Contacts of the strand formed by residues 195 - 200 (chain g) in PDB entry 5FLX
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 LEU 195 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168g CYS* 3.5 39.0 - - + -
169g GLY 3.3 22.5 + - - +
170g TRP* 2.8 33.1 + - - -
172g LYS* 5.4 1.3 - - - -
173g LEU 4.5 5.4 - - - +
174g VAL* 3.6 17.5 - - + -
191g HIS* 3.5 42.6 - - + +
193g GLY 3.8 3.8 + - - -
194g TYR* 1.3 69.6 - - - +
196g ASN* 1.3 56.8 + - - +
197g THR 4.0 8.7 - - - +
198g VAL* 5.3 0.4 - - + -
209g SER* 4.6 4.3 - - - +
210g GLY 3.2 17.9 - - - +
211g GLY* 3.6 4.3 - - - -
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Residues in contact with ASN 196 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152g SER* 2.6 29.9 + - - -
153g CYS* 4.7 0.7 - - - +
170g TRP* 4.7 10.6 - - - +
194g TYR* 3.3 13.9 - - - +
195g LEU* 1.3 73.2 - - - +
197g THR* 1.3 55.7 + - - +
210g GLY 2.6 9.3 + - - -
211g GLY* 4.2 4.3 - - - -
212g LYS* 4.4 1.7 + - - +
235g ILE* 3.4 32.4 - - - +
236g ILE 2.8 29.2 + - - +
237g ASN* 3.7 20.8 + - - +
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Residues in contact with THR 197 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153g CYS* 4.4 7.0 - - - +
155g ARG* 4.3 10.2 + - - -
168g CYS* 3.7 8.1 - - - -
195g LEU* 3.6 3.8 - - - +
196g ASN* 1.3 75.4 - - - +
198g VAL* 1.3 74.7 + - - +
209g SER* 3.3 22.0 - - - -
210g GLY 3.5 6.7 + - - +
236g ILE 4.8 1.3 - - - +
237g ASN 3.3 24.5 - - - +
238g ALA* 3.6 4.8 - - - +
239g LEU* 3.4 42.6 + - + +
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Residues in contact with VAL 198 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153g CYS* 4.0 12.1 - - - +
155g ARG* 3.0 40.2 + - + -
166g VAL* 4.0 23.8 - - + +
167g SER 4.7 3.6 - - - +
168g CYS* 3.4 23.5 - - - -
174g VAL* 5.1 4.5 - - + -
195g LEU* 5.3 0.4 - - + -
197g THR* 1.3 83.7 + - - +
199g THR* 1.3 66.2 + - - +
207g CYS* 3.5 22.7 - - - -
208g ALA 3.4 13.5 - - - +
209g SER* 4.2 9.2 - - - +
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Residues in contact with THR 199 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155g ARG* 4.1 11.3 + - - -
198g VAL* 1.3 76.1 - - - +
200g VAL* 1.3 72.1 + - - +
207g CYS* 3.5 4.9 - - - -
208g ALA* 2.9 43.3 + - + +
239g LEU* 3.3 38.9 + - + +
240g CYS* 3.6 18.3 - - - +
241g PHE* 3.5 20.7 + - + -
248g LEU* 5.0 0.4 - - + -
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Residues in contact with VAL 200 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155g ARG* 4.2 11.0 - - + +
156g PHE 3.8 20.4 - - - +
157g SER* 4.2 20.4 - - - +
166g VAL* 3.8 28.0 - - + -
199g THR* 1.3 80.3 + - - +
201g SER* 1.3 70.5 + - - +
202g PRO* 3.9 1.0 - - - +
204g GLY* 5.1 2.9 - - - -
206g LEU 3.7 5.8 - - - +
207g CYS* 4.1 10.1 - - + -
221g LEU* 4.9 5.4 - - + -
241g PHE* 3.3 14.0 + - - +
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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