Contacts of the strand formed by residues 452 - 459 (chain A) in PDB entry 4JWE
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 LYS 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A LEU* 3.3 3.3 - - - -
442A GLN* 2.8 48.9 + - - +
451A ASN* 1.3 69.7 - - - +
453A SER* 1.3 73.8 + - - +
454A LEU* 3.5 2.3 + - + -
506A GLY* 3.9 38.4 - - - +
507A LEU* 3.8 30.7 - - + -
515A MET* 4.6 2.8 - - - +
702A SO4 3.4 22.5 + - - +
502B LYS* 5.6 7.7 - - - +
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Residues in contact with SER 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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439A HIS* 2.8 33.1 + - - -
440A VAL 3.7 5.2 - - - -
441A LEU* 4.0 5.4 - - - -
451A ASN 3.6 2.0 + - - -
452A LYS* 1.3 89.0 + - - +
454A LEU* 1.3 60.5 + - - +
455A GLY* 3.8 7.3 + - - -
456A GLN* 5.1 1.4 + - - -
702A SO4 2.5 32.4 + - - -
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Residues in contact with LEU 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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399A LEU* 3.7 30.7 - - + -
440A VAL* 2.9 19.4 + - + +
441A LEU 4.6 0.2 - - - -
442A GLN* 4.0 20.0 - - + +
452A LYS* 4.1 4.3 - - + +
453A SER* 1.3 79.7 - - - +
455A GLY* 1.3 58.8 + - - +
484A LEU* 4.1 17.7 - - + -
499A ILE* 5.1 0.9 - - - +
501A ILE* 4.0 34.8 - - + +
505A SER* 4.2 8.7 + - - -
506A GLY* 3.7 35.4 - - - +
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Residues in contact with GLY 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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439A HIS* 3.6 3.8 - - - -
440A VAL* 2.9 33.2 + - - +
453A SER* 3.6 6.5 + - - -
454A LEU* 1.3 80.7 - - - +
456A GLN* 1.3 62.7 + - - +
499A ILE* 4.2 13.9 - - - -
501A ILE* 5.0 0.7 - - - -
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Residues in contact with GLN 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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437A THR* 3.7 21.4 - - + +
438A ILE 3.1 14.4 - - - +
439A HIS* 3.9 28.1 + - + -
440A VAL 4.7 0.2 - - - +
455A GLY* 1.3 76.1 - - - +
457A PHE* 1.3 70.0 + - - +
458A ASN* 5.1 3.2 + - - +
499A ILE* 4.1 11.5 - - - +
508B ASN* 5.1 7.4 + - - +
14D ARG* 5.2 13.5 - - - +
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Residues in contact with PHE 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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437A THR* 3.6 1.4 - - - +
438A ILE* 2.8 73.0 + - + +
440A VAL* 4.9 0.9 - - + -
456A GLN* 1.3 78.0 - - - +
458A ASN* 1.3 69.3 + - - +
459A LEU* 5.1 0.9 - - + -
486A VAL* 3.8 14.4 - - + -
487A SER 4.1 2.0 - - - -
488A ALA* 3.8 15.7 - - + -
497A GLN* 3.4 54.7 - - + -
498A LYS 4.7 3.1 - - - +
499A ILE* 3.6 38.6 - - + -
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Residues in contact with ASN 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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435A ALA* 5.7 0.9 - - + -
436A VAL 3.4 4.7 - - - +
437A THR* 2.8 31.5 + - - +
456A GLN* 5.1 2.9 + - - +
457A PHE* 1.3 78.8 - - - +
459A LEU* 1.3 60.9 + - - +
460A ASP* 4.2 4.7 - - + +
497A GLN* 3.4 24.4 + - - +
13D PRO* 3.4 26.4 - - + +
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Residues in contact with LEU 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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435A ALA* 3.2 3.0 - - - -
436A VAL* 2.9 42.0 + - + -
438A ILE* 5.2 0.7 - - + -
457A PHE* 4.3 1.8 + - + -
458A ASN* 1.3 73.6 - - - +
460A ASP* 1.4 63.2 + - - +
462A ILE* 3.8 6.3 - - + +
472A ILE* 3.8 27.8 - - + -
488A ALA* 3.9 16.6 - - + +
490A ASP* 3.8 29.4 - - + +
495A LYS* 3.5 37.7 - - + +
496A GLU* 3.7 17.9 - - - +
497A GLN* 3.8 8.1 - - + +
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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