Contacts of the strand formed by residues 449 - 455 (chain B) in PDB entry 2ETM
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 LEU 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B ILE* 3.5 4.9 - - - -
441B TYR* 2.9 52.7 + - + +
443B SER* 3.8 14.4 - - - +
446B ASN* 6.1 0.9 - - + -
447B PRO 3.9 4.7 - - - +
448B ALA* 1.3 76.0 - - - +
450B ALA* 1.3 74.4 + - - +
451B VAL* 3.7 18.8 - - + -
487B ILE* 4.6 15.7 - - + -
500B GLU* 5.6 4.3 - - + -
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Residues in contact with ALA 450 (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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438B GLN 5.1 1.1 - - - +
439B GLY 3.9 10.1 - - - +
440B ILE* 4.3 4.3 - - + +
449B LEU* 1.3 81.5 - - - +
451B VAL* 1.3 65.5 + - - +
500B GLU* 5.2 0.2 - - - +
501B LEU* 3.5 31.5 + - + +
503B THR* 5.2 6.5 - - + -
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Residues in contact with VAL 451 (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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422B ILE* 4.8 0.4 - - + -
438B GLN 3.1 25.8 - - - -
439B GLY 3.2 5.8 + - - +
440B ILE* 3.8 8.3 - - - +
441B TYR* 3.6 30.3 - - + +
449B LEU* 3.7 21.5 - - + -
450B ALA* 1.3 80.1 - - - +
452B ALA* 1.3 58.4 + - - +
453B ILE* 4.2 7.4 - - + +
487B ILE* 3.9 17.5 - - + -
498B ILE* 3.7 18.4 - - + -
499B MET 2.9 20.0 - - - +
500B GLU* 4.2 0.7 - - - -
501B LEU* 3.6 10.0 - - - +
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Residues in contact with ALA 452 (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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132B 7PY 3.3 53.4 - - + +
428B ILE* 4.5 0.9 - - + -
436B VAL* 4.4 3.1 - - + -
437B HIS 3.4 7.4 - - - +
451B VAL* 1.3 74.9 - - - +
453B ILE* 1.3 63.1 + - - +
454B LYS 4.1 0.7 - - - -
498B ILE* 3.5 2.3 - - - +
499B MET* 2.9 33.6 + - + +
500B GLU 4.0 2.7 - - - +
501B LEU* 3.9 8.9 - - + +
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Residues in contact with ILE 453 (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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422B ILE* 3.2 31.6 - - + -
424B LEU* 4.0 11.7 - - + -
435B ASP 3.9 0.5 - - - +
436B VAL* 3.3 4.9 - - - +
437B HIS* 2.7 43.2 + - + +
439B GLY* 3.9 26.9 - - - +
451B VAL* 4.2 10.3 - - + +
452B ALA* 1.3 80.1 - - - +
454B LYS* 1.3 61.8 + - - +
455B THR* 3.7 6.1 + - + +
496B TRP* 4.0 28.7 - - + -
497B ILE 3.7 2.9 - - - -
498B ILE* 3.6 22.7 - - + -
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Residues in contact with LYS 454 (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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132B 7PY 3.8 33.7 + - + +
431B GLY* 4.7 9.9 - - - -
432B GLN 5.8 1.0 - - - +
435B ASP 4.1 2.7 - - - -
436B VAL* 3.5 20.6 - - + +
452B ALA 4.1 0.4 - - - -
453B ILE* 1.3 71.9 - - - +
455B THR* 1.3 61.0 + - - +
468B PHE* 3.6 19.5 - - + -
471B GLU* 2.7 39.9 + - - +
496B TRP* 3.2 9.2 - - - +
497B ILE* 2.9 36.8 + - + +
499B MET* 4.0 13.2 - - + +
564B ASP* 5.4 5.9 + - - +
566B GLY* 5.9 0.4 - - - -
568B SER* 6.3 0.8 - - - -
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Residues in contact with THR 455 (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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424B LEU* 5.9 1.8 - - + -
433B PHE* 3.7 1.8 - - - +
434B GLY* 3.4 19.8 + - - +
435B ASP* 2.5 39.1 + - + +
437B HIS* 4.8 13.9 - - + -
453B ILE* 4.4 8.3 - - + +
454B LYS* 1.3 77.0 - - - +
456B CYS* 1.3 63.0 + - - +
457B LYS* 6.1 0.3 - - - +
468B PHE* 3.9 7.6 - - - -
494B PRO* 6.1 1.3 - - - -
495B VAL 3.9 5.4 - - - -
496B TRP* 3.5 29.2 - - + +
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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