Contacts of the strand formed by residues 450 - 456 (chain A) in PDB entry 5E97
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 LEU 450 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LEU* 3.4 33.7 - - + -
435A LEU* 4.1 9.4 - - + -
436A HIS 3.7 6.3 - - - +
438A THR* 2.9 9.6 + - - -
449A ASP* 1.3 72.8 - - - +
451A THR* 1.3 60.3 + - - +
452A LEU 4.0 0.2 - - - -
470A PHE* 3.9 23.8 - - + -
532A PHE 3.7 0.5 - - - +
533A VAL* 3.3 2.1 - - - -
534A ILE* 2.8 61.0 + - + +
537A ALA* 4.0 3.6 - - + -
539A VAL* 3.8 26.7 - - + -
542A CYS* 3.9 14.8 - - - -
43B PHE* 4.3 10.8 - - + -
45B THR* 4.4 3.1 - - + -
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Residues in contact with THR 451 (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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413A LEU* 2.8 38.2 + - + +
414A VAL* 4.1 22.0 - - + -
434A TYR 4.1 0.2 - - - +
435A LEU* 3.6 5.3 - - - -
436A HIS* 2.9 38.6 + - - -
437A CYS 4.6 0.2 - - - -
438A THR* 2.9 22.4 + - - +
450A LEU* 1.3 71.9 + - - +
452A LEU* 1.3 70.2 - - - +
453A TYR* 4.1 4.0 + - + -
531A PHE* 4.2 7.9 - - + -
532A PHE 3.5 6.3 - - - +
533A VAL* 3.7 9.1 - - + +
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Residues in contact with LEU 452 (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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421A ALA* 4.2 11.0 - - + -
433A VAL* 4.3 10.8 - - + -
434A TYR 3.3 17.3 - - - +
435A LEU* 3.9 10.6 - - + +
450A LEU 4.0 0.8 - - - -
451A THR* 1.3 73.6 - - - +
453A TYR* 1.3 70.6 + - - +
454A ALA* 5.0 1.1 - - + -
464A LEU* 4.6 4.7 - - + -
466A LEU* 4.3 7.6 - - + -
522A LEU* 3.9 24.5 - - + -
531A PHE* 3.2 4.7 - - - +
532A PHE* 2.8 53.5 + - + +
534A ILE* 4.9 5.1 - - + +
41B LEU* 3.8 22.4 - - + -
43B PHE* 4.2 20.0 - - + -
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Residues in contact with TYR 453 (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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366A LEU* 3.6 26.5 - - + -
369A LEU 4.1 0.7 + - - -
370A GLY* 3.3 22.4 - - - -
410A PHE* 3.5 29.5 - + - -
414A VAL* 4.0 18.4 - - + -
432A ARG 4.0 0.2 - - - +
433A VAL* 3.5 1.6 - - - -
434A TYR* 2.9 69.3 + + + +
436A HIS* 2.9 39.6 + + - -
451A THR 4.3 4.9 - - - -
452A LEU* 1.3 78.7 - - - +
454A ALA* 1.3 62.3 + - - +
530A SER 3.2 10.1 - - - +
531A PHE* 3.6 18.6 - + + -
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Residues in contact with ALA 454 (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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366A LEU* 4.5 1.0 - - - +
431A LEU* 5.5 0.2 - - + -
432A ARG 3.2 9.4 - - - +
433A VAL* 4.0 14.8 - - + -
452A LEU* 5.0 2.2 - - + -
453A TYR* 1.3 79.2 - - - +
455A ILE* 1.3 64.0 + - - +
464A LEU* 4.2 11.7 - - + -
524A LEU* 3.6 21.6 - - + +
529A TYR* 3.1 5.9 - - - +
530A SER 2.9 33.6 + - - +
532A PHE* 4.6 8.1 - - + -
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Residues in contact with ILE 455 (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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316A LEU* 5.5 0.4 - - + -
363A PHE* 3.6 34.8 - - + +
366A LEU* 3.9 21.3 - - + -
367A ASP* 3.6 48.2 - - + +
430A LYS 3.4 1.0 - - - +
431A LEU* 3.4 8.5 - - - +
432A ARG* 2.9 40.5 + - + +
434A TYR* 4.6 7.2 - - + -
453A TYR 5.9 0.2 - - - -
454A ALA* 1.3 78.3 - - - +
456A ASN* 1.3 62.3 + - - +
457A LEU* 3.8 20.2 - - + -
524A LEU* 3.9 2.2 - - - -
528A SER 3.6 4.0 - - - -
529A TYR* 4.1 5.4 - - + -
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Residues in contact with ASN 456 (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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363A PHE* 4.2 1.9 - - - -
430A LYS 3.6 1.1 - - - -
431A LEU* 4.1 3.6 - - + -
455A ILE* 1.3 73.4 - - - +
457A LEU* 1.3 60.8 + - - +
458A HIS* 2.8 39.8 + - - +
460A VAL 3.0 21.6 + - - -
462A LYS* 3.6 12.8 - - - +
524A LEU* 2.9 41.7 + - + +
525A PRO 3.1 15.5 + - - +
526A ALA 3.7 0.2 - - - +
527A PHE* 3.0 27.0 + - - -
528A SER 2.9 12.0 + - - +
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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
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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