Contacts of the helix formed by residues 252 - 257 (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 LEU 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LEU* 3.1 22.1 + - + +
248B LEU* 3.7 36.1 - - + +
251B LEU* 1.3 75.2 - - - +
253B PRO* 1.3 69.6 - - + +
255B HIS* 2.8 42.1 + - + +
271B VAL* 4.6 3.8 - - + -
284B PRO* 4.1 2.9 - - + +
285B VAL* 4.1 37.2 - - + +
288B ALA* 3.8 30.1 - - + -
289B LEU* 5.6 1.1 - - + +
292B TYR* 3.4 9.2 - - + +
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Residues in contact with PRO 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 4.1 16.6 - - + +
213B TYR* 3.8 21.3 - - - +
248B LEU 3.5 13.5 - - - +
249B LYS* 3.3 20.6 - - - +
250B VAL 3.4 11.4 - - - +
252B LEU* 1.3 89.6 - - + +
254B LEU* 1.3 58.8 - - - +
255B HIS 3.0 6.1 - - - -
256B LYS* 3.1 28.6 + - + +
257B VAL 4.2 0.7 + - - -
292B TYR* 3.8 22.0 - - + +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 4.0 30.1 - - + -
211B PHE* 3.7 36.1 - - + -
212B ILE* 3.7 15.0 - - + +
221B ILE* 4.6 4.9 - - + -
225B LEU* 4.0 25.8 - - + -
250B VAL 3.2 20.3 + - - +
251B LEU* 3.5 11.9 - - + +
252B LEU 3.1 1.2 + - - -
253B PRO* 1.3 75.4 - - - +
255B HIS* 1.3 60.4 + - - +
256B LYS 3.2 0.7 + - - -
257B VAL* 3.6 5.4 + - - -
260B LEU* 3.8 1.9 - - - +
263B TYR* 2.7 33.6 + - + +
267B LEU* 3.9 17.9 - - + -
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Residues in contact with HIS 255 (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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251B LEU 3.4 9.2 + - - -
252B LEU* 2.8 35.8 + - + +
253B PRO 3.0 0.8 - - - -
254B LEU* 1.3 78.0 - - - +
256B LYS* 1.3 57.9 + - - +
257B VAL 3.4 0.6 + - - +
260B LEU* 3.4 24.0 - - + +
264B HIS* 4.1 11.2 - + - -
267B LEU* 3.5 26.9 - - + +
271B VAL* 4.0 10.3 - - + -
288B ALA* 6.3 0.2 - - - +
289B LEU* 3.7 19.3 - - + +
292B TYR* 3.8 26.6 - + + +
304B PHE* 4.3 6.2 - + + -
307B GLU* 2.8 41.2 + - - -
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 4.2 26.8 + - + +
213B TYR* 4.4 14.7 - - - +
216B GLU* 5.4 4.4 + - - -
253B PRO* 3.1 26.6 + - + +
255B HIS* 1.3 77.0 - - - +
257B VAL* 1.3 69.8 + - + +
258B LYS* 3.6 2.4 + - - -
292B TYR* 3.7 34.7 - - + +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.7 33.4 - - + -
212B ILE* 4.1 28.5 - - + +
216B GLU* 4.5 27.1 - - + +
253B PRO 4.2 4.0 - - - +
254B LEU 3.6 5.8 + - - +
255B HIS 3.4 2.1 - - - +
256B LYS* 1.3 83.2 - - + +
258B LYS* 1.3 71.5 + - + +
259B SER* 3.2 8.5 - - - +
260B LEU* 3.0 22.5 + - - +
263B TYR* 3.4 19.7 - - - +
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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
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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