Contacts of the strand formed by residues 492 - 498 (chain A) in PDB entry 6KC4
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 TYR 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A LEU* 3.6 21.3 - - + +
461A TYR* 4.1 24.0 + + - -
482A VAL* 4.4 4.5 - - + -
483A ARG 3.5 12.3 - - - -
484A GLU* 4.7 6.7 - - + -
490A GLY 4.5 2.9 - - - -
491A GLU* 1.3 79.2 + - - +
493A VAL* 1.3 62.1 - - - +
506A ILE* 3.5 7.4 - - - +
507A ILE* 2.9 40.4 + - + +
514A TYR* 4.4 18.8 - + - -
524A ILE* 3.4 30.7 - - + -
464E ALA 3.7 2.9 + - - -
466E PRO* 3.5 20.9 - - + +
486E HIS* 3.0 44.4 + + - -
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Residues in contact with VAL 493 (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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481A LEU 3.9 0.2 - - - +
482A VAL* 3.2 7.1 - - - +
483A ARG* 2.8 56.0 + - + +
485A SER* 3.6 34.1 - - - +
492A TYR* 1.3 80.4 - - - +
494A LEU* 1.3 67.0 - - - +
495A SER* 3.6 20.3 + - - +
504A HIS* 3.9 5.2 - - + -
505A PHE 3.3 10.1 - - - +
506A ILE* 4.1 2.7 - - + -
507A ILE* 4.2 4.3 - - - -
3B PTR 3.7 25.4 - - + +
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Residues in contact with LEU 494 (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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480A PHE* 4.0 27.6 - - + -
481A LEU 3.6 14.8 - - - +
482A VAL* 4.0 13.2 - - + -
493A VAL* 1.3 70.9 - - - +
495A SER* 1.3 60.0 + - - +
496A VAL* 3.7 12.3 - - + -
504A HIS* 3.6 1.0 - - - -
505A PHE* 2.8 45.3 + - + +
507A ILE* 4.0 7.3 - - + +
516A PHE* 3.5 36.1 - - + -
528A ILE* 4.1 8.7 - - + -
538A ILE* 3.6 33.2 - - + -
546A LEU* 4.1 4.0 - - + -
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Residues in contact with SER 495 (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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470A ALA* 4.6 0.9 - - - -
474A LEU* 3.5 22.0 - - - +
480A PHE* 3.2 4.0 - - - -
481A LEU* 2.9 44.6 + - - -
483A ARG* 3.0 21.9 + - - +
493A VAL* 3.6 4.2 - - - +
494A LEU* 1.3 70.0 - - - +
496A VAL* 1.3 62.1 + - - +
503A ARG 3.4 5.2 - - - -
504A HIS* 2.8 27.6 + - - -
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Residues in contact with VAL 496 (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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474A LEU* 4.3 5.8 - - - -
478A GLY* 4.3 8.7 - - - -
479A ASP 3.1 14.8 - - - +
480A PHE* 3.9 3.8 - - + -
494A LEU* 3.7 25.1 - - + -
495A SER* 1.3 79.5 - - - +
497A TYR* 1.3 74.4 + - - +
498A SER* 4.0 1.5 + - - -
501A GLN 3.7 0.3 - - - +
502A ARG* 3.3 5.5 - - - +
503A ARG* 2.8 37.2 + - + +
505A PHE* 4.5 9.4 - - + -
544A VAL* 3.6 28.9 - - + -
545A VAL 4.9 0.2 - - - +
546A LEU* 3.8 16.8 - - + -
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Residues in contact with TYR 497 (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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474A LEU* 3.3 24.8 - - + +
475A LYS 3.4 20.4 - - - +
476A LYS* 3.4 35.9 - - - +
477A GLN* 3.7 4.7 - - - -
478A GLY 2.8 28.6 + - - -
479A ASP* 3.0 8.9 + - + -
496A VAL* 1.3 73.8 - - - +
498A SER* 1.3 66.7 + - - +
500A GLY* 3.4 37.1 + - - -
501A GLN 3.4 13.7 - - - -
502A ARG* 3.8 29.7 + - + -
521I PHE* 3.8 11.6 - - - -
526I GLN* 3.3 17.1 + - - +
530I HIS* 5.2 6.2 - - + +
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Residues in contact with SER 498 (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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477A GLN* 3.5 17.6 + - - -
478A GLY 5.2 0.7 - - - -
496A VAL* 4.0 1.3 - - - -
497A TYR* 1.3 77.3 - - - +
499A ASP* 1.3 80.0 + - - +
500A GLY 3.2 2.0 - - - -
501A GLN* 2.8 25.8 + - - +
503A ARG* 4.1 14.5 + - - -
542A SER 5.2 0.9 + - - -
543A GLY 5.7 0.2 - - - -
544A VAL* 3.7 38.9 - - - +
545A VAL 5.5 0.2 + - - -
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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