Contacts of the strand formed by residues 218 - 225 (chain A) in PDB entry 5F2R
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ARG* 5.5 12.8 - - + +
215A GLU* 3.4 26.7 + - - +
216A GLY* 4.4 4.3 - - - +
217A GLU* 1.3 81.7 + - - +
219A ASN* 1.3 66.1 + - - +
220A ILE* 4.0 3.3 + - + -
236A THR* 3.2 8.6 - - - -
237A ILE* 3.0 51.1 + - + +
357A ASP* 3.4 32.1 - - + +
358A GLU* 5.0 13.5 - - + +
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLU* 5.2 2.6 - - - +
218A LYS* 1.3 73.0 - - - +
220A ILE* 1.3 60.9 + - - +
221A LEU 4.2 0.2 - - - -
234A LEU* 4.9 1.3 - - + +
235A LEU 3.7 3.6 - - - +
236A THR* 3.3 23.2 - - - +
351A LEU* 3.9 32.5 - - + +
355A ASP* 3.0 30.1 + - - +
356A ILE* 3.8 13.0 - - + +
357A ASP* 2.7 37.1 + - - +
358A GLU 3.1 7.4 + - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA* 4.5 4.9 - - + -
211A LEU* 4.1 18.6 - - + -
218A LYS 4.6 0.9 - - - -
219A ASN* 1.3 77.8 - - - +
221A LEU* 1.3 60.5 + - - +
222A VAL* 4.1 14.1 - - + -
233A SER 3.5 1.6 - - - +
234A LEU* 3.5 6.8 - - - +
235A LEU* 2.8 49.8 + - + +
237A ILE* 3.8 30.5 - - + +
242A PHE* 4.1 22.0 - - + -
356A ILE* 4.6 0.4 - - - -
358A GLU* 3.3 24.2 - - + +
360A VAL* 3.9 24.9 - - + -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE* 1.3 71.9 - - - +
222A VAL* 1.3 74.5 + - - +
223A PHE* 4.0 14.1 - - + +
232A VAL* 3.5 26.9 - - + -
233A SER 3.6 6.3 - - - +
234A LEU* 4.5 10.1 - - + -
342A VAL* 4.3 9.4 - - + -
345A VAL* 3.7 18.2 - - + -
346A LEU* 4.7 4.3 - - + -
356A ILE* 3.8 23.6 - - + +
358A GLU 2.9 7.0 + - - +
359A ILE* 3.4 7.3 - - + +
360A VAL 3.0 23.2 + - - +
379A PHE* 3.9 28.7 - - + -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PRO* 3.7 45.8 - - + +
206A ALA* 5.4 0.4 - - + -
220A ILE* 4.1 17.5 - - + -
221A LEU* 1.3 75.9 - - - +
223A PHE* 1.3 61.6 + - - +
224A ASP* 3.9 5.4 - - + -
231A ASP 3.7 1.0 - - - +
232A VAL* 3.3 9.4 - - - +
233A SER* 2.9 40.7 + - - +
235A LEU* 4.3 7.6 - - + -
360A VAL* 3.4 13.9 - - + +
362A VAL* 3.5 31.9 - - + -
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.9 11.2 + - + -
222A VAL* 1.3 70.9 - - - +
224A ASP* 1.3 58.4 + - - +
225A LEU* 4.3 10.5 - - + -
230A PHE* 3.6 24.7 - + - -
231A ASP 4.0 2.2 - - - -
232A VAL* 4.9 1.1 - - + +
338A THR* 3.4 31.9 - - + -
339A MET* 4.2 6.3 - - + -
342A VAL* 3.8 26.7 - - + -
359A ILE* 5.4 0.9 - - + -
360A VAL 2.9 11.9 + - - +
361A LEU* 3.6 10.7 - - + -
362A VAL 2.9 25.2 + - - +
366A THR* 3.8 10.7 - - + +
371A ILE* 4.0 17.9 - - + -
375A VAL* 3.8 36.3 - - + -
379A PHE* 6.0 1.1 - + - -
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Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLU* 4.2 11.6 - - - +
202A PRO* 6.0 0.9 - - + +
222A VAL* 4.7 6.7 - - + -
223A PHE* 1.3 71.1 - - - +
225A LEU* 1.3 59.8 + - - +
226A GLY* 3.8 5.9 + - - -
229A THR* 3.9 1.0 - - - +
230A PHE* 3.5 5.6 - - - -
231A ASP* 2.8 54.8 + - + +
362A VAL* 3.2 36.4 - - + +
363A GLY* 3.7 6.9 - - - -
501A ACP 3.5 18.3 + - - -
502A MG 3.8 7.5 - - - -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.9 6.2 + - + -
224A ASP* 1.3 74.2 - - - +
226A GLY* 1.3 57.5 + - - +
229A THR 4.1 0.2 - - - -
230A PHE* 3.8 32.8 - - + -
253A LEU* 4.0 3.6 - - + +
254A GLY* 4.0 20.6 - - - +
258A PHE* 4.0 11.7 - - + -
338A THR* 4.2 16.8 - - + -
362A VAL 3.0 7.5 + - - -
363A GLY 3.5 7.8 - - - +
365A SER* 3.2 42.2 + - - +
366A THR* 4.0 12.3 + - + -
371A ILE* 3.8 35.2 - - + -
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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