Contacts of the strand formed by residues 492 - 497 (chain E) in PDB entry 6T8G
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438E THR* 4.6 12.3 - - - +
439E VAL* 4.8 8.7 - - + -
483E ILE* 5.0 6.1 - - + -
487E SER* 4.3 20.6 - - - +
488E THR 2.8 8.5 + - - +
489E PRO* 3.3 5.7 - - - +
490E SER 3.7 0.2 - - - -
491E GLU* 1.3 78.5 - - + +
493E ARG* 1.3 66.9 + - - +
494E LEU* 6.3 0.4 - - + -
512E HIS* 3.1 22.7 - - - -
588E PRO* 4.6 0.6 - - - +
589E THR* 3.3 17.9 - - - +
591E VAL* 6.2 0.9 - - + -
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Residues in contact with ARG 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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489E PRO* 2.7 40.2 + - - +
490E SER* 4.0 2.6 - - - +
492E ALA* 1.3 75.3 - - - +
494E LEU* 1.3 63.9 + - - +
511E PRO 3.3 15.4 + - - -
512E HIS* 3.3 18.8 - - - +
513E LEU 3.0 29.2 + - - +
514E LEU* 3.6 24.5 - - + -
588E PRO* 4.4 14.2 - - + +
589E THR 2.8 16.1 + - - +
590E ILE* 3.3 28.9 - - + +
591E VAL 3.3 3.8 + - - -
715E ASP* 2.8 32.3 + - - +
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Residues in contact with LEU 494 (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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480E LEU* 3.9 19.3 - - + -
483E ILE* 4.8 18.2 - - + -
484E LEU* 5.0 11.0 - - + -
492E ALA* 6.3 0.2 - - + -
493E ARG* 1.3 75.7 - - - +
495E ILE* 1.3 71.7 + - - +
496E MET* 3.8 26.9 - - + -
510E ILE* 4.4 13.2 - - + -
512E HIS* 2.4 33.1 + - + +
513E LEU* 3.3 29.8 - - + +
514E LEU* 3.4 4.5 + - - +
590E ILE* 5.2 0.7 - - - -
591E VAL* 3.5 36.1 - - + +
593E VAL* 4.9 1.1 - - + -
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Residues in contact with ILE 495 (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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494E LEU* 1.3 80.5 - - - +
496E MET* 1.3 57.6 + - - +
497E ILE* 4.1 22.9 - - + -
513E LEU* 4.5 2.5 - - - -
514E LEU* 3.9 20.2 - - + -
515E CYS* 4.0 20.6 - - - -
518E VAL* 5.1 0.4 - - + -
527E ALA* 4.7 9.2 - - + +
530E TRP* 3.7 31.4 - - + -
531E SER* 4.9 3.1 - - - +
590E ILE* 4.4 10.8 - - + -
591E VAL 3.4 5.7 + - - +
592E VAL* 3.5 16.6 - - + +
593E VAL* 2.8 33.3 + - - +
720E ILE* 3.8 13.2 - - + -
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Residues in contact with MET 496 (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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480E LEU* 3.8 19.5 - - + -
494E LEU* 3.8 26.5 - - + -
495E ILE* 1.3 75.5 - - - +
497E ILE* 1.3 63.8 + - - +
498E ASP 4.1 0.7 - - - -
504E LEU* 4.3 19.5 - - + +
507E TYR* 3.6 51.6 - - + -
510E ILE* 4.3 5.6 - - + -
513E LEU* 4.6 15.0 - - + +
515E CYS* 5.3 1.6 - - - -
516E PRO 4.4 1.4 + - - +
517E VAL* 3.9 19.4 - - + -
518E VAL* 3.2 24.8 + - - +
593E VAL* 3.4 17.3 - - + +
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Residues in contact with ILE 497 (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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495E ILE* 4.1 11.7 - - + +
496E MET* 1.3 78.3 - - - +
498E ASP* 1.3 63.4 + - - +
499E PRO* 4.1 1.0 - - - +
504E LEU* 5.1 0.7 - - - +
518E VAL* 3.8 16.4 - - + -
524E ALA* 4.2 12.6 - - + +
527E ALA* 3.9 22.0 - - + -
528E LEU* 4.7 11.9 - - + -
592E VAL* 3.9 16.2 - - + -
593E VAL* 2.6 14.1 + - - +
594E VAL* 3.3 24.7 - - + +
595E ASP* 3.2 23.9 + - - +
600E MET* 3.6 33.4 - - + -
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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