Contacts of the helix formed by residues 548 - 555 (chain I) in PDB entry 3BTW
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 ALA 548 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521I TYR* 3.7 33.6 - - + +
530I CYS* 4.7 7.0 - - + +
547I SER* 1.3 72.0 - - - +
549I GLU* 1.3 70.5 + - - +
551I CYS* 3.2 5.0 + - - +
552I LEU* 2.8 40.5 + - + +
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Residues in contact with GLU 549 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547I SER* 3.2 19.5 + - - +
548I ALA* 1.3 83.5 + - - +
550I ASP* 1.3 60.1 + - - +
552I LEU* 3.3 8.4 + - + +
553I ARG* 2.9 50.8 + - - +
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Residues in contact with ASP 550 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545I PHE* 4.0 16.4 - - + -
546I LYS* 4.5 9.9 + - - +
547I SER* 3.1 30.4 + - - +
549I GLU* 1.3 76.3 - - - +
551I CYS* 1.3 63.9 + - - +
553I ARG* 3.1 27.2 + - - +
554I THR* 3.0 30.2 + - - +
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Residues in contact with CYS 551 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521I TYR* 4.2 2.2 - - + -
522I PHE* 3.7 3.1 - - - -
523I TYR* 3.6 26.5 - - - -
530I CYS* 2.0 48.7 - - + -
545I PHE* 3.5 28.4 - - + -
547I SER 3.2 11.0 + - - +
548I ALA* 3.4 6.3 - - - +
550I ASP* 1.3 80.9 - - - +
552I LEU* 1.3 55.7 + - - +
554I THR* 4.1 0.3 - - - -
555I CYS* 2.9 29.1 + - - +
556I GLY 3.5 2.6 + - - -
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Residues in contact with LEU 552 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523I TYR* 5.2 2.0 - - + -
528I GLY 5.6 1.6 - - - +
529I LEU* 5.1 6.3 - - + -
530I CYS* 3.9 24.9 - - + +
548I ALA* 2.8 30.4 + - + +
549I GLU* 3.9 7.6 - - + +
551I CYS* 1.3 72.9 - - - +
553I ARG* 1.3 60.0 + - - +
556I GLY* 2.8 39.3 + - - +
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Residues in contact with ARG 553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549I GLU* 2.9 40.7 + - - +
550I ASP* 3.1 28.2 + - - +
552I LEU* 1.3 78.7 - - - +
554I THR* 1.3 62.4 + - - +
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Residues in contact with THR 554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504I PHE* 3.8 30.1 - - + -
505I CYS* 4.1 4.0 - - - -
545I PHE* 3.6 25.8 - - + -
550I ASP* 3.0 16.7 + - - +
553I ARG* 1.3 80.5 - - - +
555I CYS* 1.3 60.3 + - - +
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Residues in contact with CYS 555 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504I PHE* 4.0 4.3 - - - -
505I CYS* 2.0 51.1 - - - -
523I TYR* 3.5 31.3 - - + -
543I ASN* 4.3 0.9 - - - -
545I PHE* 3.8 24.9 - - - -
551I CYS 2.9 11.9 + - - +
554I THR* 1.3 75.2 - - - +
556I GLY* 1.3 69.2 + - - +
557I GLY 3.1 0.3 + - - -
558I ALA* 3.1 22.8 + - - +
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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