Contacts of the strand formed by residues 486 - 501 (chain A) in PDB entry 3Q0F
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 TYR 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLU* 3.1 8.3 - - - +
376A PHE* 2.8 49.6 + - + +
377A GLN 3.9 16.8 - - - -
378A TYR 4.1 7.4 - - - -
379A ARG* 3.5 33.9 + - + +
382A LEU* 4.7 4.5 - - + -
411A VAL* 4.1 12.8 - - + -
413A SER* 4.2 13.1 + - - -
469A ILE* 3.7 24.0 - - + -
470A ARG 3.2 4.3 - - - -
471A GLY* 3.9 11.9 - - - -
472A ILE* 3.9 1.3 - - - +
484A LYS 3.7 1.0 - - - -
485A ASN* 1.3 95.1 - - + +
487A VAL* 1.3 63.5 + - - +
7B A 3.9 5.9 + - - -
8B G 2.5 31.0 + - - -
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY* 3.6 33.2 - - - +
374A ASP 3.4 1.8 - - - +
375A GLU* 3.9 11.9 - - + +
376A PHE* 5.0 0.7 - - - -
469A ILE* 3.2 8.3 - - - -
470A ARG* 2.9 34.1 + - + +
472A ILE* 3.4 38.8 - - + -
486A TYR* 1.3 76.5 - - - +
488A TYR* 1.3 67.3 + - - +
489A ASP* 3.4 1.4 + - - +
522A LEU* 4.5 21.1 - - + -
523A PRO* 5.9 1.8 - - + -
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Residues in contact with TYR 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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366A THR* 4.6 9.5 + - + +
367A VAL 5.9 1.8 - - - -
370A VAL* 4.0 26.5 - - + -
371A GLU 3.5 24.0 - - - +
372A VAL* 3.7 15.9 - - + -
373A GLY* 2.9 28.6 + - - -
374A ASP* 3.0 15.9 + - + +
376A PHE* 4.3 12.9 - - + -
387A ILE* 4.5 14.8 - - + -
467A ARG* 3.8 26.4 - - + +
468A VAL 3.8 7.2 - - - -
469A ILE* 4.5 6.7 - - + -
487A VAL* 1.3 73.2 - - - +
489A ASP* 1.3 58.9 + - - +
490A GLY* 3.5 30.4 - - - -
491A LEU* 3.2 29.6 - - - +
522A LEU* 4.0 1.6 - - - +
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Residues in contact with ASP 489 (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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372A VAL* 4.4 1.1 - - - -
468A VAL* 2.8 25.0 + - + +
470A ARG* 2.8 34.7 + - + -
487A VAL 3.4 1.3 + - - +
488A TYR* 1.3 73.9 - - - +
490A GLY* 1.3 59.5 + - - +
492A TYR* 2.6 29.7 + - - -
515A ARG* 2.9 35.7 + - - -
522A LEU* 3.6 23.2 - - + +
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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
----------------------------------------------------------
372A VAL* 3.6 11.3 - - - +
467A ARG* 3.7 1.0 - - - -
468A VAL 3.2 23.9 + - - -
488A TYR* 3.5 30.6 - - - -
489A ASP* 1.3 80.7 - - - +
491A LEU* 1.3 61.0 + - - -
492A TYR* 4.0 2.6 - - - -
519A GLN* 3.4 11.7 - - - -
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Residues in contact with LEU 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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365A GLY* 3.8 16.8 - - - -
366A THR* 3.7 24.7 - - - +
465A PRO* 4.3 15.7 - - + -
466A VAL 3.4 4.0 - - - +
467A ARG* 3.7 25.1 - - + +
488A TYR* 3.2 22.0 - - - +
490A GLY* 1.3 71.7 - - - -
492A TYR* 1.3 67.6 + - - +
515A ARG* 3.7 0.7 - - - +
516A ILE* 3.0 27.2 + - + +
519A GLN* 2.7 40.0 + - - +
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Residues in contact with TYR 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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423A SER 4.8 3.6 + - - -
424A ASP 3.8 8.5 - - - -
426A LEU* 4.3 17.0 - - + -
465A PRO* 3.5 5.2 - - - +
466A VAL* 2.7 35.2 + - - +
468A VAL* 3.5 28.3 - - + -
470A ARG* 3.1 14.8 + - - -
489A ASP* 2.6 40.2 + - - -
490A GLY 4.0 1.3 - - - -
491A LEU* 1.3 78.8 - - - +
493A LEU* 1.3 63.4 + - - +
513A LEU* 4.0 24.5 - - + -
514A ARG 3.3 14.1 - - - +
515A ARG* 3.3 48.3 - - + +
516A ILE* 4.2 1.3 - - - +
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Residues in contact with LEU 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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463A LYS* 3.7 27.1 - - + +
464A ASN 3.6 24.5 - - - +
465A PRO* 3.8 7.4 - - + -
492A TYR* 1.3 80.6 - - - +
494A VAL* 1.3 67.7 + - - +
495A GLU* 3.4 7.9 + - + +
513A LEU* 3.2 4.3 - - - -
514A ARG* 2.9 34.0 + - + +
516A ILE* 3.8 24.5 - - + -
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Residues in contact with VAL 494 (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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456A LEU* 3.7 33.4 - - + +
459A SER* 4.0 18.7 + - - +
460A ILE* 3.4 49.4 - - + +
463A LYS* 6.0 0.5 - - - +
464A ASN 4.9 2.6 + - - -
466A VAL* 4.2 7.2 - - + -
493A LEU* 1.3 72.1 - - - +
495A GLU* 1.3 64.4 + - - +
496A GLU 4.1 12.3 - - - +
511A PHE* 4.4 17.9 - - + -
512A LYS 3.8 5.2 - - - +
513A LEU* 3.9 15.0 - - + -
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Residues in contact with GLU 495 (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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460A ILE* 3.8 11.8 - - - +
493A LEU* 4.0 9.6 - - + +
494A VAL* 1.3 75.0 - - - +
496A GLU* 1.3 63.3 + - + +
512A LYS* 2.8 49.3 + - - +
514A ARG* 3.2 50.8 + - + +
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Residues in contact with GLU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ILE* 3.7 14.8 - - - -
494A VAL* 3.5 4.9 - - - +
495A GLU* 1.3 83.3 - - + +
497A TYR* 1.3 71.0 + - - +
498A TRP* 4.0 18.5 - - + +
511A PHE* 3.5 1.9 - - - -
512A LYS* 2.9 63.1 + - + +
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Residues in contact with TYR 497 (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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449A LEU* 4.1 9.7 - - + +
457A LYS* 2.8 46.8 + - + +
460A ILE* 3.7 17.3 - - + -
496A GLU* 1.3 84.9 - - - +
498A TRP* 1.3 90.5 + - - +
499A GLU* 5.3 4.3 - - - -
509A PHE* 4.2 25.8 - + - -
510A LYS 3.1 14.6 - - - +
511A PHE* 3.5 26.5 - + + -
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Residues in contact with TRP 498 (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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427A ILE* 3.9 31.9 - - + -
496A GLU* 4.0 20.6 - - - +
497A TYR* 1.3 93.9 - - - +
499A GLU* 1.3 76.1 + - - +
500A GLU* 3.3 25.9 + - + +
509A PHE* 3.5 3.8 - - - -
510A LYS* 2.9 50.3 + - + +
512A LYS* 4.0 24.9 - - + -
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Residues in contact with GLU 499 (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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497A TYR* 5.3 4.5 - - + -
498A TRP* 1.3 86.9 - - - +
500A GLU* 1.3 64.4 + - - +
507A LEU* 3.5 41.7 - - + +
508A VAL 3.3 8.3 - - - +
509A PHE* 3.8 17.3 - - + -
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Residues in contact with GLU 500 (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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498A TRP* 3.3 33.7 + - + +
499A GLU* 1.3 74.9 - - - +
501A THR* 1.3 67.9 + - - +
502A GLY 4.2 0.4 - - - -
507A LEU* 3.4 8.1 - - - +
508A VAL* 2.7 38.9 + - + +
510A LYS* 3.5 30.6 - - + +
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Residues in contact with THR 501 (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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500A GLU* 1.3 82.2 + - - +
502A GLY* 1.3 78.3 + - - +
505A GLY* 3.6 27.1 - - - +
506A LYS 3.6 3.4 - - - +
507A LEU* 4.2 11.3 - - - +
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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