Contacts of the strand formed by residues 494 - 501 (chain B) in PDB entry 3B2T
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 GLN 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486B PRO* 4.9 13.8 - - + +
493B GLY* 1.3 75.7 - - - +
495B VAL* 1.3 65.8 + - - +
496B VAL* 4.3 14.8 - - + +
516B VAL 3.6 1.4 - - - +
517B LYS* 3.5 3.3 - - - +
518B MET* 2.9 67.0 + - + +
519B LEU 4.5 3.2 - - - +
520B LYS* 4.1 23.2 - - + +
1996B M33 5.7 0.4 - - - -
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B PRO* 3.6 1.9 - - - +
487B LEU* 2.7 41.6 + - + -
493B GLY 5.8 0.4 - - - -
494B GLN* 1.3 78.6 - - - +
496B VAL* 1.3 69.0 + - - +
515B ALA* 4.0 13.0 - - + -
516B VAL 3.3 11.9 - - - +
517B LYS* 4.0 21.1 - - + +
564B VAL* 5.8 1.8 - - + -
1996B M33 3.5 64.9 - - + +
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 4.0 16.6 - - + -
484B GLY 3.9 10.3 - - - +
485B LYS 3.5 9.6 - - - +
486B PRO* 3.6 22.2 - - + -
487B LEU* 4.0 5.8 - - - +
494B GLN* 4.3 19.5 - - - +
495B VAL* 1.3 81.4 - - - +
497B MET* 1.3 72.9 + - - +
515B ALA* 3.4 2.1 - - - -
516B VAL* 2.8 34.3 + - + +
518B MET* 3.7 26.0 - - + -
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Residues in contact with MET 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B GLY* 2.7 31.6 + - - -
485B LYS* 2.8 46.5 + - + +
487B LEU* 3.4 22.3 - - + +
496B VAL* 1.3 78.8 - - - +
498B ALA* 1.3 54.1 + - - +
499B GLU* 5.0 5.4 - - - +
513B THR* 3.9 22.0 - - + -
514B VAL 3.5 6.3 - - - +
566B TYR* 3.8 34.3 - - + -
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LEU* 4.1 6.1 - - + -
482B THR 3.2 16.4 - - - +
483B LEU* 4.0 8.1 - - + -
484B GLY* 4.0 2.0 - - - +
497B MET* 1.3 78.9 - - - +
499B GLU* 1.3 72.8 + - - +
513B THR* 3.5 0.7 - - - +
514B VAL* 2.9 36.7 + - + +
516B VAL* 3.6 28.3 - - + -
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Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LYS 3.6 2.1 - - - +
481B LEU* 3.5 5.2 - - - +
482B THR* 2.9 44.0 + - + +
497B MET* 5.0 4.9 - - - +
498B ALA* 1.3 83.3 - - - +
500B ALA* 1.3 59.9 + - - +
501B VAL* 4.1 2.4 - - + +
511B ALA* 3.8 22.6 - - + +
512B VAL 3.5 15.9 - - - +
513B THR* 2.9 25.7 + - - +
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Residues in contact with ALA 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B PHE* 3.8 17.5 - - + -
480B LYS 3.5 5.2 - - - -
481B LEU* 3.9 13.5 - - + -
498B ALA 4.1 0.2 - - - -
499B GLU* 1.3 73.2 - - - +
501B VAL* 1.3 64.8 + - - +
502B GLY 3.5 2.1 + - - -
503B ILE* 3.8 31.3 - - + +
510B GLU 3.7 0.5 - - - +
512B VAL 2.9 31.6 + - - +
514B VAL* 4.1 8.1 - - + -
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Residues in contact with VAL 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B PHE* 3.4 14.6 - - - -
480B LYS* 2.9 48.4 + - + +
482B THR* 6.1 0.7 - - - +
499B GLU* 5.3 2.2 - - + +
500B ALA* 1.3 71.0 - - - +
502B GLY* 1.3 64.0 + - - +
503B ILE 3.3 0.2 - - - -
508B PRO 3.8 11.2 - - - +
509B LYS* 3.7 23.8 - - - +
510B GLU 3.7 3.8 - - - -
511B ALA* 3.8 20.0 - - + +
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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