Contacts of the strand formed by residues 215 - 221 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92N LEU* 3.6 8.1 - - - +
93N GLY* 3.0 18.0 + - - -
171N ILE* 3.8 32.1 - - + -
182N SER* 3.1 25.8 - - - +
183N VAL 4.0 0.2 - - - +
184N PHE* 3.6 14.4 - - + +
201N MET* 4.1 14.1 - - - -
206N VAL* 4.5 6.3 - - + +
207N ILE* 3.5 26.2 - - + +
214N LYS* 1.3 81.2 - - - +
216N ALA* 1.3 73.7 + - - +
217N LEU* 4.2 1.6 + - + +
254N PHE* 5.6 0.4 - - + -
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Residues in contact with ALA 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91N THR* 4.0 28.0 - - - +
92N LEU* 4.1 5.5 - - + +
93N GLY 4.3 5.2 - - - +
94N ARG 4.3 1.1 - - - +
96N ILE* 6.0 2.5 - - + -
182N SER 3.1 6.5 + - - +
183N VAL* 3.7 20.3 - - + -
184N PHE* 2.9 28.5 + - - +
215N VAL* 1.3 78.8 - - - +
217N LEU* 1.3 62.9 + - - +
218N VAL* 4.2 2.9 - - + -
239N ILE* 4.6 6.3 - - + -
243N PHE* 6.1 0.4 - - + -
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Residues in contact with LEU 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N GLY 6.0 0.2 - - - -
94N ARG 3.0 17.8 + - - +
95N ILE* 3.2 11.7 - - + -
96N ILE* 2.7 32.8 + - - +
184N PHE* 3.6 26.2 - - + -
197N LEU* 4.4 4.3 - - + -
198N TYR* 3.6 34.3 - - + +
201N MET* 3.7 32.8 - - + -
207N ILE* 4.9 6.3 - - + -
215N VAL* 4.2 6.5 + - + +
216N ALA* 1.3 81.5 - - - +
218N VAL* 1.3 56.6 + - - +
219N PHE* 3.9 21.8 - - + -
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Residues in contact with VAL 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N ILE* 3.2 25.4 - - + +
97N ASN 4.2 4.7 - - - +
183N VAL* 4.6 7.9 - - + -
184N PHE* 3.0 13.8 + - - +
185N THR* 4.1 16.6 - - + +
186N GLY 2.7 32.1 + - - -
216N ALA* 5.2 2.0 - - + -
217N LEU* 1.3 77.7 - - - +
219N PHE* 1.3 62.6 + - - +
220N GLY 3.8 1.6 + - - +
232N VAL* 4.2 5.4 - - + +
235N THR* 4.0 28.7 - - + -
236N GLY* 4.1 19.5 - - - -
239N ILE* 4.9 6.1 - - + -
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Residues in contact with PHE 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J ILE* 5.0 12.8 - - + -
95N ILE* 3.4 43.3 - - + -
96N ILE 3.1 10.2 + - - +
97N ASN* 4.2 14.1 - - - +
98N VAL 4.9 0.5 + - - -
103N ILE* 5.9 0.9 - - + -
184N PHE* 4.8 5.2 - + - -
186N GLY* 3.9 1.6 - - - -
189N GLU* 3.7 27.1 - - + -
194N GLY* 3.6 38.4 - - - -
197N LEU* 4.0 23.3 - - + -
198N TYR* 5.1 1.1 - - + -
217N LEU* 3.9 19.5 - - + -
218N VAL* 1.3 77.2 - - - +
220N GLY* 1.3 56.3 + - - +
221N GLN* 3.0 28.3 + - + +
224N GLU* 4.1 7.1 - - - +
232N VAL* 5.0 0.2 - - - -
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Residues in contact with GLY 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N VAL 5.8 0.2 - - - -
186N GLY 2.7 18.0 + - - -
188N GLY* 2.9 24.6 + - - -
189N GLU* 4.1 0.7 - - - -
218N VAL* 3.8 2.0 + - - +
219N PHE* 1.3 68.1 - - - +
221N GLN* 1.3 68.5 + - - +
224N GLU* 3.9 5.4 - - - -
229N ARG* 3.9 3.8 - - - +
232N VAL* 3.5 35.5 - - - +
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Residues in contact with GLN 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J GLY* 4.9 2.4 - - - -
138J ILE* 3.2 36.7 + - + +
97N ASN* 5.7 4.2 - - - +
103N ILE* 5.7 3.6 - - - +
189N GLU* 3.4 12.3 - - + +
191N THR* 3.6 27.7 + - - +
219N PHE* 3.0 24.2 + - + +
220N GLY* 1.3 83.2 - - - +
222N MET* 1.3 65.2 + - - +
223N ASN* 3.5 15.2 + - - +
224N GLU* 3.0 37.7 + - - +
229N ARG* 3.6 8.1 - - - +
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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