Contacts of the helix formed by residues 399 - 404 (chain B) in PDB entry 2O8C
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 PRO 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372B TRP* 3.6 41.7 - - + +
397B TYR* 3.4 37.2 - - + +
398B VAL* 1.3 88.6 - - + +
400B GLU* 1.3 57.7 + - - +
401B ASP* 3.3 19.1 - - - +
402B PHE* 2.8 28.6 + - + +
403B LEU* 3.2 10.9 + - - +
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Residues in contact with GLU 400 (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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397B TYR* 4.6 5.8 + - - +
398B VAL 3.3 5.0 + - - -
399B PRO* 1.3 71.5 - - - +
401B ASP* 1.3 60.0 + - - +
402B PHE 3.4 1.0 + - - -
403B LEU* 3.8 9.4 + - + +
404B ASN* 3.3 43.1 + - - +
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Residues in contact with ASP 401 (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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399B PRO* 3.3 17.3 - - - +
400B GLU* 1.3 77.5 - - - +
402B PHE* 1.3 63.6 + - - +
404B ASN* 4.5 7.3 - - - +
405B SER* 4.0 13.5 + - - -
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Residues in contact with PHE 402 (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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366B TYR* 3.5 27.4 - + - -
370B LEU* 3.9 13.9 - - + -
372B TRP* 3.5 36.3 - + + +
398B VAL* 3.7 11.0 - - + -
399B PRO* 2.8 25.5 + - + +
401B ASP* 1.3 79.7 + - - +
403B LEU* 1.3 69.2 + - + +
404B ASN 3.3 0.2 - - - -
405B SER* 2.9 20.1 + - - -
406B CYS* 3.4 26.4 - - - -
414B TRP* 3.6 34.8 - + - -
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Residues in contact with LEU 403 (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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398B VAL* 3.6 42.4 - - + +
399B PRO 3.2 3.3 + - - +
400B GLU* 4.0 11.9 - - + +
402B PHE* 1.3 78.8 - - - +
404B ASN* 1.3 57.4 + - - +
406B CYS* 2.9 32.2 + - - +
411B ARG* 3.7 44.5 + - + +
414B TRP* 3.7 28.9 - - + +
415B GLN* 4.6 11.7 - - + +
418B SER* 6.3 1.8 - - - -
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Residues in contact with ASN 404 (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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400B GLU* 3.3 30.5 + - - +
401B ASP* 4.8 5.8 - - - +
402B PHE 3.3 0.8 - - - -
403B LEU* 1.3 75.2 - - - +
405B SER* 1.3 58.2 + - - +
406B CYS 3.4 3.2 - - - +
411B ARG* 2.5 36.5 + - - +
504B LYS* 4.4 7.8 + - - -
505B TYR* 3.6 18.8 + - - +
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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