Contacts of the strand formed by residues 240 - 242 (chain V) in PDB entry 3EXG
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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144V VAL 3.2 15.5 - - - +
145V VAL* 3.7 13.9 - - + +
156V LEU* 5.2 1.6 - - - +
194V PRO 5.0 0.2 + - - -
195V ILE* 3.8 2.1 - - + -
196V GLY* 2.8 40.0 + - - +
197V LYS 4.3 0.5 + - - -
238V MET* 2.6 26.7 + - - +
239V ARG* 1.3 78.9 - - - +
241V ILE* 1.3 60.7 + - - +
242V ARG 3.4 24.9 - - - +
243V PRO* 3.6 10.3 - - + +
244V MET* 3.7 14.6 - - - +
245V ASP 4.8 0.4 + - - -
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Residues in contact with ILE 241 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133V ALA* 3.3 34.5 - - + +
137V GLY* 4.1 4.3 - - - -
144V VAL* 2.6 31.4 + - + +
146V SER* 4.0 15.3 - - - -
212V HIS* 3.9 38.4 - - + +
238V MET* 4.6 7.9 - - + -
239V ARG 5.3 0.4 - - - +
240V THR* 1.3 77.5 - - - +
242V ARG* 1.3 57.9 + - - +
244V MET* 3.4 27.5 + - + +
271V VAL* 4.4 9.0 - - + -
268X GLN* 5.3 0.9 - - - +
269X PHE* 3.9 19.8 - - + -
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Residues in contact with ARG 242 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340U TYR* 3.8 15.2 + - - +
136V TYR 4.6 1.8 - - - -
137V GLY* 2.9 37.3 + - - +
138V HIS 3.6 12.3 + - - -
139V CYS 3.4 23.8 + - - -
140V PRO* 3.3 21.0 - - - +
142V LEU 3.9 11.4 - - - -
143V LYS* 3.4 5.2 - - - +
144V VAL* 2.7 34.1 + - - +
240V THR* 3.4 5.2 - - - +
241V ILE* 1.3 80.8 - - - +
243V PRO* 1.3 71.3 - - + +
244V MET 3.4 0.4 - - - +
268X GLN* 2.8 36.4 - - - +
269X PHE* 5.3 0.4 - - + -
299X ASP* 2.9 31.7 + - - -
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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
------------------------------------------------------------
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