Contacts of the strand formed by residues 215 - 220 (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 VAL 215 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92V LEU* 3.9 1.3 - - - -
93V GLY* 2.7 30.1 + - - -
175V ALA* 6.4 0.7 - - + -
182V SER* 3.1 31.6 - - - +
184V PHE* 4.3 10.1 - - + +
201V MET* 3.6 37.7 - - + -
206V VAL* 3.8 10.1 - - + -
207V ILE* 3.4 19.6 - - + +
214V LYS* 1.3 79.8 - - + +
216V ALA* 1.3 68.4 + - - +
217V LEU* 4.1 10.8 - - + -
254V PHE* 6.1 0.9 - - + -
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Residues in contact with ALA 216 (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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91V THR* 3.3 34.1 - - + +
92V LEU* 4.0 13.0 - - + -
93V GLY 4.1 0.7 - - - +
182V SER 2.9 6.3 + - - -
183V VAL* 3.3 25.3 - - + +
184V PHE 3.0 25.3 + - - -
215V VAL* 1.3 76.6 - - - +
217V LEU* 1.3 63.2 + - - +
218V VAL* 5.3 0.9 - - + -
239V ILE* 4.8 2.7 - - + -
243V PHE* 5.5 1.1 - - + -
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Residues in contact with LEU 217 (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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93V GLY 6.0 1.8 - - - -
94V ARG 2.9 29.9 + - - +
95V ILE* 4.1 15.5 - - + -
96V ILE* 3.0 18.2 + - - +
184V PHE* 3.7 26.9 - - + +
197V LEU* 4.8 1.8 - - + -
198V TYR* 3.9 29.4 - - + -
201V MET* 3.5 33.7 - - + -
207V ILE* 5.7 4.0 - - + -
215V VAL* 4.1 9.0 - - + +
216V ALA* 1.3 75.8 - - - +
218V VAL* 1.3 68.0 + - - +
219V PHE* 4.2 20.9 - - + -
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Residues in contact with VAL 218 (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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91V THR* 5.8 2.0 - - + -
96V ILE* 3.1 23.8 - - + +
97V ASN 4.0 3.4 - - - +
183V VAL* 4.6 10.5 - - + -
184V PHE 3.0 10.9 + - - +
185V THR* 4.2 10.3 - - + -
186V GLY 2.7 30.5 + - - -
216V ALA* 5.3 0.9 - - + -
217V LEU* 1.3 80.6 - - - +
219V PHE* 1.3 64.5 + - - +
232V VAL* 4.2 20.4 - - + +
235V THR* 4.0 23.8 - - + -
236V GLY* 4.0 18.4 - - - +
239V ILE* 4.7 8.7 - - + -
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Residues in contact with PHE 219 (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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138U ILE* 4.4 20.4 - - + -
95V ILE* 4.2 24.0 - - + +
96V ILE 3.1 8.5 + - - -
97V ASN* 3.5 25.0 - - - +
103V ILE* 4.1 8.1 - - + +
184V PHE* 4.2 22.4 - + - -
186V GLY* 3.9 10.8 - - - -
189V GLU* 5.2 2.2 - - + -
194V GLY* 3.6 33.4 - - - -
197V LEU* 4.3 8.1 - - + -
217V LEU* 4.2 27.6 - - + -
218V VAL* 1.3 91.6 - - - +
220V GLY* 1.3 57.5 + - - +
221V GLN* 3.5 29.6 - - + +
224V GLU* 4.4 2.6 - - - +
232V VAL* 3.9 4.5 - - - -
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Residues in contact with GLY 220 (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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98V VAL 5.6 0.7 - - - -
186V GLY 2.9 9.6 + - - +
187V VAL* 3.9 1.0 - - - -
188V GLY* 2.9 23.0 + - - -
219V PHE* 1.3 74.7 - - - +
221V GLN* 1.3 66.6 + - - +
224V GLU* 3.2 20.6 - - - -
229V ARG* 3.8 7.4 - - - +
232V VAL* 3.5 17.0 - - - +
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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