Contacts of the strand formed by residues 419 - 424 (chain A) in PDB entry 2ADS
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A LEU* 4.6 9.0 - - + -
353A SER 3.5 5.3 + - - +
354A VAL* 4.1 25.8 - - + -
355A GLU* 2.9 24.5 + - - +
387A LEU* 4.1 6.3 - - + -
417A VAL* 4.4 0.2 - - - +
418A ASP* 1.3 77.6 + - - +
420A VAL* 1.3 72.5 + - - +
421A ILE* 3.9 24.5 - - + -
452A PRO* 3.9 23.3 - - + +
454A GLN* 4.2 15.0 - - + +
477A VAL* 3.6 36.3 - - + +
480A LYS* 5.7 0.4 - - + -
481A THR* 4.3 11.7 - - + -
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Residues in contact with VAL 420 (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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355A GLU* 3.5 5.4 - - + -
357A ILE* 3.8 8.3 - - + -
413A LYS* 3.5 36.8 - - + +
417A VAL* 4.2 10.5 - - + -
419A LEU* 1.3 81.2 - - - +
421A ILE* 1.3 62.7 + - - +
422A VAL* 3.8 9.1 - - + +
446A LEU* 4.3 4.9 - - + -
451A ILE* 3.5 42.2 - - + -
452A PRO 3.3 12.9 + - - +
453A SER 4.2 0.2 - - - -
454A GLN* 3.2 26.2 + - - +
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Residues in contact with ILE 421 (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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354A VAL* 3.4 28.5 - - + -
355A GLU 3.0 11.9 + - - +
356A ILE* 4.5 6.1 - - + -
357A ILE* 3.0 24.4 + - - +
373A LEU* 4.5 14.1 - - + -
376A LEU* 4.4 20.0 - - + -
387A LEU* 4.6 4.9 - - + -
419A LEU* 3.9 18.4 - - + -
420A VAL* 1.3 72.3 - - - +
422A VAL* 1.3 69.1 + - - +
423A PHE* 3.6 34.1 - - + -
454A GLN* 3.5 11.2 - - + -
456A ILE* 3.8 16.6 - - + -
477A VAL* 5.3 0.7 - - + -
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Residues in contact with VAL 422 (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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357A ILE* 3.6 25.8 - - + +
359A VAL* 5.4 0.4 - - + -
406A LYS* 6.0 1.3 - - + -
410A VAL* 6.2 2.0 - - + -
413A LYS* 4.2 6.1 - - - +
420A VAL* 3.8 24.9 - - + +
421A ILE* 1.3 80.5 - - - +
423A PHE* 1.3 58.3 - - - +
424A LEU* 3.0 34.5 + - + +
442A VAL* 4.4 13.9 - - + -
446A LEU* 4.4 12.6 - - + -
454A GLN 3.0 11.1 + - - +
455A VAL* 4.4 6.7 - - + -
456A ILE* 3.0 24.2 + - - -
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Residues in contact with PHE 423 (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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356A ILE* 3.8 25.4 - - + -
357A ILE 3.5 4.8 + - - -
358A SER* 3.6 17.2 - - - -
359A VAL* 3.0 28.4 + - - +
369A LYS* 4.5 24.5 - - + -
372A PHE* 3.9 26.5 - + - -
373A LEU* 4.5 23.8 - - + -
376A LEU* 5.2 1.8 - - + -
421A ILE* 3.6 20.2 - - + -
422A VAL* 1.3 70.9 - - - +
424A LEU* 1.3 60.6 + - - +
456A ILE* 3.5 32.5 - - + -
458A ASN* 3.5 26.3 + - - +
461A LEU* 5.5 1.3 - - + -
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Residues in contact with LEU 424 (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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359A VAL* 3.9 10.1 - - + -
406A LYS* 3.3 29.2 - - - +
422A VAL* 3.5 28.9 - - + +
423A PHE* 1.3 69.8 - - - +
425A GLU* 1.3 57.4 + - - +
429A LYS* 4.7 5.8 - - - +
435A SER 5.5 0.4 - - - +
438A LEU* 4.3 3.8 - - + +
439A TYR* 4.1 22.9 - - - +
442A VAL* 4.2 12.1 - - + -
455A VAL* 3.4 26.2 - - + -
456A ILE 2.9 6.0 + - - +
457A LEU* 3.5 19.8 - - + +
458A ASN* 2.8 34.7 + - - -
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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