Contacts of the helix formed by residues 486 - 496 (chain A) in PDB entry 4BWM
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 SER 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A ASN* 3.0 32.2 + - - +
484A LEU 3.4 0.2 - - - -
485A ASN* 1.3 75.9 - - - +
487A ARG* 1.3 58.3 + - - +
488A ASP* 3.4 9.0 + - - +
489A GLN* 3.1 30.2 + - - +
490A LEU* 2.9 32.2 + - - +
536A ARG* 5.8 0.2 - - - -
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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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485A ASN 3.8 4.2 + - - -
486A SER* 1.3 71.5 + - - +
488A ASP* 1.3 95.4 + - - +
490A LEU* 3.6 8.4 - - - +
491A GLU* 2.8 53.7 + - - +
506A THR* 3.7 15.2 - - - +
511A LYS* 3.9 9.3 - - - +
512A ARG 2.8 29.3 + - - -
514A THR* 3.9 18.4 - - - +
536A ARG* 4.3 6.3 - - - +
108B G 3.1 32.5 + - - +
109B C 3.1 26.8 + - - +
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Residues in contact with ASP 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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486A SER* 3.2 7.5 + - - +
487A ARG* 1.3 111.5 + - - +
489A GLN* 1.3 63.4 + - + +
491A GLU* 3.4 5.7 + - - +
492A ARG* 3.2 20.6 + - - +
511A LYS* 4.3 13.5 - - - +
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Residues in contact with GLN 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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482A PHE* 3.5 13.5 - - + +
483A ASN* 2.9 48.0 + - - +
486A SER* 3.1 21.1 + - - +
488A ASP* 1.3 77.7 - - + +
490A LEU* 1.3 63.8 + - - +
492A ARG* 3.3 33.2 + - - +
493A VAL* 3.1 28.2 + - - +
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Residues in contact with LEU 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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482A PHE* 3.7 20.4 - - + -
484A LEU* 3.1 40.2 - - + +
486A SER 2.9 24.9 + - - +
487A ARG* 3.6 8.5 - - - +
489A GLN* 1.3 72.3 - - - +
491A GLU* 1.3 67.3 + - - +
493A VAL* 3.2 3.1 + - + +
494A LEU* 2.9 45.7 + - + +
514A THR* 4.3 10.5 - - + -
528A ILE* 6.3 0.2 - - + -
532A ILE* 4.0 33.0 - - + -
536A ARG* 4.4 14.4 - - - +
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Residues in contact with GLU 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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487A ARG* 2.8 44.8 + - - +
488A ASP* 3.6 7.4 - - - +
489A GLN 3.3 0.2 - - - -
490A LEU* 1.3 74.2 - - - +
492A ARG* 1.3 58.2 + - - +
495A PHE* 2.9 43.1 + - + +
496A ASP 3.9 0.2 + - - -
511A LYS* 3.9 12.0 - - - +
512A ARG* 2.9 63.7 + - - +
514A THR* 3.9 13.0 - - + +
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Residues in contact with ARG 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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480A HIS* 4.3 7.7 - - - -
482A PHE* 3.9 16.4 - - - +
488A ASP 3.2 10.0 + - - +
489A GLN* 3.5 51.3 + - - +
490A LEU 3.2 0.4 - - - -
491A GLU* 1.3 79.8 - - - +
493A VAL* 1.3 62.6 + - - +
496A ASP* 2.9 49.6 + - + +
497A GLU* 2.9 33.4 + - + +
512A ARG* 4.9 0.4 - - - +
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Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A ALA* 4.1 22.4 - - + -
480A HIS* 4.2 2.0 - - + -
482A PHE* 3.9 38.4 - - + -
489A GLN 3.1 16.6 + - - +
490A LEU* 3.7 4.7 - - + +
492A ARG* 1.3 87.1 - - - +
494A LEU* 1.3 62.1 + - + +
497A GLU* 3.5 21.8 - - - +
498A LEU* 2.8 45.8 + - + +
528A ILE* 4.5 5.4 - - + -
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Residues in contact with LEU 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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490A LEU* 2.9 41.9 + - + +
491A GLU 4.2 0.2 - - - +
493A VAL* 1.3 77.4 - - + +
495A PHE* 1.3 78.3 + - + +
498A LEU* 3.7 5.5 - - + -
499A GLY 3.4 4.9 + - - -
500A LEU* 2.9 43.5 + - + +
514A THR* 4.5 13.5 - - + -
519A LEU* 3.7 32.3 - - + -
522A LEU* 6.0 1.3 - - + -
528A ILE* 3.9 28.9 - - + -
529A VAL* 4.6 4.9 - - + -
532A ILE* 4.9 7.0 - - + -
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Residues in contact with PHE 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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491A GLU* 2.9 33.1 + - + +
494A LEU* 1.3 94.5 - - + +
496A ASP* 1.3 65.7 + - - +
499A GLY* 3.4 17.1 - - - -
500A LEU* 3.3 23.5 - - + +
501A PRO 3.7 17.0 - - - -
502A ALA* 3.7 15.7 - - + -
503A ILE 5.2 0.2 - - - -
512A ARG* 3.5 37.5 + - + +
513A SER 3.4 25.8 - - - -
514A THR* 4.0 16.4 - - + -
518A VAL* 4.4 9.0 - - + -
519A LEU* 5.3 0.2 - - + -
522A LEU* 4.0 13.5 - - + -
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Residues in contact with ASP 496 (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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492A ARG* 2.9 30.5 + - + +
495A PHE* 1.3 77.4 - - - +
497A GLU* 1.3 68.0 - - + +
499A GLY* 3.5 8.3 + - - -
512A ARG* 2.9 38.5 + - - -
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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