Contacts of the strand formed by residues 432 - 436 (chain A) in PDB entry 4OE5
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 CYS 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A PHE* 3.5 4.8 - - - -
404A LEU* 3.6 32.5 - - + -
407A ALA* 5.4 0.2 - - - -
415A ILE* 3.8 11.9 - - - -
417A ALA 3.4 11.4 - - - +
419A GLY* 3.8 13.0 - - - +
430A GLU 4.1 2.7 - - - +
431A PRO* 1.3 75.4 - - - +
433A ILE* 1.3 65.5 + - - +
434A VAL* 3.7 24.0 - - - -
451A PRO 2.9 15.3 + - - +
452A VAL* 3.5 4.6 - - - -
453A LEU 2.8 27.0 + - - -
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU* 4.1 21.3 - - + -
341A PHE* 4.0 12.6 - - + -
368A LEU* 4.5 20.4 - - + +
369A LEU* 4.7 4.0 - - + -
372A HIS* 3.8 28.3 - - + -
415A ILE* 3.6 2.6 - - - +
416A LEU* 2.7 53.3 + - + -
417A ALA* 3.0 17.2 + - + +
432A CYS* 1.3 78.8 - - - +
434A VAL* 1.3 58.5 + - - +
453A LEU* 3.4 14.1 - - + +
455A VAL* 4.0 24.5 - - + -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ALA* 3.8 22.4 - - + -
413A LEU* 4.0 25.1 - - + -
414A THR 3.5 12.1 - - - +
415A ILE* 4.3 2.9 - - + -
416A LEU* 4.6 2.0 - - - -
432A CYS* 3.7 21.8 - - - -
433A ILE* 1.3 80.7 - - - +
435A GLU* 1.3 67.0 + - - +
443A ILE* 4.3 18.4 - - + -
452A VAL* 4.4 5.4 - - + -
453A LEU 2.8 14.6 + - - +
454A SER* 3.3 3.9 - - - +
455A VAL* 2.7 34.4 + - - +
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Residues in contact with GLU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A TRP* 3.9 21.8 + - + -
365A LYS* 5.1 3.1 + - - -
412A SER 3.7 1.0 - - - +
413A LEU* 3.3 5.4 - - - -
414A THR* 2.9 43.5 + - - +
416A LEU* 4.0 24.8 - - + +
434A VAL* 1.3 76.1 - - - +
436A SER* 1.3 69.7 + - - +
437A LYS* 4.2 1.4 - - - +
455A VAL* 3.4 14.1 - - + +
457A VAL* 3.3 29.3 + - + +
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Residues in contact with SER 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A SER 3.5 3.5 + - - -
413A LEU* 3.6 15.2 - - - +
434A VAL 4.0 0.8 + - - -
435A GLU* 1.3 80.2 - - - +
437A LYS* 1.3 60.8 + - - +
438A ASP 2.4 33.6 + - - -
441A GLU* 3.5 9.5 - - - +
443A ILE* 4.7 2.0 - - - -
444A MET* 4.1 20.2 - - - -
454A SER* 5.6 0.2 - - - -
455A VAL 2.8 17.5 + - - +
456A TYR* 3.3 19.2 - - - -
457A VAL 4.7 0.7 + - - -
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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