Contacts of the strand formed by residues 454 - 462 (chain A) in PDB entry 2ID5
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 GLY 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A PRO* 4.0 5.4 - - - -
452A ASP 3.7 1.0 + - - -
453A ASN* 1.3 78.7 - - - +
455A THR* 1.3 59.5 + - - -
456A TYR* 3.9 6.2 - - - -
471A ALA 3.8 0.5 - - - +
472A HIS* 3.4 0.3 - - - -
473A LEU* 2.8 40.4 + - - -
491A NAG 3.1 22.8 + - - -
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Residues in contact with THR 455 (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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421A SER 4.0 2.1 - - - +
422A PRO* 3.2 24.6 - - - +
454A GLY* 1.3 70.3 - - - -
456A TYR* 1.3 71.6 + - - +
457A LEU* 4.2 4.6 + - + -
470A PRO* 4.0 13.2 - - + -
471A ALA 3.3 5.8 - - - +
472A HIS* 2.8 36.7 + - + +
491A NAG 3.2 7.6 + - - -
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Residues in contact with TYR 456 (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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405A PHE* 4.2 11.7 - + + -
419A TRP* 3.8 17.3 - + + -
420A LEU 3.2 18.8 - - - +
421A SER* 3.8 9.2 - - - -
422A PRO* 3.4 22.6 - - + +
427A VAL* 6.0 1.8 - - + -
435A LEU* 4.1 26.4 - - + +
443A LEU* 3.7 19.7 - - + -
445A VAL* 4.8 2.3 - - + +
452A ASP* 2.8 47.1 + - - +
454A GLY 3.9 8.5 - - - -
455A THR* 1.3 80.0 - - - +
457A LEU* 1.3 61.3 + - - +
470A PRO* 3.5 4.0 - - - +
471A ALA* 2.6 40.8 + - + +
473A LEU* 4.1 16.9 - - + +
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Residues in contact with LEU 457 (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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418A LEU 3.7 0.3 - - - +
419A TRP* 3.2 10.6 - - - -
420A LEU* 2.8 66.2 + - + +
455A THR* 4.2 4.6 + - + -
456A TYR* 1.3 73.3 - - - +
458A CYS* 1.3 61.0 + - - +
459A ILE* 3.8 15.7 + - + +
468A SER* 4.0 20.6 - - - +
469A MET 3.7 9.9 - - - +
470A PRO* 4.2 19.5 - - + -
117D VAL* 4.6 7.2 - - + -
118D ILE* 4.2 6.5 - - + -
141D VAL* 4.1 18.8 - - + -
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Residues in contact with CYS 458 (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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387A ILE* 3.6 8.4 - - + +
393A GLN* 5.6 0.9 - - - +
407A CYS* 2.0 51.8 - - - -
417A ILE* 3.6 17.5 - - - -
418A LEU 3.7 2.2 - - - -
419A TRP* 3.7 22.3 - - + -
457A LEU* 1.3 71.6 - - - +
459A ILE* 1.3 63.4 + - - +
460A ALA 4.1 0.2 - - - -
468A SER* 2.9 8.3 - - - -
469A MET* 2.8 44.6 + - + +
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Residues in contact with ILE 459 (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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416A ALA 3.4 2.4 - - - +
417A ILE* 3.5 1.6 - - - -
418A LEU* 2.7 60.2 + - + +
419A TRP 4.7 0.4 - - - -
420A LEU* 3.7 37.9 - - + +
426A LEU* 4.8 4.3 - - + -
457A LEU* 3.9 20.6 - - + +
458A CYS* 1.3 80.1 - - - +
460A ALA* 1.3 64.2 + - - +
461A ALA* 4.9 0.4 - - + -
467A ASP 3.3 5.2 - - - +
468A SER* 4.4 1.1 - - - -
118D ILE* 3.4 35.0 - - + -
120D LEU* 4.3 18.6 - - + -
142D TYR* 5.2 3.4 - - + -
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Residues in contact with ALA 460 (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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385A ALA* 3.9 10.8 - - + +
387A ILE* 3.7 17.5 - - + +
409A ALA* 3.6 32.1 - - + -
415A PRO* 4.5 1.6 - - + -
416A ALA 3.4 4.5 - - - -
417A ILE* 3.9 8.7 - - + -
459A ILE* 1.3 72.3 - - - +
461A ALA* 1.3 61.1 + - - +
466A ASN* 3.1 5.6 - - - +
467A ASP* 2.7 40.1 + - + +
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Residues in contact with ALA 461 (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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385A ALA* 4.1 3.5 - - - +
416A ALA* 2.9 44.6 + - + +
418A LEU* 5.6 5.6 - - + -
459A ILE* 4.9 2.2 - - + -
460A ALA* 1.3 76.3 - - - +
462A ASN* 1.3 62.9 + - - +
465A GLY 3.6 4.9 - - - -
466A ASN* 3.9 3.6 - - + -
120D LEU* 3.5 30.7 - - + -
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Residues in contact with ASN 462 (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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383A ARG 2.9 24.9 + - - -
385A ALA* 3.2 22.9 + - - +
411A GLY* 3.9 3.2 - - - -
412A ASP 3.6 10.5 + - - +
413A PRO* 3.1 33.0 + - + +
414A PRO 4.9 1.1 - - - +
415A PRO* 4.1 6.3 - - + +
461A ALA* 1.3 75.8 - - - +
463A ALA* 1.3 57.8 + - - +
464A GLY* 2.9 13.6 + - - +
465A GLY* 2.7 34.4 + - - +
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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