Contacts of the helix formed by residues 438 - 443 (chain B) in PDB entry 2O2C
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 438 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B TYR* 4.0 1.3 - - + -
437B GLY* 1.3 68.8 + - - -
439B ASN* 1.3 65.2 + - - +
440B GLY 3.1 3.1 - - - -
441B GLN* 2.9 41.6 + - - +
442B HIS* 3.5 4.2 - - - -
476B PHE* 3.8 24.0 - - + -
479B ASN* 3.8 26.2 - - + +
205C ILE* 3.5 6.1 - - - +
234C ASN* 3.0 10.6 + - - -
235C VAL* 3.9 6.5 - - + -
265C GLU* 2.8 30.9 + - - +
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Residues in contact with ASN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLN* 4.0 4.1 - - - +
435B GLU* 5.5 4.7 - - + -
436B ALA* 3.3 12.2 + - - +
438B THR* 1.3 77.2 + - - +
440B GLY* 1.3 62.6 + - - +
442B HIS* 3.0 17.8 + - - +
443B ALA* 3.4 11.0 + - - +
205C ILE* 3.9 18.5 - - + +
206C GLY* 5.1 1.9 - - - -
209C ASP* 4.3 7.9 + - - -
210C LEU* 6.3 0.2 - - - +
233C SER* 2.7 35.4 + - - -
234C ASN* 3.3 31.4 + - - +
239C HIS* 5.0 0.6 - - - -
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Residues in contact with GLY 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLU* 4.9 5.8 - - - +
436B ALA 3.6 8.9 + - - -
437B GLY* 4.6 0.4 - - - -
438B THR 3.1 1.6 + - - -
439B ASN* 1.3 78.6 - - - +
441B GLN* 1.3 55.8 + - - +
443B ALA* 3.0 10.2 + - - -
444B PHE* 3.0 41.4 + - - -
445B TYR* 3.0 26.9 + - - -
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Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TYR* 2.6 37.9 + - - +
438B THR* 2.9 24.2 + - - +
440B GLY* 1.3 75.8 - - - +
442B HIS* 1.3 64.6 + - + +
443B ALA 3.3 1.2 + - - -
445B TYR* 3.5 37.0 + - + +
479B ASN* 3.2 31.6 - - - +
483B GLN* 3.5 22.7 + - - +
265C GLU* 3.9 4.7 - - - +
411C GLU* 4.4 0.3 - - - +
567C VAL* 3.5 27.0 - - + +
571C LYS* 6.0 1.7 - - - +
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B THR 3.5 17.9 - - - -
439B ASN 3.0 7.4 + - - +
441B GLN* 1.3 83.6 + - + +
443B ALA* 1.3 57.1 + - - +
205C ILE* 3.6 17.0 - - + +
206C GLY* 3.6 18.0 - - - +
263C THR* 3.8 14.4 - - + -
265C GLU* 2.6 38.4 + - - -
407C GLN* 2.9 12.6 + - - -
411C GLU* 3.6 7.2 - - - -
567C VAL* 5.3 1.7 - - - +
571C LYS* 4.5 18.2 - - - -
5003C G6Q 2.8 52.9 + - - +
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Residues in contact with ALA 443 (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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435B GLU* 6.2 0.4 - - + -
439B ASN 3.7 9.9 - - - +
440B GLY* 3.0 11.0 + - - +
441B GLN 3.3 1.4 + - - -
442B HIS* 1.3 80.0 - - - +
444B PHE* 1.3 75.9 + - + +
445B TYR 3.9 0.4 - - - -
206C GLY* 5.8 0.2 - - - -
210C LEU* 4.5 12.6 - - + -
403C ALA 5.5 1.1 - - - +
406C GLN* 5.6 0.4 - - + +
407C GLN* 3.3 28.7 - - + +
411C GLU* 3.3 28.6 + - - +
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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
------------------------------------------------------------
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