Contacts of the strand formed by residues 474 - 479 (chain A) in PDB entry 3DLX
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 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A HIS* 4.1 2.5 - - + -
469A ILE 3.7 1.4 - - - +
471A THR* 2.8 44.0 + - - +
472A GLU 3.9 0.2 - - - -
473A LYS* 1.3 75.5 - - - +
475A VAL* 1.3 62.4 + - - +
476A PHE* 3.8 20.6 - - + -
486A LEU* 3.1 30.3 - - + -
488A GLU 3.4 4.9 - - - -
498A VAL* 4.1 11.0 - - + -
515A MET* 4.6 1.3 - - - -
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Residues in contact with VAL 475 (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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308A ARG* 3.7 40.4 - - + +
468A ARG* 3.8 31.2 - - + -
469A ILE 3.3 4.3 - - - +
470A ILE* 4.4 7.2 - - + -
474A ALA* 1.3 77.7 - - - +
476A PHE* 1.3 63.4 + - - +
486A LEU* 3.7 3.3 - - - +
487A ILE* 2.9 43.2 + - + +
488A GLU* 3.0 29.6 + - + +
515A MET* 4.1 7.2 - - + -
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Residues in contact with PHE 476 (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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443A HIS* 3.7 9.6 - + - -
452A ILE* 3.7 33.9 - - + -
468A ARG* 3.3 9.2 - - - +
469A ILE* 2.9 49.2 + - + +
471A THR* 5.2 0.7 - - + -
474A ALA* 3.8 6.7 - - + -
475A VAL* 1.3 76.8 - - - +
477A ASP* 1.3 67.2 + - - +
484A LEU* 4.1 22.7 - - + -
485A THR 3.1 7.9 - - - +
486A LEU* 3.6 37.7 - - + -
487A ILE* 4.9 0.2 - - - -
498A VAL* 3.7 23.8 - - + -
502A THR* 4.0 9.4 - - + -
506A PHE* 3.9 22.2 - + + -
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Residues in contact with ASP 477 (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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467A ASN 3.7 6.7 - - - +
468A ARG* 2.8 35.1 + - - -
476A PHE* 1.3 74.1 - - - +
478A VAL* 1.3 60.4 + - - +
483A GLY 3.8 0.7 - - - +
484A LEU* 3.4 5.0 - - - -
485A THR* 2.9 36.8 + - - +
487A ILE* 3.0 34.6 - - + +
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Residues in contact with VAL 478 (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 SER 4.5 1.1 - - - +
406A LYS 4.0 9.6 - - - +
407A TYR 3.8 6.1 - - - +
408A GLY* 3.6 28.9 - - - +
466A VAL* 3.2 26.1 - - + +
467A ASN* 2.9 32.1 + - - +
468A ARG* 4.0 2.2 - - - +
469A ILE* 3.7 30.5 - - + -
476A PHE 4.1 0.9 - - - +
477A ASP* 1.3 80.8 - - - +
479A ASP* 1.3 61.0 + - - +
480A LYS 4.3 0.2 + - - -
483A GLY 3.6 2.2 - - - -
484A LEU* 3.9 11.2 - - + -
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Residues in contact with ASP 479 (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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407A TYR* 3.8 10.1 - - - -
477A ASP 4.2 0.4 - - - -
478A VAL* 1.3 74.4 - - - +
480A LYS* 1.3 65.6 + - - +
481A LYS* 3.2 11.1 + - - +
482A LYS* 3.1 48.6 + - + +
483A GLY* 2.8 36.1 + - - +
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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