Contacts of the strand formed by residues 272 - 278 (chain B) in PDB entry 1ZVM
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLU* 4.1 41.4 + - + +
77A MET* 4.3 6.9 - - - +
79A HIS* 6.1 2.2 - - + -
114A THR 5.0 0.5 - - - +
115A GLN* 3.8 9.8 - - - +
116A THR* 2.8 48.8 + - - +
236B GLN 3.0 13.0 + - - +
237B THR* 3.0 26.3 - - + -
238B LEU 2.9 26.2 + - - -
266B ILE* 3.9 1.0 - - - +
270B ASN 5.6 1.6 - - - -
271B ILE* 1.3 78.1 + - - +
273B PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 273 (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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114A THR* 4.6 13.5 - - - +
116A THR* 2.7 24.9 + - + +
237B THR* 5.4 0.2 - - - -
238B LEU* 3.4 17.7 - - + -
240B ALA* 4.0 12.1 - - + -
259B ILE* 3.8 28.3 - - + -
262B LEU* 3.6 35.4 - - + -
263B GLU* 3.6 42.2 - - + +
266B ILE* 4.0 27.1 - - + -
272B GLN* 1.3 74.7 - - - +
274B SER* 1.3 71.9 + - - +
275B CYS* 4.1 11.7 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 6.1 1.1 - - - -
237B THR* 4.7 9.0 - - - -
238B LEU 3.0 7.2 + - - +
239B GLU* 2.9 37.6 + - - +
240B ALA 2.8 23.6 + - - -
273B PHE* 1.3 82.3 - - - +
275B CYS* 1.3 64.0 + - - +
276B LYS* 3.8 11.6 + - - -
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Residues in contact with CYS 275 (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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240B ALA* 3.4 9.6 - - - -
242B VAL* 3.7 19.1 - - - -
254B CYS* 2.0 57.2 - - + +
259B ILE* 4.0 10.3 - - + -
273B PHE* 4.1 15.0 - - + -
274B SER* 1.3 77.6 + - - +
276B LYS* 1.3 76.1 + - - +
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Residues in contact with LYS 276 (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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111A LYS* 5.8 7.1 - - - +
239B GLU* 3.7 33.2 - - + +
240B ALA 2.8 9.6 + - - +
241B TRP* 3.4 13.1 - - + +
242B VAL 2.9 24.9 + - - -
254B CYS* 3.7 4.0 - - - -
274B SER* 3.8 9.2 + - - -
275B CYS* 1.3 83.2 + - - +
277B ASN* 1.3 67.3 + - - +
278B ILE* 4.3 2.9 - - + +
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Residues in contact with ASN 277 (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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242B VAL* 3.8 4.3 - - - +
244B HIS* 2.8 22.1 + - - +
252B ASP* 2.7 28.9 + - - -
253B LEU* 3.0 23.9 + - - +
254B CYS* 3.8 8.9 + - - -
276B LYS* 1.3 77.8 - - - +
278B ILE* 1.3 63.5 + - - +
279B TYR* 3.5 41.7 + - + -
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Residues in contact with ILE 278 (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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241B TRP* 3.5 38.8 - - + -
242B VAL 3.0 15.1 + - - +
243B ILE* 3.5 19.3 - - + -
244B HIS* 3.1 23.6 + - - -
276B LYS* 4.3 4.5 - - + +
277B ASN* 1.3 79.6 - - - +
279B TYR* 1.3 60.8 + - - +
280B ARG 4.1 2.0 - - - +
281B PRO* 4.0 16.7 - - + +
284B PHE* 3.9 50.0 - - + -
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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