Contacts of the strand formed by residues 240 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A MET* 4.8 3.8 - - - -
140A ARG* 4.8 1.7 + - - -
205A VAL* 3.2 15.3 - - + +
207A PRO* 3.5 26.0 - - + -
220A PRO* 3.5 14.1 - - + +
223A LEU* 3.5 30.7 - - + -
224A HIS* 3.9 22.0 - - - +
227A LEU* 3.7 21.5 - - + -
239A ASP* 1.3 80.9 - - - +
241A HIS* 1.3 59.8 + - - +
242A ILE* 4.2 6.3 - - + -
266A ARG* 3.1 10.9 + - + +
267A VAL* 3.8 24.9 - - + -
268A LYS* 3.0 28.7 + - - +
269A SER* 3.8 2.6 + - - -
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Residues in contact with HIS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA 4.5 0.9 - - - -
130A CYS* 4.7 1.0 - - - -
133A GLY* 3.9 18.1 - - - +
137A MET* 4.1 24.0 - - + -
166A TRP* 3.5 31.5 - + - -
205A VAL 3.0 5.9 + - - -
206A VAL* 3.4 11.2 - - + +
207A PRO* 3.4 14.6 - - - +
240A MET* 1.3 73.7 - - - +
242A ILE* 1.3 71.7 + - - +
243A ASP 4.0 0.4 - - - -
269A SER* 2.8 33.4 + - - +
270A ILE 3.6 21.5 - - - -
271A SER* 2.7 32.8 + - - -
287A VAL* 4.2 3.4 - - + -
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 3.6 26.2 - - + +
209A PHE* 3.8 28.0 - - + -
220A PRO* 3.6 28.9 - - + -
240A MET* 4.4 3.4 - - + -
241A HIS* 1.3 76.1 + - - +
243A ASP* 1.3 61.3 + - - +
244A ALA* 3.3 7.0 + - + -
260A TRP* 3.5 29.2 - - + +
267A VAL* 3.8 28.3 - - + -
269A SER 3.2 6.1 + - - -
270A ILE* 3.4 11.9 - - + +
271A SER 3.1 24.9 + - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A SER* 5.1 1.3 + - - -
130A CYS* 4.1 13.2 - - - -
163A GLN* 4.4 10.3 + - - +
165A CYS* 4.2 2.9 - - - -
166A TRP* 2.7 38.7 + - + +
206A VAL* 3.9 11.7 - - + -
207A PRO 3.1 10.7 + - - +
208A THR* 3.5 15.8 + - - +
209A PHE 2.7 31.1 + - - -
241A HIS* 3.6 1.8 + - - -
242A ILE* 1.3 71.1 - - - +
244A ALA* 1.3 53.2 + - - +
245A ALA* 3.2 27.1 + - - +
271A SER* 4.0 8.8 + - - +
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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