Contacts of the strand formed by residues 272 - 276 (chain B) in PDB entry 2JG7
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 ASN 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLY 4.2 4.2 - - - -
271B ASN* 1.3 76.7 + - - +
273B ALA* 1.3 60.4 + - - +
301B CYS 2.8 26.4 + - - -
302B THR 3.1 10.0 - - - +
303B THR 2.9 23.3 + - - +
304B THR* 3.6 2.1 - - - -
305B ARG* 2.8 33.5 + - - +
306B ARG 3.0 7.0 + - - +
426B LEU* 3.6 9.2 + - - +
427B SER* 2.9 42.1 + - - +
458B THR* 3.8 16.8 - - + -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ASN 3.6 1.0 + - - -
272B ASN* 1.3 74.4 - - - +
274B ILE* 1.3 64.2 + - - +
275B ILE* 4.1 2.6 - - + +
306B ARG* 3.1 19.3 - - + +
308B MET* 3.7 27.6 - - + -
419B ASN* 3.4 21.4 + - + +
427B SER 3.8 5.3 + - - -
428B SER* 3.5 2.1 - - - -
429B SER 3.0 26.2 + - - +
458B THR* 3.5 4.3 - - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ALA* 1.3 74.8 - - - +
275B ILE* 1.3 58.2 + - - +
276B VAL* 3.9 7.4 - - + -
285B VAL* 5.7 0.7 - - + -
289B ALA* 4.3 22.9 - - + +
292B ALA* 4.5 0.2 - - + -
304B THR* 3.3 34.3 - - + +
306B ARG 2.8 6.7 + - - -
307B LEU* 3.5 22.8 - - + +
308B MET* 2.7 33.6 + - - +
429B SER* 3.4 10.8 - - - +
431B PHE* 3.6 28.7 - - + -
457B PRO* 4.2 21.8 - - + -
458B THR* 4.0 9.9 - - + -
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ALA* 4.8 2.9 - - + -
274B ILE* 1.3 78.0 - - - +
276B VAL* 1.3 63.7 + - - +
277B PHE* 3.5 22.5 + - + -
308B MET* 3.5 17.7 - - + -
409B PHE* 3.6 13.5 - - + -
415B ALA* 3.6 42.4 - - + +
416B PHE* 4.5 1.6 - - + -
419B ASN* 4.0 17.7 - - + +
429B SER 2.8 11.8 + - - +
430B ILE* 3.2 23.3 - - + +
431B PHE 2.8 27.4 + - - +
441B TRP* 4.0 12.3 - - + -
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 3.9 17.7 - - + -
275B ILE* 1.3 76.0 - - - +
277B PHE* 1.3 72.6 + - - +
280B ALA* 3.8 14.6 - - + -
282B LEU* 4.6 4.9 - - + -
285B VAL* 3.6 35.4 - - + -
307B LEU* 4.0 4.0 - - + -
308B MET 2.8 12.7 + - - +
309B LEU* 3.7 22.4 - - + -
310B HIS 3.1 25.6 + - - -
313B VAL* 4.5 11.0 - - + -
317B VAL* 5.1 1.1 - - + -
409B PHE* 3.3 4.4 - - - -
431B PHE* 4.0 3.8 - - + -
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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