Contacts of the strand formed by residues 319 - 325 (chain B) in PDB entry 2AX1
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 ASP 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B ARG* 4.4 2.6 + - - -
219B TYR 5.2 0.4 - - - -
314B LEU 3.9 0.7 - - - +
315B VAL* 3.4 6.7 - - - +
316B ASN* 2.9 42.7 + - + +
318B ASP* 1.3 84.4 + - - +
320B LEU* 1.3 63.2 + - - +
365B SER* 3.5 9.5 - - - -
366B CYS* 2.6 57.3 + - - +
367B SER 4.4 1.2 + - - -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PHE* 5.9 0.2 - - + -
218B SER* 3.1 9.0 - - - -
219B TYR* 3.0 60.3 + - + +
295B CYS* 4.0 18.6 - - - -
299B ALA* 3.4 25.4 - - + -
313B MET* 4.0 12.1 - - + -
314B LEU 3.7 1.8 - - - +
315B VAL* 3.9 22.9 - - + -
318B ASP 3.5 2.2 + - - -
319B ASP* 1.3 81.1 + - - +
321B VAL* 1.3 78.2 + - - +
322B VAL* 4.0 13.9 - - + -
339B PHE* 4.2 9.0 - - + -
343B MET* 4.7 1.3 - - + -
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Residues in contact with VAL 321 (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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200B ARG* 4.6 1.8 - - - +
204B LEU* 4.4 11.0 - - + -
217B PHE 3.4 13.0 - - - +
218B SER* 4.6 0.7 - - - -
312B THR 4.0 0.3 - - - +
313B MET* 3.4 3.8 - - - -
314B LEU* 3.0 59.4 + - + +
319B ASP* 5.8 0.2 - - - +
320B LEU* 1.3 74.8 - - - +
322B VAL* 1.3 71.2 + - - +
323B ILE* 4.8 9.9 - - + -
363B ILE* 3.8 27.6 - - + -
365B SER* 3.5 25.6 - - - +
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Residues in contact with VAL 322 (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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215B MET 4.0 0.2 - - - +
216B GLY* 3.0 5.0 - - - -
217B PHE* 2.9 68.6 + - + -
303B CYS* 4.4 7.4 - - - -
308B LEU* 4.8 0.4 - - + -
311B CYS* 4.0 28.5 - - + -
312B THR 3.5 7.6 - - - +
313B MET* 3.8 22.0 - - + -
320B LEU* 4.0 16.6 - - + -
321B VAL* 1.3 80.3 - - - +
323B ILE* 1.3 70.3 + - - +
324B CYS* 4.7 2.7 - - + +
339B PHE* 5.0 1.1 - - + -
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Residues in contact with ILE 323 (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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203B PHE* 6.4 0.2 - - + -
204B LEU* 4.0 39.5 - - + +
207B THR* 3.8 31.2 - - + -
208B TRP* 3.6 35.7 - - + -
211B LYS* 3.5 23.6 - - + -
214B PRO* 4.8 0.2 - - + -
215B MET 3.4 7.0 - - - +
216B GLY* 4.7 1.6 - - - -
312B THR 2.9 31.4 + - - +
321B VAL* 4.8 9.4 - - + -
322B VAL* 1.3 77.4 - - - +
324B CYS* 1.3 63.4 + - - +
360B LEU* 4.5 5.6 - - + -
363B ILE* 5.2 1.3 - - + -
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Residues in contact with CYS 324 (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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211B LYS* 3.7 10.4 - - - +
214B PRO* 3.6 6.6 - - - +
215B MET* 2.8 63.9 + - - -
217B PHE* 5.2 1.1 - - - -
308B LEU* 4.7 17.3 - - + -
309B GLN 3.1 13.9 - - - +
310B ASP 3.5 8.1 - - - +
311B CYS* 4.1 15.0 - - - -
322B VAL* 4.7 4.0 - - + -
323B ILE* 1.3 75.9 - - - +
325B GLU* 1.3 70.3 + - - +
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Residues in contact with GLU 325 (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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210B SER 4.4 1.6 - - - +
211B LYS* 3.3 11.9 - - + +
212B LYS* 2.7 31.3 + - - +
213B ASN* 3.0 28.8 + - - +
309B GLN* 3.0 42.3 + - + +
310B ASP* 3.8 25.5 - - + +
324B CYS* 1.3 85.2 - - - +
326B SER* 1.3 65.6 + - - +
327B ALA* 3.6 1.7 + - - +
332B ASP* 4.6 1.2 - - - +
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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
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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