Contacts of the helix formed by residues 163 - 168 (chain V) in PDB entry 3FKS
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 LYS 163 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375U ARG* 4.1 16.9 - - - +
155V LEU* 4.9 9.4 - - + +
156V PHE* 3.1 34.8 - - - +
162V GLY* 1.3 79.6 - - - +
164V THR* 1.3 61.6 + - - +
165V VAL 3.3 0.9 - - - -
166V PHE* 3.6 9.6 + - + +
167V ILE* 3.4 29.1 + - + +
257V ASN* 5.1 4.5 - - - +
309V ALA* 5.6 6.5 - - + -
310V VAL 4.2 15.0 - - - +
311V TYR* 3.9 34.9 - - - +
312V VAL 6.0 0.2 - - - +
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Residues in contact with THR 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375U ARG* 3.8 9.0 + - - -
162V GLY* 3.0 3.3 - - - -
163V LYS* 1.3 78.0 - - - +
165V VAL* 1.3 65.8 + - - +
166V PHE 3.2 0.4 - - - -
167V ILE* 3.3 29.4 - - + +
168V GLN* 3.2 38.0 - - - +
189V GLU* 5.7 1.1 - - - +
193V GLU* 2.9 44.6 + - + +
196V ASP* 6.4 0.9 - - + -
197V LEU* 5.9 0.4 - - + -
424V PHE* 6.3 2.9 - - - -
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Residues in contact with VAL 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162V GLY* 3.9 16.6 - - - +
163V LYS 3.3 0.2 - - - -
164V THR* 1.3 81.2 - - - +
166V PHE* 1.3 60.8 + - - +
168V GLN* 4.8 0.2 - - - -
169V GLU* 3.8 16.6 + - - +
345V TYR* 6.3 3.8 - - + -
418V PHE* 5.8 7.0 - - + -
420V VAL* 3.9 14.3 - - + +
421V ALA* 3.8 37.2 - - + +
424V PHE* 4.2 34.5 - - + -
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Residues in contact with PHE 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138V ILE* 3.7 24.5 - - + -
141V VAL* 4.2 13.5 - - + -
147V TYR* 4.9 0.4 - - - -
155V LEU* 3.5 24.2 - - + -
156V PHE 6.0 0.2 - - - -
162V GLY 4.3 1.5 + - - +
163V LYS* 3.6 15.6 + - + +
164V THR 3.2 0.4 - - - -
165V VAL* 1.3 78.9 - - - +
167V ILE* 1.3 64.2 + - - +
169V GLU* 3.1 20.7 + - + +
170V LEU* 3.5 23.8 + - + +
333V THR* 4.0 29.6 - - - -
346V PRO* 3.4 41.1 - - + -
418V PHE* 4.8 6.1 - + - -
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Residues in contact with ILE 167 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155V LEU* 3.7 31.9 - - + -
163V LYS 3.4 12.8 + - - +
164V THR* 3.3 33.9 - - + +
166V PHE* 1.3 76.6 - - - +
168V GLN* 1.3 73.3 + - + +
169V GLU 3.0 0.2 - - - -
170V LEU* 2.9 26.8 + - - +
171V ILE* 3.4 15.4 + - + +
184V PHE* 4.8 17.0 - - + -
189V GLU* 5.8 1.1 - - - +
197V LEU* 5.2 3.4 - - + -
254V PHE* 5.8 1.6 - - + -
256V ASP* 3.8 20.6 - - + +
309V ALA* 4.3 11.0 - - + -
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Residues in contact with GLN 168 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164V THR* 3.2 36.0 + - - +
165V VAL* 4.8 0.3 - - - -
166V PHE 3.3 0.6 - - - -
167V ILE* 1.3 83.9 - - + +
169V GLU* 1.3 59.0 + - - +
170V LEU 3.4 0.2 - - - -
171V ILE* 4.0 11.1 - - + +
172V ASN* 3.9 15.4 + - - +
193V GLU 4.9 1.2 + - - -
196V ASP* 4.5 7.5 - - - +
197V LEU* 3.3 46.7 - - + +
200V GLU* 4.3 20.7 - - + +
420V VAL* 3.2 35.2 - - + +
424V PHE* 5.6 4.3 - - - -
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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