Contacts of the strand formed by residues 212 - 216 (chain D) in PDB entry 1FP1
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 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D ILE* 3.6 4.0 - - - +
211D SER* 1.3 80.3 + - - +
213D LEU* 1.3 60.8 + - - +
214D VAL* 4.4 3.6 - - + -
235D LYS* 3.3 18.7 - - + +
237D ILE* 4.0 20.2 - - + -
267D GLN 3.9 22.7 - - - +
268D GLY* 3.9 6.1 - - - -
269D ASP* 3.0 31.5 + - - +
270D ALA 3.4 9.2 + - - +
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PHE* 3.9 26.0 - - + -
210D ILE* 4.0 6.3 - - + -
212D THR* 1.3 73.0 - - - +
214D VAL* 1.3 63.2 + - - +
215D ASP 3.9 0.3 + - - -
224D LEU* 3.7 25.9 - - + +
227D ILE* 3.9 13.9 - - + -
234D ILE* 3.6 19.2 - - + +
235D LYS 2.9 7.3 + - - -
236D GLY* 3.5 3.6 - - - -
237D ILE* 2.9 23.7 + - - +
270D ALA* 3.4 31.0 - - + +
271D MET 4.0 3.1 - - - +
272D ILE* 4.0 25.6 - - + +
303D ILE* 4.8 7.2 - - + -
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D THR* 4.4 2.2 - - + -
213D LEU* 1.3 76.2 - - - +
215D ASP* 1.3 60.7 + - - +
216D VAL* 3.3 19.3 + - + -
237D ILE* 3.3 23.3 - - + +
239D PHE* 4.1 9.0 - - + -
265D VAL* 4.3 0.2 - - + -
266D PRO* 3.7 33.2 - - + +
267D GLN 3.6 25.8 - - - +
268D GLY* 4.1 4.9 - - - -
270D ALA 2.9 11.1 + - - +
271D MET* 3.2 14.1 - - + +
272D ILE* 2.9 27.5 + - - -
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Residues in contact with ASP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU 3.9 1.8 + - - -
214D VAL* 1.3 71.2 - - - +
216D VAL* 1.3 61.6 + - - +
217D GLY 4.0 0.3 - - - -
218D GLY* 3.1 31.1 + - - +
221D GLY* 5.8 0.3 - - - -
223D ASN* 4.1 19.9 + - - +
224D LEU* 3.7 31.2 + - + +
237D ILE 2.8 9.8 + - - +
238D ASN* 4.0 3.2 + - - +
239D PHE 2.9 28.7 + - - +
272D ILE* 3.3 26.6 - - + +
274D LYS* 4.9 3.8 + - - +
1699D SAH 4.2 7.1 + - - -
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D VAL* 4.1 13.7 - - + +
215D ASP* 1.3 68.3 - - - +
217D GLY* 1.3 66.2 + - - +
239D PHE* 3.9 10.1 - - + -
261D MET* 4.1 33.9 - - + -
265D VAL* 3.6 32.5 - - + -
271D MET* 4.2 4.5 - - + -
272D ILE 3.0 11.2 + - - +
273D LEU* 3.7 33.4 - - + +
276D VAL* 3.4 17.2 - - - +
288D PHE* 5.6 0.4 - - + -
292D CYS* 4.2 7.2 - - - -
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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