Contacts of the strand formed by residues 482 - 495 (chain A) in PDB entry 3R2W
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 VAL 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A ASN 5.7 0.2 - - - +
460A SER* 3.2 28.5 - - - +
462A LYS* 5.2 6.1 - - + -
480A GLY 3.7 10.5 - - - +
481A ALA* 1.3 76.5 - - - +
483A LEU* 1.3 63.6 + - - +
484A GLU* 3.3 14.9 + - + +
486A LYS* 5.2 0.7 - - - +
479B PRO* 2.7 39.9 + - + +
480B GLY* 4.7 4.5 - - - -
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Residues in contact with LEU 483 (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 VAL* 5.1 2.0 - - + -
460A SER 2.8 12.0 + - - +
461A LEU* 3.7 12.3 - - + -
462A LYS 2.9 27.0 + - - +
465A VAL* 3.2 23.6 - - + +
467A ILE* 3.9 22.0 - - + -
477A ILE* 3.9 28.0 - - + -
481A ALA* 4.5 6.1 - - + -
482A VAL* 1.3 71.1 - - - +
484A GLU* 1.3 58.8 - - - +
486A LYS* 4.5 17.3 - - + -
488A VAL* 4.3 16.8 - - + -
478B PRO* 3.8 29.8 - - + -
479B PRO* 5.6 0.2 - - + -
494B ILE* 5.1 2.9 - - + -
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LYS* 3.3 24.0 - - + +
463A GLY* 5.4 0.2 - - - -
482A VAL* 3.3 13.8 + - + +
483A LEU* 1.3 71.7 - - - +
485A ASN* 1.3 77.0 + - + +
486A LYS* 2.9 18.7 - - + +
496B ASP* 4.9 1.6 - - - +
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Residues in contact with ASN 485 (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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462A LYS 3.2 8.7 + - - -
463A GLY* 3.0 28.2 - - - -
464A THR* 3.0 32.3 + - - +
483A LEU 4.0 0.4 + - - -
484A GLU* 1.3 78.2 - - + +
486A LYS* 1.3 58.7 + - - +
496B ASP* 4.0 2.6 - - - +
497B HIS* 2.9 41.3 + - + +
420C LYS* 4.1 6.5 - - - +
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Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A THR 2.9 7.5 + - - +
465A VAL* 3.4 8.1 - - - +
466A ILE* 3.0 23.3 + - - -
482A VAL 5.2 2.0 - - - +
483A LEU* 4.5 16.4 - - + -
484A GLU* 2.9 33.8 - - + +
485A ASN* 1.3 75.1 - - - +
487A ILE* 1.3 65.0 + - - +
488A VAL* 3.9 3.4 + - + +
479B PRO* 3.8 22.5 - - + +
494B ILE* 3.6 47.2 + - + +
495B LEU 3.4 9.2 - - - +
496B ASP* 4.5 12.6 - - - +
497B HIS 4.6 1.1 + - - +
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Residues in contact with ILE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ILE* 3.4 35.9 - - + +
468A ILE* 6.0 3.1 - - + -
486A LYS* 1.3 73.9 - - - +
488A VAL* 1.3 64.7 - - - +
489A SER* 3.6 11.2 + - - -
493B ARG 3.7 5.7 - - - +
494B ILE* 4.5 0.4 - - - -
495B LEU* 2.9 47.1 + - + +
496B ASP 3.9 7.4 - - - +
497B HIS* 3.5 32.8 - - - +
420C LYS* 4.9 3.4 - - + -
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 5.5 0.2 - - + -
466A ILE 2.6 12.1 + - - +
467A ILE* 3.1 29.8 - - + -
468A ILE* 2.8 26.3 + - - +
475A ILE* 3.8 13.2 - - + -
477A ILE* 3.7 21.3 - - + -
483A LEU* 4.3 24.2 - - + -
486A LYS* 4.8 5.4 - - + +
487A ILE* 1.3 72.4 - - - +
489A SER* 1.3 65.4 + - - +
492B LEU* 4.1 15.3 - - + -
493B ARG 4.8 1.6 - - - -
494B ILE* 4.1 23.1 - - + -
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Residues in contact with SER 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ILE* 3.2 23.9 + - - +
470A ASN* 5.2 4.9 + - - -
475A ILE* 4.0 2.2 - - - -
487A ILE* 3.6 15.6 + - - -
488A VAL* 1.3 79.3 - - - +
490A GLY* 1.3 63.3 + - - +
492B LEU* 3.2 23.8 - - - +
493B ARG 3.7 10.2 + - - +
495B LEU* 6.0 2.9 - - - -
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Residues in contact with GLY 490 (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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468A ILE 3.9 4.5 + - - +
469A ALA* 4.7 4.0 - - - -
470A ASN 6.2 0.2 - - - -
473A ASP* 4.8 5.9 - - - +
474A ARG 4.7 0.5 - - - -
475A ILE* 3.1 23.9 - - - +
489A SER* 1.3 81.2 + - - +
491A ASN* 1.3 59.5 + - - -
491B ASN* 3.5 12.3 - - - -
492B LEU* 3.5 2.9 - - - -
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Residues in contact with ASN 491 (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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473A ASP* 3.3 33.7 + - - +
474A ARG 2.9 30.6 + - - +
490A GLY* 1.3 71.9 - - - -
492A LEU* 1.3 52.3 + - - +
493A ARG* 3.4 24.8 + - - +
490B GLY* 3.3 15.8 - - - -
491B ASN* 2.5 44.4 + - - +
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Residues in contact with LEU 492 (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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474A ARG 2.8 22.4 + - - +
475A ILE* 4.2 0.9 - - - +
476A ASP* 3.0 47.5 + - - +
478A PRO* 5.3 5.8 - - + -
490A GLY 4.0 2.0 + - - -
491A ASN* 1.3 73.0 - - - +
493A ARG* 1.3 61.0 + - - +
494A ILE* 4.1 18.4 - - + -
475B ILE* 3.6 30.1 - - + -
476B ASP 4.4 5.8 - - - +
477B ILE* 5.5 3.1 - - + -
478B PRO* 6.3 1.3 - - + -
488B VAL* 3.9 8.3 - - + -
489B SER 3.6 11.0 - - - +
491B ASN 4.3 2.0 - - - +
492B LEU* 3.3 39.5 - - + +
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Residues in contact with ARG 493 (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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452A ASP* 5.7 0.4 + - - -
472A GLY 3.1 28.9 + - - -
473A ASP* 4.0 3.0 + - - +
474A ARG* 3.4 33.3 - - + +
476A ASP* 3.2 7.2 - - - +
491A ASN* 3.4 24.5 + - - +
492A LEU* 1.3 76.5 - - - +
494A ILE* 1.3 61.5 + - - +
495A LEU* 4.2 6.1 - - + +
487B ILE 3.8 0.2 - - - +
488B VAL* 3.5 4.7 - - - +
489B SER* 2.9 45.7 + - - +
490B GLY* 5.7 0.2 - - - -
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Residues in contact with ILE 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASP* 2.8 34.6 + - + +
478A PRO* 3.8 36.8 - - + -
479A PRO* 5.5 1.6 - - + -
492A LEU* 4.1 8.3 - - + -
493A ARG* 1.3 78.8 - - - +
495A LEU* 1.3 63.2 + - - +
496A ASP* 4.9 2.6 - - - +
483B LEU* 4.3 6.1 - - + -
486B LYS* 3.9 31.2 - - + -
487B ILE 3.3 3.4 - - - -
488B VAL* 3.7 24.9 - - + -
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ARG* 4.2 5.8 - - + -
494A ILE* 1.3 75.6 - - - +
496A ASP* 1.3 71.1 + - - +
486B LYS* 3.3 10.7 - - - +
487B ILE* 3.0 46.0 + - + +
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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