Contacts of the strand formed by residues 296 - 299 (chain B) in PDB entry 1JS6
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 SER 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 4.7 1.3 - - - -
155B ALA* 3.6 2.4 - - - +
267B TRP* 3.0 22.5 + - - -
268B LEU 3.4 1.8 + - - +
269B HIS* 2.8 29.2 + - - +
270B VAL 2.9 24.6 + - - -
294B ALA* 3.4 6.8 - - - +
295B ASP* 1.3 81.7 - - - +
297B PHE* 1.3 60.6 + - - +
314B MET* 3.7 19.5 - - - -
315B TRP 3.1 12.6 - - - -
316B VAL* 3.8 5.2 - - - -
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.8 25.8 - - + -
128B LEU* 3.8 17.0 - - + -
132B PHE* 4.7 9.6 - - + -
270B VAL* 3.5 20.9 - - + -
272B ALA* 3.8 23.3 - - + -
276B GLY* 4.9 0.2 - - - -
279B PHE* 4.5 6.1 - + - -
288B LEU* 3.7 26.9 - - + -
291B VAL* 3.9 22.9 - - + -
294B ALA* 5.1 0.2 - - + -
296B SER* 1.3 74.4 - - - +
298B ASN* 1.3 66.0 + - - +
299B PHE* 4.1 20.4 - + + -
313B ALA 3.8 0.5 - - - +
314B MET* 3.4 3.4 - - - +
315B TRP* 2.9 52.8 + + + +
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Residues in contact with ASN 298 (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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148B ALA* 3.4 23.7 - - - +
151B ALA* 3.3 26.0 - - + +
152B THR* 5.2 0.3 + - - -
269B HIS* 3.8 20.9 + - + +
270B VAL 3.0 8.8 + - - +
271B ASP* 5.0 3.9 - - - +
272B ALA* 2.9 30.7 + - - +
273B ALA 3.8 0.2 + - - -
297B PHE* 1.3 81.6 - - - +
299B PHE* 1.3 67.7 + - - +
312B SER* 2.9 21.2 + - - -
313B ALA 2.6 30.2 + - - -
314B MET* 3.8 4.7 - - + +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.7 37.5 - - + -
126B LEU* 3.4 33.7 - - + -
272B ALA* 3.2 22.9 - - + +
273B ALA* 3.8 5.8 - - - +
276B GLY* 3.8 8.7 - - - -
277B SER* 3.3 44.6 - - - -
280B ILE* 5.6 0.4 - - + -
297B PHE* 4.1 6.5 - + + -
298B ASN* 1.3 79.1 + - - +
300B ASN* 1.3 68.0 + - - +
301B PRO* 3.1 21.1 - - + +
305B LEU* 4.4 4.9 - - + -
313B ALA* 2.9 28.6 + - + +
315B TRP* 4.0 11.4 - + - -
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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