Contacts of the strand formed by residues 236 - 241 (chain F) in PDB entry 5IJ7
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 LYS 236 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 5.1 2.0 - - - +
230F TYR* 3.4 4.4 - - - +
231F ASP* 2.8 59.6 + - - +
234F GLY 3.5 0.8 - - - -
235F GLU* 1.3 85.5 + - + +
237F ILE* 1.3 61.9 + - - +
248F LEU* 3.7 17.5 - - + -
249F TRP 3.5 8.7 - - - +
250F ARG* 4.1 12.8 - - + +
251F ILE* 4.0 3.1 - - - +
300F TRP* 3.4 35.9 + - + -
303F ASP* 3.4 19.6 + - - -
326F ILE* 3.7 26.2 - - + +
327F ASP* 4.7 14.9 + - - +
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Residues in contact with ILE 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F LEU* 3.6 45.8 - - + -
201F LEU* 4.8 3.1 - - + -
203F LEU* 5.3 1.8 - - + -
215F PHE* 4.3 11.9 - - + -
228F ALA* 4.2 5.4 - - + -
229F ASP 3.4 9.2 - - - +
230F TYR* 3.7 27.8 - - + +
236F LYS* 1.3 74.0 - - - +
238F MET* 1.3 70.6 + - - +
239F SER 4.2 0.2 - - - -
247F LYS 3.9 0.2 - - - +
248F LEU* 3.4 7.4 - - - +
249F TRP* 2.8 49.4 + - + +
251F ILE* 3.7 26.0 - - + -
300F TRP* 4.1 1.8 - - - -
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Residues in contact with MET 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F ALA* 3.2 2.9 - - - -
229F ASP* 3.0 31.3 + - + +
237F ILE* 1.3 73.3 - - - +
239F SER* 1.3 61.4 - - - +
246F LEU* 4.3 11.4 - - + +
247F LYS 3.3 35.2 - - - +
248F LEU* 3.7 20.6 - - + -
285F PHE* 5.0 1.8 - - + -
298F VAL* 3.4 29.8 - - + +
300F TRP* 3.7 30.2 - - + +
305F ILE* 3.7 33.7 - - + -
317F TRP* 4.6 6.5 - - + -
319F PRO* 4.6 10.3 - - + -
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Residues in contact with SER 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F LEU* 3.7 29.2 - - - -
221F HIS* 2.7 27.2 + - - -
225F VAL* 4.1 1.6 - - - -
227F SER 3.4 8.1 - - - -
228F ALA* 4.2 0.7 - - - -
237F ILE* 4.2 0.6 - - - -
238F MET* 1.3 74.6 - - - +
240F CYS* 1.3 62.2 + - - +
246F LEU* 3.1 6.9 - - - +
247F LYS* 2.7 33.3 + - - +
249F TRP* 2.8 24.2 + - - -
298F VAL* 4.3 1.6 - - - -
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Residues in contact with CYS 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F HIS* 3.8 6.1 - - - -
225F VAL* 3.4 3.8 - - - +
226F LEU 2.9 20.8 + - - -
227F SER* 3.0 35.3 + - - -
239F SER* 1.3 76.6 - - - +
241F GLY* 1.3 59.7 + - - +
245F SER 3.1 12.3 - - - +
246F LEU* 3.7 13.2 - - + -
295F VAL* 3.2 37.5 - - + -
297F CYS 3.9 2.7 - - - -
298F VAL* 3.7 14.4 - - + -
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Residues in contact with GLY 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F HIS* 3.7 3.3 - - - -
224F GLU 3.2 12.8 - - - -
225F VAL* 4.2 2.0 - - - -
226F LEU* 3.9 5.2 - - - -
240F CYS* 1.3 75.8 - - - +
242F MET* 1.3 60.7 - - - -
243F ASP* 3.2 9.2 - - - -
244F HIS 3.4 6.9 + - - -
245F SER 3.2 10.3 + - - -
295F VAL* 2.8 35.3 + - - +
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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