Contacts of the strand formed by residues 475 - 488 (chain A) in PDB entry 3M8D
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 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A ASP* 3.2 6.8 - - - +
472A THR* 2.9 48.3 + - - +
473A GLY 3.2 3.7 - - - +
474A PRO* 1.3 89.1 - - + +
476A THR* 1.3 60.6 + - - +
477A HIS* 3.8 14.0 - - + +
507A LEU* 4.1 14.8 - - + -
508A ASP 3.4 3.1 - - - -
509A TRP* 3.6 37.9 - - + -
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Residues in contact with THR 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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469A ASN* 5.8 1.8 - - + -
470A PHE 4.1 2.0 - - - +
471A ASP* 2.5 27.7 + - - +
474A PRO 4.0 2.6 + - - -
475A LEU* 1.3 71.5 - - - +
477A HIS* 1.3 66.3 + - - +
478A THR* 4.2 13.7 - - - +
506A GLN 3.5 1.6 - - - +
507A LEU* 3.3 7.8 - - - +
508A ASP* 2.7 56.3 + - - +
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Residues in contact with HIS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA 4.7 0.2 - - - -
469A ASN* 3.1 8.5 - - - +
470A PHE* 2.8 84.5 + + + +
472A THR* 2.8 32.9 + - + +
475A LEU* 3.8 13.8 - - + +
476A THR* 1.3 76.9 - - - +
478A THR* 1.3 63.5 + - - +
479A VAL* 4.3 0.4 - - + -
505A TYR* 2.6 37.1 + - + -
506A GLN 3.6 4.0 - - - -
507A LEU* 3.3 12.9 - - + +
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Residues in contact with THR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ALA 3.7 3.4 - - - +
469A ASN* 4.2 13.4 - - + +
476A THR* 4.2 11.6 - - - +
477A HIS* 1.3 76.4 + - - +
479A VAL* 1.3 62.5 + - - +
504A LYS 4.0 0.5 - - - +
505A TYR* 3.4 2.7 - - - -
506A GLN* 2.8 50.7 + - + +
508A ASP* 4.8 5.4 + - - -
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Residues in contact with VAL 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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466A ALA 4.1 0.2 - - - +
467A THR* 3.4 3.8 - - - -
468A ALA* 2.9 50.1 + - + +
470A PHE* 4.8 11.9 - - + -
477A HIS 5.5 0.2 - - - -
478A THR* 1.3 77.4 - - - +
480A SER* 1.3 69.7 + - - +
503A VAL* 5.1 7.0 - - + -
504A LYS 3.2 12.8 - - - +
505A TYR* 4.0 22.2 - - + -
704A C8E 4.5 16.4 - - - +
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Residues in contact with SER 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG 4.9 1.4 + - - -
50A PRO* 4.3 19.2 - - - +
465A GLU* 5.8 0.2 - - - -
466A ALA 3.2 10.8 - - - -
467A THR* 3.7 15.5 - - - -
479A VAL* 1.3 78.1 - - - +
481A TYR* 1.3 64.5 + - - +
482A ASP* 4.9 2.2 + - - -
502A GLN 3.9 0.4 - - - +
503A VAL* 3.5 7.1 - - - +
504A LYS* 2.9 60.5 + - - +
704A C8E 4.9 1.1 - - - -
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A VAL* 4.7 5.4 - - + -
465A GLU* 3.5 3.1 - - - +
466A ALA* 2.8 38.6 + - + +
480A SER* 1.3 76.7 - - - +
482A ASP* 1.3 73.2 + - - +
483A TYR* 3.3 31.3 - - + +
501A GLN* 2.6 37.8 + - + -
502A GLN 3.4 12.6 - - - -
503A VAL* 4.0 17.5 - - + -
704A C8E 4.0 62.6 - - - -
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Residues in contact with ASP 482 (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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50A PRO* 3.8 5.3 - - - +
51A GLY* 2.8 43.9 + - - -
52A VAL 4.2 0.2 + - - -
464A VAL 3.4 3.0 - - - +
465A GLU* 3.9 17.0 - - - +
480A SER* 4.9 2.1 + - - -
481A TYR* 1.3 83.3 - - - +
483A TYR* 1.3 60.6 + - - +
484A VAL* 4.1 12.6 - - + -
500A LYS 3.8 0.2 - - - +
501A GLN* 3.2 7.7 - - - -
502A GLN* 3.0 41.3 + - + +
504A LYS* 4.1 17.3 - - - +
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Residues in contact with TYR 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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436A TYR* 4.1 0.9 + - - -
462A LYS 3.7 17.7 - - - -
463A GLY* 3.0 6.3 - - - -
464A VAL* 2.7 57.5 + - + +
481A TYR* 3.3 29.5 - - + +
482A ASP* 1.3 71.4 - - - +
484A VAL* 1.3 67.1 + - - +
485A ASP* 3.7 25.9 + - + +
500A LYS* 3.6 25.9 + - + -
501A GLN* 4.2 14.4 - - + -
704A C8E 5.4 4.3 - - - -
706A C8E 4.1 21.1 - - - -
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Residues in contact with VAL 484 (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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51A GLY* 5.8 3.1 - - - +
69A ARG* 4.1 3.6 - - - -
70A GLY* 3.5 35.7 - - - +
436A TYR* 3.6 13.5 - - - +
461A ILE* 4.0 13.9 - - + -
462A LYS 3.8 2.5 - - - -
463A GLY* 4.4 0.7 - - - -
482A ASP* 4.7 13.2 - - + -
483A TYR* 1.3 83.1 - - - +
485A ASP* 1.3 57.7 + - - +
486A ALA* 3.7 9.4 + - + +
498A ARG* 5.6 4.2 - - + +
499A ALA 4.4 10.9 - - - +
500A LYS* 3.0 35.2 + - - +
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ARG* 3.4 7.6 + - - +
461A ILE* 3.3 2.9 - - - -
462A LYS* 2.9 53.1 + - + +
483A TYR* 3.7 25.2 + - + +
484A VAL* 1.3 69.1 - - - +
486A ALA* 1.3 57.3 + - - +
487A ARG* 2.7 43.4 + - - +
500A LYS* 4.6 10.6 - - - -
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Residues in contact with ALA 486 (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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70A GLY 3.8 22.0 - - - +
460A ARG 3.7 3.6 - - - -
461A ILE* 4.1 10.8 - - + +
484A VAL* 3.7 14.3 + - + -
485A ASP* 1.3 71.7 + - - +
487A ARG* 1.3 65.6 + - - +
494A PRO* 3.5 4.7 - - - +
495A LEU* 3.0 27.4 + - + +
498A ARG* 3.9 18.4 - - + -
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Residues in contact with ARG 487 (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 ALA* 3.2 8.5 - - - +
460A ARG* 3.0 48.2 + - - +
485A ASP* 2.7 35.4 + - - +
486A ALA* 1.3 80.6 - - - +
488A ASN* 1.3 67.2 + - - +
489A ALA* 3.6 0.7 - - - -
492A ASP* 2.7 53.0 + - - +
493A THR 3.4 10.8 - - - +
494A PRO* 3.8 24.8 - - + +
495A LEU* 3.9 8.6 - - - +
500A LYS* 4.8 14.5 - - - +
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Residues in contact with ASN 488 (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 GLY* 6.4 0.4 - - - -
458A LYS 3.5 14.2 + - - +
487A ARG* 1.3 69.0 - - - +
489A ALA* 1.3 55.5 + - - +
490A ILE* 3.1 22.5 + - - +
491A THR* 3.3 30.7 + - - +
492A ASP* 2.6 34.8 + - - -
493A THR* 3.0 17.0 + - - +
495A LEU* 3.8 15.9 - - + +
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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