Contacts of the strand formed by residues 487 - 493 (chain E) in PDB entry 4K4I
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 ARG 487 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382E ASP 4.0 4.4 + - - -
383E PHE* 4.1 6.7 - - - -
385E GLU* 3.9 25.7 + - - +
386E ARG 4.1 2.0 + - - -
387E MET* 3.4 48.7 - - + +
388E PRO* 4.3 3.4 - - - +
391E GLU* 2.6 42.4 + - - +
395E ILE* 4.1 16.6 - - + -
426E GLY 6.0 0.2 - - - -
476E VAL* 3.4 2.1 - - - -
477E CYS* 2.7 41.0 + - - +
478E ARG* 5.8 0.7 - - - -
479E LEU 6.2 0.4 - - - +
485E ARG* 3.7 41.5 - - - +
486E HIS* 1.3 82.9 - - - +
488E ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E TRP* 3.1 24.8 - - + +
383E PHE* 3.7 38.7 - - + -
426E GLY 5.1 3.1 + - - +
427E ASP* 3.4 23.0 + - + +
428E VAL* 3.2 23.9 + - - +
461E LEU* 3.7 23.3 - - - +
474E LEU* 4.1 5.6 - - - +
475E GLY 2.8 36.7 + - - +
476E VAL* 4.6 0.2 - - - +
487E ARG* 1.3 76.0 - - - +
489E LEU* 1.3 71.7 + - - +
490E ASP* 2.8 36.3 + - - -
6G C 2.8 29.5 + - - -
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Residues in contact with LEU 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E ILE* 4.1 13.5 - - + -
399E VAL* 3.9 4.5 - - + -
428E VAL* 3.5 9.2 - - + +
430E VAL* 3.8 21.1 - - + -
456E PHE* 3.9 28.0 - - + -
457E LEU* 4.0 13.2 - - + -
473E TYR* 3.7 4.2 - - + +
474E LEU* 3.6 0.7 - - - -
475E GLY 2.9 37.2 + - - +
476E VAL 5.2 0.2 - - - -
477E CYS* 4.1 17.9 - - + -
487E ARG 3.5 0.8 + - - -
488E ARG* 1.3 76.6 + - - +
490E ASP* 1.3 79.7 + - - +
491E ILE* 3.8 28.7 - - + -
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Residues in contact with ASP 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ASP* 3.4 4.9 - - - +
428E VAL 3.0 9.8 + - - +
429E ASP* 3.2 11.4 - - + +
430E VAL 2.8 28.9 + - - -
472E LYS* 5.6 3.4 - - + -
473E TYR 3.1 4.7 - - - -
474E LEU* 2.9 24.3 - - + +
488E ARG* 2.8 35.7 + - - -
489E LEU* 1.3 80.3 - - - +
491E ILE* 1.3 56.9 + - - +
492E ILE* 5.8 1.1 - - + -
506E PHE* 5.9 3.6 - - + -
603E CA 2.4 31.4 - - - -
6G C 3.7 9.5 - - - +
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Residues in contact with ILE 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E VAL* 4.4 10.5 - - + -
430E VAL* 3.4 7.0 - - + +
432E ILE* 3.8 27.4 - - + -
444E PHE* 3.6 16.6 - - + -
447E LEU* 4.2 8.3 - - + -
448E LEU* 4.0 22.4 - - + -
451E LEU* 4.4 17.5 - - + -
457E LEU* 4.9 1.3 - - + -
472E LYS* 3.5 3.2 - - - +
473E TYR* 2.7 53.4 + - + +
489E LEU* 3.8 29.6 - - + -
490E ASP* 1.3 77.7 - - - +
492E ILE* 1.3 63.5 + - - +
493E VAL* 4.8 0.7 - - + -
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Residues in contact with ILE 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429E ASP 5.9 1.3 - - - -
430E VAL 2.9 18.1 + - - +
431E LEU* 3.2 23.9 - - + +
432E ILE* 2.7 36.0 + - - +
467E ASN* 5.1 1.8 - - - +
470E GLN* 3.4 25.8 - - + +
471E GLN 3.3 13.9 - - - +
472E LYS* 4.0 19.3 - - + -
490E ASP* 5.9 0.9 - - + -
491E ILE* 1.3 75.1 - - - +
493E VAL* 1.3 60.3 + - - +
494E VAL* 3.5 14.8 - - + -
506E PHE* 3.5 40.2 - - + -
529E GLU* 6.3 0.2 - - + -
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Residues in contact with VAL 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432E ILE* 3.3 28.9 - - + +
440E HIS* 3.6 39.5 - - + +
443E ILE* 5.2 6.3 - - + -
444E PHE* 3.5 33.7 - - + -
447E LEU* 5.3 0.9 - - + -
469E GLN 3.8 2.4 - - - +
470E GLN* 3.3 2.3 - - - -
471E GLN* 2.9 49.6 + - - +
491E ILE* 4.8 0.2 - - + -
492E ILE* 1.3 77.4 - - - +
494E VAL* 1.3 66.7 + - - +
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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