Contacts of the strand formed by residues 492 - 496 (chain D) in PDB entry 6T8B
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 ALA 492 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D THR* 4.5 5.4 - - + +
439D VAL* 5.0 7.0 - - + -
483D ILE* 4.7 16.4 - - + -
487D SER* 4.0 22.9 - - - +
488D THR 3.5 4.0 + - - +
489D PRO* 3.1 11.2 + - - +
491D GLU* 1.3 79.0 - - - +
493D ARG* 1.3 65.6 + - - +
512D HIS* 3.0 25.5 - - + +
588D PRO* 3.7 0.6 - - - +
589D THR 3.5 9.9 - - - +
591D VAL* 6.1 1.3 - - + -
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Residues in contact with ARG 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D PRO 3.7 10.9 + - - -
492D ALA* 1.3 89.4 - - - +
494D LEU* 1.3 72.3 + - - +
511D PRO 4.5 4.0 - - - -
512D HIS* 3.3 28.4 - - - +
513D LEU 4.1 3.2 - - - +
514D LEU* 3.3 51.9 - - + +
588D PRO* 3.7 27.0 - - + +
589D THR 2.7 13.0 + - - +
590D ILE* 4.3 3.4 - - + -
591D VAL* 3.2 22.2 + - - +
715D ASP* 3.1 41.5 + - - +
717D ILE* 5.3 5.1 - - - +
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Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D LEU* 4.2 28.3 - - + +
483D ILE* 4.8 13.0 - - + -
484D LEU* 5.6 3.4 - - + -
493D ARG* 1.3 83.9 - - - +
495D ILE* 1.3 72.4 + - - +
496D MET* 4.9 9.2 - - + -
507D TYR* 6.1 4.9 - - + -
510D ILE* 5.2 4.5 - - + -
512D HIS* 2.9 38.3 + - + +
513D LEU* 3.8 17.2 - - + -
514D LEU* 3.1 23.6 + - - +
515D CYS 4.2 0.2 + - - -
591D VAL* 3.5 34.1 - - + +
593D VAL* 4.8 2.7 - - + -
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Residues in contact with ILE 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D LEU* 1.3 81.9 - - - +
496D MET* 1.3 62.8 + - - +
497D ILE* 3.9 26.2 - - + -
513D LEU* 5.1 1.6 - - - -
514D LEU* 3.8 23.3 - - + -
515D CYS* 3.6 28.9 - - - -
527D ALA* 5.0 7.0 - - + +
530D TRP* 4.0 22.7 - - + -
531D SER* 5.1 5.6 - - - -
590D ILE* 4.0 4.5 - - + -
591D VAL 3.3 5.7 + - - -
592D VAL* 3.5 28.8 - - + +
593D VAL* 3.0 28.4 + - - +
720D ILE* 5.3 2.2 - - + -
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Residues in contact with MET 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D LEU* 4.6 7.9 - - - -
494D LEU* 4.9 8.1 - - + -
495D ILE* 1.3 74.6 - - - +
497D ILE* 1.3 64.2 + - - +
498D ASP 4.1 0.7 - - - -
504D LEU* 3.8 28.5 - - + +
507D TYR* 3.2 53.2 - - + +
513D LEU* 3.5 29.9 - - + +
515D CYS* 4.9 2.8 + - - -
516D PRO 4.1 1.0 - - - +
517D VAL* 3.6 20.1 - - + +
518D VAL* 2.9 25.6 + - - +
593D VAL* 3.5 22.2 - - + -
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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