Contacts of the strand formed by residues 454 - 459 (chain A) in PDB entry 4A8W
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 454 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A THR 4.7 3.8 - - - +
410A TYR* 4.3 0.2 - - - -
450A SER* 3.7 0.9 - - - -
451A LYS 2.9 36.1 + - - +
452A SER 4.1 0.5 - - - +
453A ASP* 1.3 81.9 + - - +
455A ALA* 1.3 72.7 + - - +
491A GLU* 4.2 6.7 - - - +
495A ALA 3.3 19.3 - - - +
496A PHE* 3.4 13.1 - - - -
497A LEU* 2.7 42.6 + - + +
498A GLY 4.6 0.7 + - - -
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Residues in contact with ALA 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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322A ALA* 3.8 1.4 - - - +
323A THR* 3.4 31.6 + - - +
410A TYR* 3.3 37.7 - - + -
449A ILE 3.3 13.2 - - - +
450A SER* 3.7 4.0 - - - -
453A ASP 4.2 1.2 + - - -
454A ASP* 1.3 83.1 + - - +
456A MET* 1.3 70.8 + - - +
457A LEU* 4.5 5.2 - - + -
491A GLU* 5.5 0.2 - - - +
495A ALA 4.9 0.7 - - - +
496A PHE* 3.8 5.4 - - - -
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Residues in contact with MET 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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314A VAL* 4.7 1.8 - - - -
317A TRP* 3.4 5.5 - - + -
320A CYS* 3.7 26.0 - - - -
321A VAL 3.4 3.1 - - - -
322A ALA* 3.8 18.6 - - + -
448A GLN* 3.4 4.7 - - - +
449A ILE* 3.0 44.7 + - + +
455A ALA* 1.3 79.2 - - - +
457A LEU* 1.3 61.4 + - - +
494A GLY* 3.9 0.9 - - - -
495A ALA 3.7 35.9 - - - +
496A PHE* 3.9 11.0 - - + +
501A LEU* 3.8 26.0 - - + -
514A PHE* 3.6 24.7 - - + -
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Residues in contact with LEU 457 (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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317A TRP* 3.6 2.5 - - - -
320A CYS* 3.4 3.8 - - - -
321A VAL* 2.8 46.9 + - + +
323A THR* 3.9 23.6 - - + +
410A TYR* 3.4 51.1 - - + +
413A MET* 4.6 11.7 - - + -
414A GLN* 3.9 13.0 - - + +
447A ARG 3.7 2.9 - - - +
448A GLN* 3.8 17.9 - - + -
455A ALA* 4.5 3.8 - - + -
456A MET* 1.3 75.0 - - - +
458A GLY* 1.3 58.7 + - - +
459A TRP* 3.3 24.9 - - + -
471A LEU* 5.2 2.9 - - + -
475A LEU* 6.3 0.2 - - + -
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Residues in contact with GLY 458 (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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317A TRP* 3.3 25.4 - - - -
319A LEU 3.3 8.1 - - - -
414A GLN* 3.3 8.3 + - - -
445A GLU 4.6 0.2 - - - -
446A ILE* 3.5 1.6 - - - -
447A ARG* 2.7 44.1 + - - -
457A LEU* 1.3 74.5 - - - +
459A TRP* 1.3 64.5 + - - -
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Residues in contact with TRP 459 (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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317A TRP* 3.7 2.4 - - - +
318A SER* 2.8 32.1 + - - -
319A LEU* 3.2 25.2 + - + -
321A VAL* 3.6 22.9 - - + -
414A GLN* 3.7 21.5 - - + -
418A THR* 3.0 40.0 + - + +
445A GLU 3.4 5.4 - - - -
446A ILE* 3.5 17.5 - - + +
457A LEU* 3.3 37.9 - - + -
458A GLY* 1.3 75.2 - - - -
460A THR* 1.3 59.7 + - - +
464A ALA* 3.4 24.5 - - + -
465A LEU* 3.7 20.2 - - + -
468A GLY* 3.6 13.9 - - - -
471A LEU* 3.9 17.9 - - + -
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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