Contacts of the strand formed by residues 240 - 243 (chain B) in PDB entry 3FZ7
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 MET 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B MET* 4.8 4.9 - - - -
140B ARG* 4.9 0.7 + - - -
205B VAL* 3.3 17.5 - - + +
207B PRO* 3.9 19.3 - - + -
220B PRO* 3.6 14.8 - - - +
223B LEU* 3.5 34.8 - - + -
224B HIS* 3.6 24.7 - - - +
227B LEU* 4.1 17.5 - - + -
239B ASP* 1.3 78.8 - - - +
241B HIS* 1.3 59.0 + - - +
242B ILE* 4.2 7.4 - - + -
266B ARG* 2.9 13.7 + - + +
267B VAL* 3.7 25.8 - - + -
268B LYS* 2.9 29.6 + - - +
269B SER* 3.6 2.8 + - - -
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Residues in contact with HIS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 4.4 1.8 - - - -
130B CYS* 4.7 1.0 - - - -
133B GLY* 4.0 18.8 - - - +
137B MET* 3.8 26.3 - - + -
166B TRP* 3.6 30.0 - + - -
205B VAL 3.2 5.3 + - - -
206B VAL* 3.3 24.6 - - - +
207B PRO* 3.4 1.3 - - - +
240B MET* 1.3 72.8 - - - +
242B ILE* 1.3 73.1 + - - +
243B ASP 3.6 1.0 + - - -
269B SER* 2.6 32.5 + - - +
270B ILE 3.7 4.3 - - - -
271B SER* 2.7 45.8 + - - -
287B VAL* 4.2 4.9 - - + -
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PRO* 3.8 31.4 - - + +
209B PHE* 3.8 28.3 - - + -
220B PRO* 3.9 13.7 - - + -
240B MET* 4.4 2.0 - - + -
241B HIS* 1.3 76.6 + - - +
243B ASP* 1.3 63.6 + - - +
244B ALA* 3.3 2.2 + - + +
260B TRP* 3.5 37.5 - - + +
267B VAL* 3.7 36.6 - - + -
269B SER 3.1 4.9 + - - -
270B ILE* 3.9 11.2 - - + +
271B SER 3.1 24.8 + - - -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B SER* 4.7 1.6 + - - -
130B CYS* 3.8 13.8 - - - -
163B GLN* 4.3 10.0 - - - +
165B CYS* 4.1 3.8 - - - -
166B TRP* 2.9 36.3 + - + +
206B VAL* 4.2 4.7 - - + -
207B PRO 2.9 17.1 + - - +
208B THR* 3.5 16.4 + - - +
209B PHE 2.7 31.5 + - - -
210B GLY 5.3 0.2 - - - +
241B HIS* 3.6 3.6 + - - -
242B ILE* 1.3 71.2 - - - +
244B ALA* 1.3 53.1 + - - +
245B ALA* 2.8 27.6 + - - +
271B SER* 4.0 7.3 + - - +
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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
------------------------------------------------------------
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