Contacts of the strand formed by residues 529 - 535 (chain I) in PDB entry 3BTM
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 529 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523I TYR* 4.1 7.3 - - - -
524I ASN* 2.8 26.7 + - - +
527I ALA* 3.3 27.6 - - + +
528I GLY* 1.3 81.7 - - - +
530I CYS* 1.3 67.7 + - - +
531I GLN* 3.3 32.1 - - + +
552I LEU* 5.0 5.8 - - + -
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Residues in contact with CYS 530 (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* 4.4 16.3 - - + -
522I PHE 3.2 4.5 - - - -
523I TYR* 3.9 10.8 - - - -
529I LEU* 1.3 81.6 - - - +
531I GLN* 1.3 62.3 + - - +
548I ALA* 4.6 8.3 - - + +
551I CYS* 2.0 62.1 - - + -
552I LEU* 3.6 20.9 - - + +
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Residues in contact with GLN 531 (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* 3.1 7.5 - - - -
522I PHE* 2.8 52.4 + - + -
524I ASN* 3.1 29.8 + - + -
527I ALA* 4.6 3.0 - - - +
529I LEU* 3.3 29.1 - - + +
530I CYS* 1.3 71.8 - - - +
532I THR* 1.3 66.4 + - - +
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Residues in contact with THR 532 (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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519I ILE* 3.8 22.4 - - + -
520I ARG 3.1 6.7 - - - +
521I TYR* 3.6 33.0 - - + +
522I PHE* 3.8 6.4 - - - -
531I GLN* 1.3 79.1 - - - +
533I PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 533 (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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509I PRO* 3.6 24.2 - - + -
510I TYR 3.7 24.0 - - - -
511I THR* 4.5 4.5 - - - -
519I ILE* 3.6 6.4 - - - +
520I ARG* 3.0 48.3 + - + -
521I TYR 3.7 20.4 - - - -
522I PHE* 3.5 32.5 - + + -
532I THR* 1.3 76.4 - - - +
534I VAL* 1.3 84.2 + - - +
535I TYR* 3.7 6.9 + - + -
543I ASN 4.2 3.6 - - - -
544I ASN* 3.8 27.6 - - + -
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Residues in contact with VAL 534 (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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151E TYR* 4.0 17.9 - - + +
192E GLN* 4.4 11.0 - - + -
511I THR* 2.8 30.9 + - + +
516I ALA 4.1 4.0 - - - +
517I ARG* 3.8 48.5 - - + +
518I ILE 3.6 3.4 - - - +
519I ILE* 5.1 5.2 - - + -
533I PHE* 1.3 82.2 - - - +
535I TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 535 (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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510I TYR 3.8 8.3 - - - -
511I THR* 3.5 9.2 - - - -
516I ALA 3.5 3.8 - - - +
518I ILE* 2.7 46.1 + - + +
520I ARG* 3.8 36.6 - - + -
533I PHE* 3.7 9.4 + - + -
534I VAL* 1.3 74.4 - - - +
536I GLY* 1.3 67.5 + - - +
537I GLY* 3.4 18.9 + - - -
538I CYS* 3.1 42.5 - - - -
539I ARG 3.4 0.6 + - - -
540I ALA* 3.1 23.2 + - + +
544I ASN* 3.4 16.8 - - - -
602I SO4 2.8 36.8 + - - -
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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