Contacts of the helix formed by residues 500 - 505 (chain B) in PDB entry 1S0V
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 500 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ILE* 3.9 41.1 - - + +
353B PRO 5.7 0.2 + - - -
496B PRO 6.0 0.2 - - - +
497B LEU 5.9 2.9 - - - +
498B GLU 4.1 0.6 - - - -
499B ASN* 1.3 70.4 - - - +
501B TRP* 1.3 66.7 + - - +
502B TRP* 3.3 5.8 - - + +
503B ALA* 2.9 22.2 + - + +
504B GLU* 3.2 13.0 + - - +
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Residues in contact with TRP 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B PHE* 4.6 11.0 - + - -
485B ASN* 2.8 42.8 - - + -
488B ASN* 3.6 45.3 + - + +
489B ILE* 3.9 16.4 - - + -
492B CYS* 4.7 5.4 - - + -
499B ASN* 3.1 8.5 + - + +
500B THR* 1.3 73.9 + - - +
502B TRP* 1.3 52.7 + - - +
504B GLU* 2.6 30.2 + - + +
505B GLN* 2.5 47.3 + - - +
511B PHE* 3.9 32.8 - + - -
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Residues in contact with TRP 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL* 4.2 13.5 - - + -
341B ILE* 4.4 15.9 - - + -
348B PRO 5.5 2.2 - - - -
349B VAL* 5.1 3.8 - - + -
492B CYS* 2.9 35.4 - - + -
496B PRO* 3.6 16.7 + - + -
499B ASN 2.9 16.9 + - - -
500B THR* 4.1 7.3 - - + +
501B TRP* 1.3 79.2 - - - +
503B ALA* 1.3 73.6 + - + +
505B GLN* 3.7 17.2 - - - +
508B PRO* 3.3 32.9 - - + +
509B PHE* 3.7 44.9 - + - -
511B PHE* 3.8 18.8 - - + -
512B LEU* 3.3 42.6 - - + -
515B CYS* 4.7 0.2 - - - -
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Residues in contact with ALA 503 (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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348B PRO 5.0 0.4 - - - +
349B VAL* 3.3 30.7 - - + +
352B ILE* 3.5 30.5 - - + -
500B THR* 2.9 22.6 + - + +
502B TRP* 1.3 98.3 - - + +
504B GLU* 1.3 61.7 + - + +
505B GLN 3.5 6.1 - - - +
508B PRO* 3.5 3.3 - - - +
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ILE* 4.4 13.8 - - + +
353B PRO 4.6 2.1 - - - +
354B ALA* 3.6 25.6 - - - +
500B THR* 3.7 15.1 + - - +
501B TRP* 2.6 41.4 + - + +
503B ALA* 1.3 71.4 - - + +
505B GLN* 1.3 74.7 + - - +
506B ASP* 4.8 1.2 - - - +
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Residues in contact with GLN 505 (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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467B CYS 3.9 9.2 - - - +
468B ALA* 4.1 19.3 - - - +
481B PHE* 4.9 2.8 - - - -
501B TRP* 2.5 50.9 + - - +
502B TRP 3.7 9.6 - - - +
503B ALA 3.4 3.1 - - - +
504B GLU* 1.3 94.5 - - - +
506B ASP* 1.3 65.7 + - - +
507B SER 3.6 0.9 - - - +
508B PRO* 3.5 10.8 - - - +
511B PHE* 3.3 42.1 - - + -
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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