Contacts of the strand formed by residues 357 - 362 (chain E) in PDB entry 6O81
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 ARG 357 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A HIS* 3.6 35.4 + - - -
357A GLU* 6.0 1.6 - - - -
331E ASP 3.7 2.8 + - - +
332E VAL* 3.5 36.8 - - + +
333E ILE 3.2 20.4 + - - -
356E PHE* 1.3 77.0 - - - +
358E VAL* 1.3 64.8 + - - +
359E VAL* 3.8 24.5 - - - +
382E PRO* 3.3 26.2 - - + +
383E ALA 6.1 0.4 - - - -
384E SER* 4.7 10.5 - - - -
394E VAL* 5.9 1.2 - - - +
397E GLU* 4.7 10.9 + - - +
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Residues in contact with VAL 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ILE* 3.3 14.8 - - + +
335E VAL* 3.8 32.3 - - + -
346E LEU* 3.8 14.1 - - + -
356E PHE* 3.7 28.7 - - + -
357E ARG* 1.3 78.9 - - - +
359E VAL* 1.3 63.7 + - - +
360E VAL* 3.9 0.3 + - - +
376E LEU* 3.7 22.7 - - + -
381E VAL* 3.8 14.1 - - + -
382E PRO 3.1 6.8 + - - +
383E ALA* 3.3 4.3 - - - +
384E SER* 2.8 26.5 + - - +
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Residues in contact with VAL 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E VAL* 3.8 15.7 - - + -
333E ILE 2.7 12.5 + - - +
334E LEU* 3.4 9.7 - - + +
335E VAL* 3.0 27.2 + - - +
357E ARG* 3.8 25.4 - - - +
358E VAL* 1.3 72.7 - - - +
360E VAL* 1.3 67.8 + - - +
361E VAL* 3.8 8.5 + - + -
384E SER* 3.3 18.4 - - - +
386E LEU* 4.6 6.1 - - + -
394E VAL* 3.8 41.7 - - + -
398E VAL* 4.6 0.9 - - + -
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Residues in contact with VAL 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E VAL* 3.8 15.5 - - + -
337E GLY 5.5 0.9 - - - +
358E VAL 4.6 2.7 - - - +
359E VAL* 1.3 73.7 - - - +
361E VAL* 1.3 67.6 + - - +
369E GLY* 4.1 20.4 - - - +
372E THR* 4.6 5.4 - - + -
373E LEU* 3.8 19.3 - - + -
376E LEU* 3.7 29.8 - - + -
383E ALA* 4.7 0.4 - - + -
384E SER 2.5 19.6 + - - +
385E TYR* 3.5 23.7 - - + -
386E LEU* 2.6 36.0 + - - +
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Residues in contact with VAL 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E LEU* 3.8 35.2 - - + -
335E VAL 3.1 12.5 + - - +
336E TYR* 3.2 28.9 - - + -
337E GLY 3.5 4.3 + - - -
359E VAL* 4.4 7.6 - - + -
360E VAL* 1.3 80.9 - - - +
362E ASP* 1.3 62.6 + - - +
386E LEU* 3.4 4.3 - - + +
387E LEU 3.3 25.6 - - - +
388E ILE* 3.7 23.8 - - + -
391E ALA* 4.2 15.0 - - + -
394E VAL* 4.9 1.1 - - + -
423E LEU* 4.6 3.8 - - + -
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Residues in contact with ASP 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ALA* 6.1 0.2 - - - +
336E TYR* 4.2 3.8 - - - -
337E GLY* 4.9 3.6 - - - -
361E VAL* 1.3 75.2 - - - +
363E SER* 1.3 71.1 + - - +
367E LEU* 3.3 25.7 - - - +
368E GLU* 3.9 5.7 + - - +
369E GLY* 3.0 30.2 + - - -
370E ARG* 3.6 2.8 + - - -
385E TYR* 2.7 42.8 + - + +
386E LEU 3.2 5.5 + - - -
387E LEU* 3.3 10.5 - - + +
388E ILE* 3.0 28.9 + - - +
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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