Contacts of the strand formed by residues 240 - 242 (chain F) in PDB entry 3EXF
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 THR 240 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F VAL 3.3 11.4 - - - +
145F VAL* 4.0 6.0 - - + +
156F LEU* 5.1 1.9 - - - +
194F PRO 4.7 0.3 + - - -
195F ILE* 3.6 10.8 - - + -
196F GLY* 2.6 38.0 + - - +
197F LYS 3.9 2.8 + - - -
238F MET* 2.8 30.4 + - - +
239F ARG* 1.3 76.5 - - - +
241F ILE* 1.3 66.7 + - - +
242F ARG 3.5 25.6 - - - +
243F PRO* 3.5 13.0 - - + +
244F MET* 3.8 10.8 - - - +
245F ASP 5.3 0.2 - - - -
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Residues in contact with ILE 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ALA* 3.7 36.1 - - + +
137F GLY* 4.0 12.3 - - - -
144F VAL* 2.4 35.2 + - + +
145F VAL* 4.0 0.2 - - - +
146F SER* 4.2 17.7 - - - -
212F HIS* 4.1 17.3 - - + +
238F MET* 3.7 28.3 - - + -
239F ARG 5.7 0.2 - - - -
240F THR* 1.3 77.1 - - - +
242F ARG* 1.3 59.3 + - - +
244F MET* 3.4 21.8 + - - +
271F VAL* 4.3 10.5 - - + -
268H GLN* 5.3 1.6 - - - +
269H PHE* 4.3 19.0 - - + -
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Residues in contact with ARG 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E TYR* 4.3 7.4 + - - +
136F TYR 4.6 1.3 - - - -
137F GLY* 2.4 45.8 + - - +
138F HIS 3.4 10.9 + - - -
139F CYS 3.6 13.9 + - - +
140F PRO* 3.5 26.3 - - - +
142F LEU 3.2 19.3 + - - +
143F LYS* 3.2 11.0 - - - +
144F VAL* 2.8 39.9 + - + +
240F THR* 3.5 6.4 - - - +
241F ILE* 1.3 77.5 - - - +
243F PRO* 1.3 67.6 - - + +
268H GLN* 3.1 35.2 - - - +
269H PHE* 6.0 0.2 - - + -
299H ASP* 2.7 31.3 + - - -
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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