Contacts of the helix formed by residues 475 - 492 (chain A) in PDB entry 4BL8
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 THR 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.4 14.4 - - + -
394A VAL* 4.2 12.5 - - + +
413A MET* 3.8 24.2 - - + -
473A PRO 4.5 0.7 - - - +
474A PRO* 1.3 74.8 - - - +
476A TRP* 1.3 66.5 + - - +
477A PRO* 3.2 3.8 - - - -
478A ALA* 3.1 18.6 + - - +
479A GLU* 3.6 3.6 + - - +
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Residues in contact with TRP 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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462A PHE* 3.9 19.1 - + - -
464A LEU* 3.7 25.4 - - + +
474A PRO* 3.7 27.8 - - + +
475A THR* 1.3 79.1 + - - +
477A PRO* 1.3 77.1 - - + +
479A GLU* 3.2 20.8 + - + +
480A LEU* 3.2 19.5 + - + +
507A LEU* 3.7 32.8 - - + -
508A ASP* 3.6 34.3 + - + +
509A ASN* 6.0 2.5 - - - +
578A MET* 3.9 17.5 - - + -
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Residues in contact with PRO 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 3.4 31.6 - - + +
462A PHE* 3.8 23.8 - - + -
464A LEU* 4.1 3.4 - - + -
474A PRO 3.6 11.2 - - - +
475A THR 3.2 6.1 - - - -
476A TRP* 1.3 125.3 - - + +
478A ALA* 1.3 64.0 + - - +
480A LEU* 3.1 7.0 + - + +
481A MET* 3.0 28.2 + - - +
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 3.8 34.5 - - + -
411A VAL* 4.2 23.7 - - + +
413A MET* 3.8 8.7 - - + -
430A TYR* 4.7 2.4 - - - -
475A THR 3.1 13.0 + - - +
477A PRO* 1.3 77.8 - - - +
479A GLU* 1.3 63.2 + - - +
481A MET* 3.3 5.2 + - - +
482A GLN* 3.1 28.1 + - + +
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Residues in contact with GLU 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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475A THR 3.6 3.1 + - - +
476A TRP* 3.2 17.2 + - + +
478A ALA* 1.3 79.2 - - - +
480A LEU* 1.3 62.5 - - - +
482A GLN* 3.1 13.4 + - - +
483A GLY* 3.1 17.0 + - - -
486A ARG* 4.0 17.3 + - - -
509A ASN* 5.7 6.7 - - - +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A PHE* 4.8 11.9 - - + -
476A TRP* 3.2 26.9 + - + +
477A PRO* 3.1 13.6 + - + +
479A GLU* 1.3 81.0 - - - +
481A MET* 1.3 57.7 + - + +
483A GLY* 2.9 17.7 + - - -
484A LEU* 3.0 13.4 + - + +
503A TRP* 3.6 37.7 - - + +
507A LEU* 4.0 30.5 - - + +
517A MET* 4.3 22.0 - - + -
540A ILE* 4.7 13.0 - - + -
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Residues in contact with MET 481 (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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408A LEU* 3.5 16.2 - - + +
411A VAL* 3.8 26.0 - - + -
430A TYR* 3.6 13.0 - - + +
432A SER* 4.4 7.4 - - - -
460A LEU* 3.6 21.7 - - + +
461A THR* 3.4 46.2 - - - +
462A PHE* 3.6 14.1 - - + +
477A PRO 3.0 16.0 + - - +
478A ALA* 3.7 7.0 - - - +
480A LEU* 1.3 72.8 - - + +
482A GLN* 1.3 61.6 + - - +
484A LEU* 3.9 4.0 - - - +
485A ALA* 2.9 31.0 + - - +
540A ILE* 4.1 14.6 - - + -
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Residues in contact with GLN 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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394A VAL* 5.4 7.9 - - + +
396A ALA* 4.8 4.8 - - - +
406A ASP* 3.6 27.6 + - + +
407A PRO* 3.6 3.8 - - - +
408A LEU* 3.2 55.0 + - - +
411A VAL* 4.6 6.9 - - - +
478A ALA 3.1 18.2 + - - +
479A GLU* 3.3 13.2 - - - +
481A MET* 1.3 77.0 - - - +
483A GLY* 1.3 56.3 + - - +
485A ALA* 3.4 2.1 + - - +
486A ARG* 3.0 52.1 + - - +
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Residues in contact with GLY 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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479A GLU* 3.1 8.8 + - - -
480A LEU* 2.9 8.7 + - - -
482A GLN* 1.3 78.4 - - - +
484A LEU* 1.3 61.0 + - - +
486A ARG* 3.5 22.3 + - - +
487A TYR* 3.1 20.4 + - - +
503A TRP* 3.9 21.0 - - - -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.9 23.1 - - + -
480A LEU* 3.0 13.1 + - + +
481A MET* 4.0 0.9 - - - +
483A GLY* 1.3 73.2 - - - +
485A ALA* 1.3 65.6 + - - +
487A TYR* 3.1 20.4 + - + +
488A VAL* 3.1 15.8 + - + +
495A PHE* 3.8 24.9 - - + -
501A VAL* 4.1 24.0 - - + -
503A TRP* 4.1 4.6 - - + -
517A MET* 4.0 22.0 - - + -
519A LEU* 4.5 9.2 - - + -
540A ILE* 3.6 35.4 - - + -
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A PRO* 3.5 21.5 - - + -
408A LEU* 3.7 24.0 - - + -
435A LEU* 4.1 20.2 - - + -
460A LEU* 4.4 0.6 - - - +
481A MET 2.9 19.3 + - - +
482A GLN 3.7 1.3 - - - +
484A LEU* 1.3 72.6 - - - +
486A ARG* 1.3 65.4 + - - +
488A VAL* 3.2 4.0 + - - +
489A PHE* 3.0 28.2 + - - -
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Residues in contact with ARG 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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400A TYR* 5.8 0.4 - - + -
405A PRO* 3.7 16.0 + - - +
406A ASP* 3.4 25.6 + - - -
407A PRO* 3.7 19.4 - - + +
479A GLU* 4.0 18.6 + - - -
482A GLN* 3.0 37.2 + - - +
483A GLY* 3.5 24.0 + - - +
485A ALA* 1.3 76.1 - - - +
487A TYR* 1.3 61.9 + - - +
489A PHE* 4.5 3.8 - - - -
490A GLN* 3.1 42.6 + - + +
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Residues in contact with TYR 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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483A GLY 3.1 13.1 + - - +
484A LEU* 3.1 20.8 + - + +
486A ARG* 1.3 78.1 - - - +
488A VAL* 1.3 57.4 + - - +
490A GLN* 4.8 1.7 - - - +
491A SER* 3.0 32.3 + - - -
493A ASN* 6.0 0.9 - - + -
495A PHE* 3.6 32.5 - + - -
501A VAL* 5.4 11.7 - - + -
502A SER 5.9 2.5 - - - -
503A TRP* 5.3 10.3 - + + -
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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
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435A LEU* 4.4 8.3 - - + -
456A PHE* 3.5 40.2 - - + -
458A PHE* 4.3 13.5 - - + -
460A LEU* 6.4 1.3 - - + -
484A LEU 3.1 13.4 + - - +
485A ALA* 3.2 7.6 + - - +
487A TYR* 1.3 75.4 - - - +
489A PHE* 1.3 60.1 + - - +
491A SER* 3.4 5.7 + - - -
492A GLU* 2.8 29.5 + - - -
493A ASN 3.7 13.8 + - - +
494A THR* 4.8 0.7 - - - -
495A PHE* 3.4 39.0 - - + -
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Residues in contact with PHE 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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400A TYR* 3.2 44.2 - + + +
407A PRO* 3.7 21.8 - - + -
434A GLY 3.9 9.2 - - - -
435A LEU* 3.6 23.1 - - + -
444A VAL* 3.8 18.6 - - + -
445A HIS* 3.6 28.3 - + - -
456A PHE* 3.7 19.3 - + - -
485A ALA 3.0 22.8 + - - +
486A ARG* 3.8 5.6 - - - +
488A VAL* 1.3 80.1 - - - +
490A GLN* 1.3 69.0 + - - +
492A GLU* 3.1 20.8 + - - +
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Residues in contact with GLN 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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400A TYR* 3.7 26.7 + - - -
486A ARG* 3.1 26.5 + - + +
487A TYR* 4.8 2.0 - - - +
489A PHE* 1.3 83.6 - - - +
491A SER* 1.3 58.7 + - - +
492A GLU* 4.5 3.3 - - - +
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TYR* 3.0 28.9 + - - -
488A VAL 3.4 2.0 + - - -
489A PHE 3.2 0.6 - - - -
490A GLN* 1.3 79.0 - - - +
492A GLU* 1.3 73.0 + - - +
493A ASN* 3.2 23.0 + - - +
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 4.2 19.9 - - + -
488A VAL 2.8 13.5 + - - -
489A PHE 3.1 13.0 + - - +
490A GLN 4.5 3.8 - - - +
491A SER* 1.3 80.3 - - - +
493A ASN* 1.3 58.2 + - - +
494A THR* 3.9 4.4 + - - +
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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
------------------------------------------------------------
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