Contacts of the strand formed by residues 272 - 278 (chain C) in PDB entry 5AJI
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 GLN 272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LYS* 4.3 6.4 + - - +
273B MET* 4.8 2.1 - - - +
274B ASP* 2.8 41.8 + - - +
276B ASN* 3.6 13.9 + - - +
231C SER* 3.1 26.8 + - - +
269C PRO* 4.3 9.4 - - + +
270C TYR 3.3 15.6 + - - +
271C PRO* 1.3 74.2 - - - +
273C MET* 1.3 62.7 + - - +
270D TYR* 3.3 50.5 - - + -
271D PRO* 3.7 21.2 - - - +
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Residues in contact with MET 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MET* 4.2 30.5 - - + +
274B ASP 3.0 9.8 + - - +
275B VAL* 3.3 7.2 - - + +
276B ASN* 2.9 27.8 + - - +
272C GLN* 1.3 80.7 + - - +
274C ASP* 1.3 71.6 + - - +
275C VAL* 3.8 15.4 + - + -
270D TYR* 4.5 0.9 - - - -
271D PRO* 3.5 20.9 - - + +
272D GLN 5.4 0.4 - - - +
273D MET* 3.1 51.1 - - + -
275D VAL* 5.2 1.1 - - + -
273E MET* 5.0 4.7 - - + -
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Residues in contact with ASP 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASN* 2.8 31.3 + - - +
278B LYS* 3.4 27.7 + - - +
273C MET* 1.3 71.2 - - - +
275C VAL* 1.3 61.4 + - - +
276C ASN* 4.3 1.3 - - - +
269D PRO* 5.1 1.0 - - - +
270D TYR* 3.7 20.1 + - - +
271D PRO 2.9 7.3 + - - +
272D GLN* 2.8 38.3 + - - +
273D MET 3.1 25.8 + - - +
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Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 3.3 31.9 - - + -
276B ASN 3.1 8.5 + - - +
277B PHE* 3.7 2.8 - - + -
278B LYS 3.1 24.3 + - - +
273C MET* 3.9 27.4 - - + -
274C ASP* 1.3 75.9 - - - +
276C ASN* 1.3 67.2 + - - +
277C PHE* 3.5 27.4 + - + -
273D MET 3.3 3.4 - - - +
275D VAL* 3.4 28.0 - - + -
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Residues in contact with ASN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LYS* 3.4 32.4 - - + +
279B ARG 5.4 4.7 - - - +
275C VAL* 1.3 80.3 + - - +
277C PHE* 1.3 64.2 + - - +
278C LYS* 4.9 1.9 - - - +
272D GLN* 3.6 21.9 + - - +
273D MET 2.9 13.7 + - - +
274D ASP* 2.6 33.6 + - - +
275D VAL 3.0 20.9 + - - +
270E TYR* 3.6 12.1 - - - -
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 3.3 52.3 - + + -
278B LYS 3.5 20.6 + - - +
279B ARG* 4.7 25.4 - - + +
275C VAL* 3.5 30.7 - - + -
276C ASN* 1.3 75.0 - - - +
278C LYS* 1.3 69.8 + - - +
275D VAL 3.5 3.8 - - - -
277D PHE* 3.2 47.1 - + + -
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Residues in contact with LYS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C ASN 4.9 1.6 - - - +
277C PHE* 1.3 81.0 - - - +
279C ARG* 1.3 62.2 + - - +
274D ASP* 5.4 8.7 + - - -
275D VAL 3.1 4.2 + - - +
276D ASN* 3.3 29.3 - - + +
277D PHE* 2.8 35.4 + - - +
272E GLN* 5.3 5.2 + - - -
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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