Contacts of the helix formed by residues 240 - 250 (chain B) in PDB entry 5JJA
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 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ARG* 6.1 0.9 - - - +
236B ALA* 5.0 7.1 + - - +
238B PRO 3.4 5.9 + - - +
239B LEU* 1.3 75.7 - - - +
241B GLU* 1.3 66.1 + - - +
242B GLU* 4.2 13.9 - - + +
243B HIS* 3.0 34.1 + - + +
244B LYS* 3.4 9.9 + - - +
674D GLU* 3.2 33.7 + - - +
675D ASP 5.2 5.7 + - - -
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Residues in contact with GLU 241 (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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239B LEU 3.7 2.0 + - - -
240B LYS* 1.3 71.7 - - - +
242B GLU* 1.3 63.3 + - - +
244B LYS* 3.2 31.8 + - - +
245B ILE* 2.9 47.8 + - + +
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Residues in contact with GLU 242 (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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198B ALA* 5.2 2.3 - - - +
201B ARG* 3.1 49.2 + - - +
202B LYS* 5.4 1.2 + - - -
240B LYS* 4.2 11.2 - - + +
241B GLU* 1.3 78.6 - - - +
243B HIS* 1.3 70.8 + - + +
245B ILE* 3.6 10.8 + - - +
246B PHE* 3.2 22.6 + - + +
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Residues in contact with HIS 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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201B ARG* 3.7 27.3 + - - -
235B PHE* 3.4 55.3 - + + -
236B ALA 5.9 0.2 - - - -
239B LEU* 4.7 4.7 - - + -
240B LYS* 3.0 32.5 + - + +
242B GLU* 1.3 91.2 - - + +
244B LYS* 1.3 61.2 + - - +
246B PHE* 3.2 8.0 + - - +
247B LEU 3.0 22.9 + - - -
274B PHE* 3.1 18.4 - - + -
674D GLU* 2.9 28.6 + - - -
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Residues in contact with LYS 244 (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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238B PRO* 6.1 1.6 - - - +
239B LEU* 3.7 32.0 + - + +
240B LYS 3.4 8.9 + - - +
241B GLU* 3.2 32.2 + - - +
243B HIS* 1.3 74.5 - - - +
245B ILE* 1.3 65.9 + - + +
247B LEU* 3.1 4.8 + - - +
248B LEU* 3.0 33.1 + - + +
274B PHE* 4.4 5.2 - - - -
278B ASP* 3.6 24.2 + - - -
280B THR* 5.6 0.4 - - - -
281B LEU* 4.2 29.8 - - + -
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Residues in contact with ILE 245 (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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209B TYR* 5.0 5.6 - - - +
241B GLU* 2.9 41.0 + - + +
242B GLU* 3.7 9.2 - - - +
244B LYS* 1.3 75.6 - - - +
246B PHE* 1.3 55.8 + - - +
248B LEU* 4.6 4.9 - - - +
249B LYS* 2.8 52.5 + - + +
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Residues in contact with PHE 246 (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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204B ILE* 5.5 0.7 - - + -
205B ASN* 3.0 35.0 - - - +
208B PHE* 4.3 5.8 - + - -
228B LEU* 3.5 41.1 - - + -
232B ILE* 4.6 5.8 - - + -
235B PHE* 5.8 3.4 - + - -
242B GLU* 3.2 15.5 + - + +
243B HIS* 3.3 14.8 - - + +
245B ILE* 1.3 76.0 - - - +
247B LEU* 1.3 65.5 + - - +
250B VAL* 3.0 50.6 + - + +
251B LEU* 3.1 35.4 + - + -
274B PHE* 4.2 14.1 - + - -
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Residues in contact with LEU 247 (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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243B HIS 3.0 13.4 + - - +
244B LYS 3.1 6.9 + - - +
246B PHE* 1.3 76.7 - - - +
248B LEU* 1.3 68.2 + - + +
251B LEU* 3.4 20.8 + - + +
252B LEU* 3.1 40.0 + - + +
271B VAL* 4.6 10.5 - - + -
274B PHE* 3.9 36.3 - - + -
281B LEU* 3.6 33.7 - - + -
285B VAL* 3.8 31.2 - - + -
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Residues in contact with LEU 248 (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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244B LYS* 3.0 24.7 + - + +
245B ILE* 4.0 3.6 - - - +
247B LEU* 1.3 91.5 - - + +
249B LYS* 1.3 71.5 + - + +
252B LEU* 3.7 27.8 - - + +
253B PRO* 3.5 14.0 - - - +
281B LEU* 4.9 12.3 - - + -
284B PRO* 4.0 28.0 - - + -
285B VAL* 5.0 0.7 - - + -
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Residues in contact with LYS 249 (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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209B TYR* 3.9 29.1 - - + +
212B ILE* 5.1 0.3 - - - +
213B TYR* 4.7 6.2 + - - -
245B ILE* 2.8 36.7 + - + +
248B LEU* 1.3 81.4 - - + +
250B VAL* 1.3 61.0 + - + +
253B PRO* 3.3 18.3 - - - +
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Residues in contact with VAL 250 (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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205B ASN* 3.6 26.0 - - - +
208B PHE* 3.4 46.0 - - + -
209B TYR* 3.7 23.8 - - + +
212B ILE* 3.7 9.2 - - + +
246B PHE* 3.0 26.7 + - + +
249B LYS* 1.3 83.4 - - + +
251B LEU* 1.3 67.5 + - - +
252B LEU 3.4 1.3 - - - -
253B PRO* 3.4 2.5 - - - +
254B LEU* 3.2 22.8 + - + +
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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