Contacts of the strand formed by residues 180 - 183 (chain E) 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 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179E ASN* 1.3 72.0 - - - +
181E CYS* 1.3 58.5 + - - +
192E VAL* 3.6 20.6 - - + -
193E GLY* 3.2 27.4 - - - +
194E VAL* 4.4 2.0 - - + +
227E VAL* 3.3 4.2 - - - +
228E ILE* 3.0 17.8 + - + -
229E GLY* 2.7 42.3 + - - +
232E ASN* 4.3 30.1 - - - +
233E LYS 4.4 0.2 - - - -
234E PRO* 3.7 42.8 - - + -
238E LEU* 5.8 1.1 - - + -
242E LYS* 6.2 5.6 - - + -
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Residues in contact with CYS 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E LEU* 1.3 73.9 - - - +
182E MET* 1.3 63.2 + - - +
183E VAL* 5.7 4.3 - - - -
191E ARG 3.7 1.3 - - - +
192E VAL* 3.2 8.8 - - - +
193E GLY 3.0 40.4 + - - -
195E ILE* 3.6 29.2 - - + -
210E VAL* 3.8 20.9 - - - -
225E ILE* 4.5 12.8 - - + -
226E PHE 3.2 12.6 - - - +
227E VAL* 3.9 12.6 - - + -
228E ILE* 3.6 5.8 - - - +
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Residues in contact with MET 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E PHE* 3.6 29.4 - - + -
102E VAL* 4.2 8.5 - - + -
103E TYR* 3.4 50.7 - - + +
181E CYS* 1.3 72.0 - - - +
183E VAL* 1.3 69.7 + - - +
190E GLY* 4.3 5.2 - - - -
191E ARG 3.2 5.2 - - - +
192E VAL* 3.6 24.9 - - + -
225E ILE* 5.0 0.2 - - - -
226E PHE* 2.4 58.9 + - + +
228E ILE* 4.2 17.3 - - + -
238E LEU* 4.6 11.2 - - + -
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Residues in contact with VAL 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E TYR* 4.0 2.3 - - - -
181E CYS* 5.7 5.4 - - - -
182E MET* 1.3 73.8 - - - +
184E ILE* 1.3 58.4 + - - +
185E GLY 3.2 25.1 - - - +
188E ASN* 3.9 7.2 - - + +
189E LEU* 3.3 6.4 - - - +
190E GLY* 2.7 31.7 + - - -
191E ARG* 2.8 39.4 + - + +
210E VAL* 5.5 5.2 - - + -
220E THR* 3.7 38.6 - - + +
224E ASN* 3.2 10.8 - - + +
225E ILE* 5.3 2.7 - - + -
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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