Contacts of the strand formed by residues 192 - 198 (chain C) in PDB entry 5FL6
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 TYR 192 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 3.5 18.7 - - + +
46C ARG 2.5 40.6 + - - -
48C LEU* 3.8 22.9 - - + +
82C LEU 4.5 5.5 + - - -
189C PHE 3.6 22.9 - - - -
190C SER 4.2 2.2 - - - -
191C ARG* 1.3 75.5 - - - +
193C PHE* 1.3 69.2 + - - +
194C GLN* 3.9 18.9 + - + -
211C THR* 3.6 23.1 - - + -
212C VAL 3.3 15.0 - - - +
213C PHE* 4.1 5.8 - + + -
214C ASN 3.9 2.7 - - - +
256C ALA* 3.5 2.8 - - - -
257C SER* 2.9 53.3 + - - -
258C PHE* 3.7 7.8 - - - -
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Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 3.9 40.8 - - + -
36C PRO* 4.1 28.7 - - + -
39C ALA* 4.3 3.6 - - + -
109C VAL* 5.4 7.6 - - + -
146C PHE* 6.1 1.1 - + - -
192C TYR* 1.3 77.6 - - - +
194C GLN* 1.3 61.2 + - - +
195C TYR* 5.7 1.1 - - + -
210C TRP 4.4 0.2 - - - -
211C THR* 3.2 5.0 - - - -
212C VAL* 2.7 50.3 + - + +
213C PHE 4.7 1.6 - - - -
214C ASN* 4.3 24.0 - - - -
254C ILE* 4.0 14.4 - - + -
255C GLU 3.3 10.8 - - - +
256C ALA* 4.1 13.2 - - + -
258C PHE* 3.7 25.6 - + - -
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Residues in contact with GLN 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 3.5 29.0 - - + +
48C LEU* 5.2 0.2 - - - +
82C LEU* 4.1 22.1 + - - +
86C ARG* 5.1 9.4 + - - -
192C TYR* 3.9 21.3 + - + -
193C PHE* 1.3 75.1 - - - +
195C TYR* 1.3 68.0 + - - +
209C ILE* 3.9 17.5 - - + +
210C TRP 3.2 12.6 - - - +
211C THR* 2.9 20.1 + - - +
253C VAL 4.5 0.3 - - - +
254C ILE* 3.8 1.2 - - - +
255C GLU* 2.9 42.5 + - + +
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Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 2.9 32.9 + - - -
32C VAL* 3.5 31.3 + - + +
34C ILE* 5.8 2.0 - - + -
107C HIS* 2.7 32.9 + + - -
193C PHE* 5.7 0.9 - - + -
194C GLN* 1.3 79.8 - - - +
196C GLU* 1.3 77.5 + - - +
197C GLY* 4.0 2.7 - - - -
209C ILE* 3.8 4.4 - - - +
210C TRP* 2.8 52.2 + - + +
212C VAL* 4.8 5.4 - - + -
249C LEU* 5.2 2.2 - - + -
252C ARG* 3.6 25.1 - - + -
253C VAL 4.8 5.6 - - - +
254C ILE* 4.4 24.5 - - + -
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Residues in contact with GLU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 4.6 2.2 - - - +
137C PRO* 3.9 19.1 - - - +
138C GLY 4.8 1.6 + - - -
195C TYR* 1.3 78.8 - - - +
197C GLY* 1.3 60.7 + - - +
207C GLY* 3.4 32.2 + - - +
208C VAL 3.3 12.6 - - - +
209C ILE* 4.5 11.8 - - + +
252C ARG* 2.9 31.0 + - - +
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Residues in contact with GLY 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.3 19.6 - - - +
30C SER* 3.3 13.0 - - - -
195C TYR* 4.0 0.7 - - - -
196C GLU* 1.3 75.3 - - - +
198C SER* 1.3 57.2 + - - -
206C GLN* 3.4 1.6 - - - +
207C GLY 3.1 12.0 + - - -
208C VAL* 2.8 32.6 + - - -
210C TRP* 4.0 3.4 - - - -
252C ARG* 3.4 5.2 - - - -
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Residues in contact with SER 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE 3.7 1.3 + - - -
29C GLN* 3.3 34.3 + - - -
30C SER* 2.9 31.8 + - - -
197C GLY* 1.3 74.6 - - - -
199C LEU* 1.3 83.2 + - - +
204C CYS 3.7 2.0 - - - -
205C ALA 3.1 15.0 - - - -
206C GLN* 4.1 0.4 - - - -
208C VAL* 3.7 8.1 - - - -
210C TRP* 2.8 22.4 + - - +
244C ARG* 3.7 0.2 + - - -
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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