Contacts of the strand formed by residues 200 - 205 (chain D) in PDB entry 5FLZ
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 ALA 200 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D LEU 3.4 3.0 + - - -
168D THR* 3.4 15.7 - - + +
169D THR 3.0 13.9 + - - -
198D SER* 3.0 15.7 + - - -
199D ASP* 1.4 78.3 - - - +
201D THR* 1.3 61.2 + - - +
202D VAL 4.3 0.2 - - - -
256D TYR* 2.9 28.7 - - + +
260D ILE* 5.5 1.1 - - + -
266D HIS* 3.5 8.3 - - + -
268D LEU* 4.1 19.1 - - + -
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Residues in contact with THR 201 (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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169D THR* 3.3 14.2 - - - +
171D SER* 3.3 27.2 + - - -
173D PHE* 5.1 1.6 - - - -
194D LEU* 5.0 7.4 - - + +
198D SER* 4.8 2.0 - - - -
200D ALA* 1.3 76.0 - - - +
202D VAL* 1.3 61.7 + - - +
203D VAL* 3.7 2.9 + - + +
266D HIS* 2.9 29.2 + - + +
267D PHE* 3.3 44.7 - - + -
268D LEU* 2.8 26.5 + - - +
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Residues in contact with VAL 202 (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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168D THR* 4.5 5.2 - - + -
169D THR 2.9 11.6 + - - +
170D TYR* 3.9 38.4 - - + +
171D SER 2.8 31.6 + - - +
201D THR* 1.3 72.8 + - - +
203D VAL* 1.3 60.6 + - - +
204D PHE* 3.5 24.9 - - + -
268D LEU* 3.8 25.6 - - + +
270D PRO* 4.3 7.0 - - + -
377D LEU* 3.8 29.2 - - + -
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Residues in contact with VAL 203 (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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171D SER 3.6 3.1 - - - -
173D PHE* 3.3 49.6 - - + -
176D ARG* 4.7 1.6 - - - +
201D THR* 4.5 4.5 - - - +
202D VAL* 1.3 72.5 - - - +
204D PHE* 1.4 67.2 + - - +
205D ASP* 4.0 2.7 - - + +
267D PHE* 3.8 28.0 - - + -
268D LEU 2.9 14.0 + - - +
270D PRO* 3.2 20.0 - - - +
304D SER* 3.0 15.7 + - - +
306D VAL* 3.5 31.4 - - + -
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Residues in contact with PHE 204 (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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170D TYR* 3.7 36.6 - + + -
171D SER 2.9 21.4 + - - +
172D VAL* 3.3 20.2 - - + +
173D PHE 2.9 23.0 + - - +
202D VAL* 3.5 30.3 - - + -
203D VAL* 1.4 72.7 - - - +
205D ASP* 1.4 63.2 + - - +
206D ASN* 3.4 2.4 + - - -
209D LEU* 4.7 13.5 - - + -
231D ILE* 4.4 23.6 - - + -
234D ILE* 3.8 36.3 - - + -
235D ILE* 4.3 7.9 - - + -
270D PRO* 3.9 14.6 - - + -
303D ASN* 4.6 7.2 - - + +
304D SER* 4.0 2.7 - - - -
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Residues in contact with ASP 205 (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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173D PHE* 3.8 5.8 - - - +
174D PRO 3.6 14.1 - - - +
175D ALA* 3.7 4.3 - - - -
176D ARG* 3.6 25.9 + - - +
203D VAL* 4.5 3.1 - - + -
204D PHE* 1.4 70.6 - - - +
206D ASN* 1.4 59.2 + - - +
207D ALA* 3.3 16.6 - - - +
208D SER* 3.2 17.0 + - - -
209D LEU* 2.9 27.5 + - - +
303D ASN 3.6 3.7 + - - +
304D SER* 3.3 9.4 + - - +
305D LEU* 3.2 45.0 - - - +
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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