Contacts of the strand formed by residues 354 - 358 (chain B) in PDB entry 1AX4
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 ALA 354 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLY 4.5 0.7 + - - +
332B VAL* 3.6 15.5 - - - +
350B THR* 4.6 1.0 - - - -
351B GLY 4.1 15.4 + - - -
353B HIS* 1.3 100.1 + - + +
355B VAL* 1.3 65.6 + - - +
356B PHE* 3.8 25.8 + - + -
414B ARG* 3.9 7.9 - - + -
415B LEU 3.1 14.1 - - - +
416B THR* 3.9 7.2 - - - -
417B ILE* 4.6 1.1 - - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 3.6 28.9 - - + +
335B LEU* 3.9 15.7 - - + -
336B GLY* 3.8 17.9 - - - +
339B LEU* 3.9 16.2 - - + -
346B ILE* 3.8 31.4 - - + -
350B THR* 4.0 7.4 - - + -
354B ALA* 1.3 77.8 - - - +
356B PHE* 1.3 64.6 + - - +
357B VAL* 4.4 2.7 - - + -
413B MET 3.6 1.6 - - - +
414B ARG* 3.7 0.5 - - - -
415B LEU* 2.8 43.1 + - + +
417B ILE* 5.8 0.2 - - + -
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Residues in contact with PHE 356 (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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194B ASN* 3.8 12.3 - - - -
195B SER* 4.7 3.1 - - - -
197B GLY* 3.2 45.1 - - - -
346B ILE* 3.2 5.5 - - - +
347B GLN* 2.9 44.9 + - + +
353B HIS* 4.7 3.6 - + - -
354B ALA* 3.8 22.9 - - + -
355B VAL* 1.3 78.0 - - - +
357B VAL* 1.3 62.3 + - - +
391B ILE* 4.1 16.2 - - + -
412B PHE* 3.3 42.2 - + + -
413B MET 3.3 3.8 - - - -
414B ARG* 3.5 30.1 - - + -
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.2 15.7 - - + -
344B ILE* 3.8 15.5 - - + -
345B PRO 3.6 5.8 - - - +
346B ILE* 4.3 4.5 - - + +
355B VAL* 4.4 1.6 - - + -
356B PHE* 1.3 74.7 - - - +
358B ASP* 1.3 61.7 - - - +
359B CYS* 3.0 11.2 + - - -
362B LEU* 3.7 29.6 - - + -
412B PHE* 3.3 3.5 - - - -
413B MET* 2.9 62.8 + - + +
415B LEU* 4.3 8.5 - - + -
434B LEU* 4.0 13.0 - - + -
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Residues in contact with ASP 358 (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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157B SER* 3.0 20.4 + - - +
345B PRO* 2.9 32.3 + - - +
346B ILE* 4.9 1.1 - - - +
356B PHE 3.7 2.8 + - - -
357B VAL* 1.3 69.8 - - - +
359B CYS* 1.3 58.3 + - - +
360B LYS* 3.2 19.1 + - - +
361B LYS* 2.9 47.3 + - + +
362B LEU* 3.8 3.5 + - - +
410B MET* 3.4 20.4 - - - +
411B GLU 4.3 1.0 + - - +
412B PHE* 3.7 15.0 - - + -
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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
------------------------------------------------------------
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