Contacts of the helix formed by residues 521 - 529 (chain B) in PDB entry 1B3U
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 521 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B THR* 2.8 20.0 + - + +
517B THR* 3.7 14.1 - - + +
520B MET* 1.3 69.9 - - - +
522B PRO* 1.3 71.9 - - + +
524B VAL* 3.0 6.7 + - + +
525B LEU* 3.0 47.4 + - + +
543B LEU* 4.1 21.5 - - + -
546B ILE* 4.3 9.6 - - + +
550B LEU* 4.3 21.5 - - + -
554B THR* 3.9 28.0 - - + -
558B GLU* 4.8 6.1 - - + -
559B VAL* 4.3 7.6 - - + -
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Residues in contact with PRO 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B THR 3.4 13.9 - - - +
518B LYS 3.9 14.8 - - - +
519B HIS 4.4 1.6 - - - -
520B MET 3.4 10.8 - - - +
521B LEU* 1.3 95.3 - - + +
523B THR* 1.3 62.6 + - - +
525B LEU* 3.3 11.2 + - + +
526B ARG* 3.0 24.1 + - - +
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B LEU* 3.2 29.3 - - + +
489B SER* 3.8 29.9 + - - +
500B THR* 4.4 9.4 - - + -
504B ILE* 4.8 2.7 - - + -
519B HIS 4.7 1.4 + - - -
520B MET 3.2 9.0 + - - -
521B LEU 3.2 0.6 - - - -
522B PRO* 1.3 80.7 - - - +
524B VAL* 1.3 54.5 + - - +
526B ARG* 3.3 6.8 + - + +
527B MET* 2.7 45.3 + - + +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B LEU* 4.2 16.2 - - + -
504B ILE* 3.8 32.1 - - + -
520B MET 3.2 15.0 + - - +
521B LEU* 3.0 8.1 + - - +
523B THR* 1.3 75.9 - - - +
525B LEU* 1.3 64.5 + - - +
527B MET* 3.2 22.4 + - - +
528B ALA 3.5 3.1 + - - -
539B VAL* 3.8 22.0 - - + +
542B SER* 4.6 6.1 - - - -
543B LEU* 3.8 28.0 - - + -
546B ILE* 4.4 8.5 - - + -
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 3.0 44.8 + - + +
522B PRO* 3.6 9.6 - - + +
524B VAL* 1.3 75.2 - - - +
526B ARG* 1.3 64.9 + - - +
528B ALA* 3.0 23.8 + - - +
539B VAL* 5.6 0.4 - - - -
543B LEU* 4.3 14.1 - - + -
558B GLU* 4.1 24.7 - - + +
559B VAL* 4.4 10.1 - - - -
562B ILE* 3.8 39.3 - - + +
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Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522B PRO 3.0 17.3 + - - +
523B THR* 3.6 8.3 - - + +
525B LEU* 1.3 76.6 - - - +
527B MET* 1.3 63.7 + - - +
528B ALA 3.0 1.0 + - - -
529B GLY* 3.3 12.6 + - - -
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Residues in contact with MET 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B SER* 4.3 16.2 - - - +
497B ARG* 3.4 38.4 - - + +
500B THR* 4.4 8.7 - - + -
501B LEU* 3.6 23.6 - - + -
523B THR* 2.7 42.0 + - + +
524B VAL* 3.3 14.1 - - - +
525B LEU 3.2 0.2 - - - -
526B ARG* 1.3 76.7 - - - +
528B ALA* 1.3 63.4 + - - +
529B GLY 3.1 0.4 - - - -
530B ASP* 2.8 31.5 + - - +
535B VAL* 4.6 7.6 - - + -
536B ARG* 4.3 0.3 - - - +
539B VAL* 3.8 16.6 - - + +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B VAL 3.5 3.9 + - - +
525B LEU 3.0 18.3 + - - +
527B MET* 1.3 77.0 - - - +
529B GLY* 1.3 56.4 + - - +
536B ARG* 3.1 25.6 - - - +
539B VAL* 4.1 15.2 - - + +
562B ILE* 4.0 28.0 - - + -
565B LYS* 6.5 1.1 - - + -
566B LEU* 4.2 15.8 - - + +
570B GLN* 5.9 0.2 - - - +
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Residues in contact with GLY 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B ARG 3.3 9.6 + - - -
527B MET 2.9 2.7 + - - -
528B ALA* 1.3 77.5 - - - +
530B ASP* 1.3 60.7 + - - +
531B PRO* 3.9 4.2 - - - +
536B ARG* 4.8 1.8 - - - -
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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