Contacts of the strand formed by residues 432 - 436 (chain B) in PDB entry 2O8C
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 PHE 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B LYS* 3.3 5.3 - - - +
429B VAL* 2.7 37.1 + - - +
430B GLY 3.2 0.8 - - - -
431B LYS* 1.3 94.7 - - + +
433B TYR* 1.3 61.2 + - - +
434B GLU* 3.9 3.1 + - - +
461B PHE* 3.5 7.0 - - - +
462B PRO* 3.6 20.4 - - + -
7E C 4.0 10.1 - + - -
8E 6OG 3.3 15.5 - + - -
23F T 3.2 75.4 - + + +
24F G 3.4 48.5 - + - -
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Residues in contact with TYR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B CYS* 3.7 27.4 - - + -
427B TYR 3.6 2.0 - - - -
428B LYS* 3.1 35.9 + - + -
432B PHE* 1.3 73.7 - - - +
434B GLU* 1.3 60.4 + - - +
460B GLY* 3.2 2.3 - - - -
461B PHE* 2.7 56.7 + + + +
463B GLU* 3.6 32.5 - - + -
466B PHE* 3.8 25.6 - + + +
482B ARG* 3.8 22.4 - - + -
483B VAL 4.4 0.2 - - - -
484B GLU* 2.1 34.7 + - - -
527B LEU* 5.0 1.4 - - + +
844B MET* 3.4 9.2 - - - +
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE 3.2 5.2 - - - +
427B TYR* 2.7 42.6 + - - +
429B VAL* 3.6 24.5 - - + +
432B PHE* 4.3 4.9 - - + +
433B TYR* 1.3 78.6 - - - +
435B LEU* 1.3 64.1 + - - +
436B TYR* 2.7 39.3 + - + +
458B HIS* 2.8 25.8 + - - +
459B SER 3.8 6.1 - - - +
22F G 4.3 5.4 + - - +
23F T 3.1 39.2 + - - +
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Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 3.9 20.9 - - + -
425B ILE 3.2 26.5 - - - +
426B CYS* 4.0 15.7 - - - -
434B GLU* 1.3 75.8 - - - +
436B TYR* 1.3 65.2 + - - +
439B ASP* 3.7 27.8 - - + +
440B ALA* 3.3 16.8 - - - +
443B GLY* 3.7 20.6 - - - +
447B LEU* 4.6 6.7 - - + -
449B LEU* 4.3 12.8 - - + -
458B HIS* 4.0 0.2 - - - -
459B SER* 2.7 28.5 + - - +
461B PHE* 4.5 14.1 - - + -
473B LEU* 5.0 2.0 - - + -
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Residues in contact with TYR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLY 5.6 0.2 - - - -
410B MET* 3.7 20.8 - - + +
413B TRP* 3.3 48.4 - + + +
427B TYR* 3.5 27.5 - + + -
429B VAL* 3.4 17.5 - - - +
434B GLU* 2.7 38.1 + - + -
435B LEU* 1.3 76.3 - - - +
437B HIS* 1.3 83.0 + - + +
438B MET 3.1 1.4 + - - -
439B ASP* 2.9 19.8 + - - +
440B ALA 3.9 0.4 - - - -
456B TRP* 3.4 21.9 - + + -
457B ALA 3.9 0.7 - - - -
458B HIS* 3.2 20.8 + + - -
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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
------------------------------------------------------------
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