Contacts of the strand formed by residues 455 - 461 (chain A) in PDB entry 3DDN
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 ILE 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A GLY* 1.3 75.4 - - - -
456A ASN* 1.3 61.8 + - - +
501A ARG* 3.4 3.8 - - - +
502A LEU* 2.7 53.4 + - + +
503A ASP 4.6 4.0 - - - +
504A GLN* 3.7 35.7 - - - +
505A ASP* 4.3 7.6 - - + +
525A VAL* 3.5 28.3 - - + -
526A VAL 3.6 4.7 - - - +
527A ASP* 4.3 19.1 - - + +
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Residues in contact with ASN 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 5.9 0.4 - - + -
440A ILE* 5.8 1.2 - - - +
450A LEU* 4.9 1.9 - - - +
451A ARG 4.7 6.1 - - - +
453A GLN 2.8 28.0 + - - +
454A GLY 2.9 16.6 + - - -
455A ILE* 1.3 77.2 - - - +
457A LEU* 1.3 60.2 + - - +
458A ILE* 4.1 3.2 + - + +
499A LEU* 3.4 30.2 - - + +
500A LEU 3.2 3.8 - - - +
501A ARG* 3.7 14.4 - - - +
524A GLU 3.8 0.7 - - - +
525A VAL* 3.3 4.8 - - - -
526A VAL* 2.6 54.0 + - + +
528A LEU* 3.8 20.5 - - + +
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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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455A ILE 4.2 0.2 - - - -
456A ASN* 1.3 72.1 - - - +
458A ILE* 1.3 65.3 + - - +
459A ILE* 3.7 25.6 - - + -
475A LEU* 4.2 21.1 - - + -
498A ILE 3.7 1.0 - - - +
499A LEU* 3.2 3.6 - - - +
500A LEU* 2.6 58.5 + - + +
502A LEU* 3.8 28.0 - - + +
506A VAL* 4.4 5.2 - - + -
514A ILE* 4.6 6.1 - - + -
523A LEU* 3.7 26.7 - - + -
524A GLU 3.3 16.8 - - - +
525A VAL* 3.9 11.2 - - + +
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Residues in contact with ILE 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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337A LEU* 4.3 11.2 - - + -
340A VAL* 4.6 9.6 - - + -
341A LEU* 3.7 33.4 - - + -
443A ILE* 5.7 1.3 - - + -
456A ASN* 4.6 2.7 - - + +
457A LEU* 1.3 78.2 - - - +
459A ILE* 1.3 66.6 + - - +
460A HIS* 4.0 16.4 - - + +
497A THR* 6.3 0.7 - - - -
498A ILE 3.3 7.6 - - - +
499A LEU* 3.7 28.9 - - + -
522A LYS* 4.0 3.9 - - + +
523A LEU* 3.5 2.1 - - - -
524A GLU* 2.8 45.9 + - + +
526A VAL* 4.0 27.4 - - + -
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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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457A LEU* 3.7 22.7 - - + -
458A ILE* 1.3 79.3 - - - +
460A HIS* 1.3 66.0 + - - +
461A TYR* 3.8 16.8 - - + -
471A ILE* 4.2 13.0 - - + -
497A THR* 3.2 5.4 - - - -
498A ILE* 2.9 51.1 + - + +
500A LEU* 4.5 0.7 - - + -
514A ILE* 3.8 26.0 - - + -
518A VAL* 4.4 6.3 - - + -
520A ALA* 3.8 21.5 - - + -
522A LYS 3.3 9.4 - - - +
523A LEU* 3.5 17.5 - - + -
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Residues in contact with HIS 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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341A LEU* 4.1 17.2 + - + +
443A ILE* 6.0 2.0 - - + -
444A ASN* 4.8 13.1 + - - -
458A ILE* 4.0 22.1 - - + +
459A ILE* 1.3 76.3 + - - +
461A TYR* 1.3 62.6 + - - +
496A ALA 3.5 5.2 - - - +
497A THR* 3.7 20.0 - - + +
520A ALA* 3.3 1.0 - - - -
521A TYR* 2.9 67.0 + + + +
522A LYS* 2.8 33.6 + - + +
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Residues in contact with TYR 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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459A ILE* 3.8 17.3 - - + -
460A HIS* 1.3 76.5 - - - +
462A VAL* 1.3 63.0 + - - +
463A ASP 3.3 21.8 - - - -
464A ARG* 4.3 3.8 + - - -
467A ALA* 3.4 31.8 - - + +
468A LEU* 5.1 1.4 + - - -
471A ILE* 4.7 6.6 - - + +
487A LEU* 4.7 14.6 - - - +
495A GLY* 3.3 4.0 - - - -
496A ALA* 2.8 66.7 + - + +
497A THR 3.9 4.7 + - - -
498A ILE* 4.0 21.4 - - + +
518A VAL* 3.5 27.4 - - + +
519A ASP 3.6 5.4 - - - -
520A ALA* 3.6 11.9 - - + +
521A TYR* 3.7 4.3 - - - -
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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