.6 1.8 - - - -
164F ALA* 3.1 18.9 + - - +
165F GLU 3.2 1.1 + - - -
166F GLY* 1.3 82.7 - - - +
168F ALA* 1.3 63.6 + - - +
169F ILE 3.3 2.5 - - - -
170F LYS* 3.6 24.1 + - + -
171F ASP* 3.0 39.3 + - - -
339F LYS* 4.6 7.1 + - - +
341F ASP* 5.8 1.6 - - - +
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F TYR 5.4 0.2 - - - +
18F PRO* 4.4 11.7 - - + -
54F GLU* 2.7 34.9 + - + +
163F LEU* 3.7 29.2 - - + -
164F ALA 3.3 4.7 + - - +
167F THR* 1.3 73.9 - - - +
169F ILE* 1.3 57.6 + - - +
171F ASP* 3.4 0.7 + - - +
172F LEU* 2.8 46.1 + - + +
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Residues in contact with ILE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PRO* 4.8 7.4 - - + -
22F VAL* 3.8 22.0 - - + -
54F GLU* 4.7 3.1 - - + -
55F PRO 3.4 25.3 + - - +
56F GLY* 3.9 14.4 - - - +
57F LEU* 3.8 30.5 - - + +
60F VAL* 4.1 22.2 - - + -
167F THR 3.3 0.4 - - - -
168F ALA* 1.3 77.1 - - + +
170F LYS* 1.3 68.7 + - - +
172F LEU* 3.0 13.6 + - - +
173F LYS* 3.0 35.4 + - + +
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Residues in contact with LYS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F THR* 3.6 24.8 + - + +
168F ALA 3.5 0.2 - - - -
169F ILE* 1.3 78.9 - - - +
171F ASP* 1.3 68.2 + - - +
173F LYS* 3.9 6.0 - - - +
174F ASN* 3.1 31.0 + - + +
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Residues in contact with ASP 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E ARG* 5.6 0.9 + - - -
161F GLU* 6.1 0.2 - - - -
162F PHE 4.8 1.6 - - - +
163F LEU* 3.9 16.1 - - - -
164F ALA* 3.0 27.2 + - - +
167F THR* 3.0 38.2 + - - +
168F ALA 3.8 3.8 - - - +
170F LYS* 1.3 86.8 + - - +
172F LEU* 1.3 61.8 + - - +
174F ASN 4.6 4.0 - - - -
175F PRO* 3.1 33.9 - - - +
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PRO* 3.8 12.3 - - + +
19F THR* 3.8 45.5 - - - +
22F VAL* 3.9 20.4 - - + -
161F GLU* 3.5 24.2 - - - +
163F LEU* 3.9 16.4 - - + -
168F ALA 2.8 25.0 + - - +
169F ILE* 3.7 3.6 - - + +
171F ASP* 1.3 77.7 - - - +
173F LYS* 1.3 60.2 + - - +
175F PRO* 3.4 10.0 - - - +
199F TYR* 6.3 2.7 - - + -
202F TRP* 2.9 28.0 + - + -
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Residues in contact with LYS 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 4.4 10.8 - - + -
25F HIS* 4.1 23.2 + - - -
26F MET* 3.7 26.6 - - + +
60F VAL* 4.4 11.3 - - - +
169F ILE* 3.0 37.4 + - + +
170F LYS* 3.9 4.3 - - - +
172F LEU* 1.3 77.7 - - - +
174F ASN* 1.3 59.4 + - + +
175F PRO* 3.1 8.8 - - - +
202F TRP* 3.2 26.0 - - - +
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Residues in contact with ASN 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F LYS* 3.1 17.1 + - + +
171F ASP* 3.5 6.8 - - - +
173F LYS* 1.3 77.3 - - + +
175F PRO* 1.4 62.8 - - - +
176F ASP* 3.7 4.3 + - - +
204F PRO* 5.9 1.9 - - - +
207F LYS* 3.2 26.1 + - - +
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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