Contacts of the strand formed by residues 355 - 359 (chain B) in PDB entry 3D0G
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 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 2.7 32.2 + - + +
326B GLY* 5.7 0.9 - - - -
330B ASN* 4.5 8.8 + - - -
350B ASP* 3.8 2.1 + - - +
351B LEU* 3.0 33.8 + - + +
352B GLY 2.8 17.5 + - - +
353B LYS 4.2 2.7 - - - +
354B GLY* 1.3 74.4 - - - +
356B PHE* 1.3 64.7 + - - +
357B ARG* 2.8 42.8 + - - +
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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
----------------------------------------------------------
324B THR* 4.4 12.3 + - + +
326B GLY 4.3 1.8 - - - -
327B PHE* 3.3 26.0 + - + +
349B TRP 3.5 5.2 - - - +
350B ASP* 3.1 38.6 - - - -
354B GLY* 3.6 30.6 + - - -
355B ASP* 1.3 73.5 + - - +
357B ARG* 1.3 67.9 + - - +
379B ILE* 4.0 18.6 - - + -
382B ASP* 3.7 27.8 - - + -
383B MET* 3.7 45.5 - - + -
386B ALA* 4.4 11.4 - - + -
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Residues in contact with ARG 357 (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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41B TYR* 4.5 2.8 + - - -
45B VAL* 4.9 8.7 - - - +
48B TRP* 3.0 51.3 - - + +
49B ASN* 5.1 0.8 + - - -
327B PHE* 3.8 4.7 - - - +
330B ASN* 3.5 40.3 + - + +
331B SER* 3.1 21.3 - - - +
349B TRP* 2.7 40.1 + - + +
351B LEU* 3.4 29.5 - - + +
355B ASP* 2.8 34.1 + - - -
356B PHE* 1.3 77.8 - - - +
358B ILE* 1.3 59.7 + - - +
379B ILE* 3.4 6.2 - - - +
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Residues in contact with ILE 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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48B TRP* 4.1 2.7 - - - -
308B PHE* 3.9 26.9 - - + -
327B PHE* 3.7 19.7 - - + -
331B SER* 3.0 10.7 + - - -
332B MET 3.1 26.9 + - - +
333B LEU* 4.0 5.5 - - + +
347B THR 3.5 12.6 - - - +
348B ALA* 4.4 2.9 - - - -
357B ARG* 1.3 79.2 - - - +
359B LEU* 1.3 70.4 + - - +
360B MET* 4.0 10.5 - - + -
375B GLU* 3.8 14.4 - - + -
376B MET* 3.6 37.0 - - + +
379B ILE* 3.7 13.2 - - + -
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Residues in contact with LEU 359 (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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48B TRP* 3.7 20.3 - - + -
51B ASN* 3.5 36.3 - - + +
52B THR* 4.0 9.9 - - + -
332B MET* 3.6 32.8 - - + -
342B ALA* 5.1 0.9 - - + -
343B VAL* 3.8 22.7 - - + +
344B CYS* 5.3 0.2 - - - -
345B HIS 4.5 2.0 - - - +
346B PRO* 3.4 2.6 - - - +
347B THR* 2.8 53.6 + - - +
349B TRP* 3.9 7.8 - - + +
358B ILE* 1.3 70.8 - - - +
360B MET* 1.3 69.5 + - - +
361B CYS* 5.2 3.8 - - - -
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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