Contacts of the strand formed by residues 281 - 287 (chain B) in PDB entry 4A0L
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 VAL 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B CYS* 3.4 20.8 - - - +
242B CYS* 3.7 8.9 - - - -
255B GLY* 3.8 23.1 - - - -
256B ASP 3.1 7.2 + - - +
259B GLY* 3.6 32.3 - - - +
260B ARG 3.8 11.0 - - - +
261B LEU* 4.7 8.1 - - + +
276B LEU* 5.9 0.2 - - + -
277B HIS* 4.0 24.2 - - + -
279B ALA 3.3 0.2 + - - -
280B LYS* 1.3 69.2 - - - +
282B THR* 1.3 60.6 + - - +
283B HIS 3.6 21.3 - - - +
284B ALA* 4.6 6.3 - - + -
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Residues in contact with THR 282 (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 CYS* 3.6 9.6 - - - +
242B CYS* 3.5 12.8 - - - +
280B LYS* 3.3 29.7 + - + +
281B VAL* 1.3 74.8 - - - +
283B HIS* 1.3 68.2 + - - +
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Residues in contact with HIS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B CYS* 3.7 13.9 - - - +
243B VAL 5.5 5.4 - - - -
244B ASP* 6.1 1.3 - - + -
281B VAL* 3.4 11.2 - - - +
282B THR* 1.3 87.7 + - - +
284B ALA* 1.3 79.4 + - - +
285B GLU* 3.3 37.1 + - + +
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Residues in contact with ALA 284 (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 CYS* 3.7 14.8 - - - +
243B VAL 4.6 2.8 - - - +
244B ASP* 3.3 23.0 + - - +
253B ALA* 4.8 13.9 - - + +
261B LEU* 3.9 28.7 - - + -
281B VAL* 4.6 2.5 - - + -
283B HIS* 1.3 86.3 + - - +
285B GLU* 1.3 62.2 + - - +
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Residues in contact with GLU 285 (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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199B LYS* 6.2 0.2 - - - +
244B ASP* 3.2 11.9 - - - +
283B HIS* 3.3 28.6 + - + +
284B ALA* 1.3 74.1 - - - +
286B PHE* 1.3 77.2 + - - +
287B ASN 3.7 1.7 + - - -
288B PRO* 4.5 12.1 - - - +
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Residues in contact with PHE 286 (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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244B ASP* 2.8 47.3 + - + +
245B VAL* 3.8 2.2 - - - +
246B SER* 3.6 38.6 - - - +
249B ARG* 4.9 8.3 - - - -
251B MET* 3.8 39.0 - - + -
252B LEU 4.1 3.1 - - - -
253B ALA* 3.7 24.5 - - + -
263B LEU* 5.5 1.6 - - + -
285B GLU* 1.3 83.9 - - - +
287B ASN* 1.3 66.9 + - - +
288B PRO* 3.3 11.1 - - + +
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Residues in contact with ASN 287 (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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112A ILE* 3.2 32.8 - - - +
285B GLU* 3.7 3.8 + - - -
286B PHE* 1.3 72.9 - - - +
288B PRO* 1.3 71.8 - - - +
289B ARG* 2.9 18.2 + - - +
290B CYS* 3.0 37.1 + - - +
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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