Contacts of the helix formed by residues 438 - 442 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 3.7 3.5 - - - +
234B ASN* 3.0 13.4 + - - -
235B VAL* 4.0 4.5 - - + -
265B GLU* 2.9 31.0 + - - +
394C TYR* 3.9 2.9 - - + -
437C GLY* 1.3 67.8 + - - -
439C ASN* 1.3 63.4 + - - +
440C GLY 3.3 3.1 - - - -
441C GLN* 3.2 41.7 + - - +
442C HIS* 3.4 6.8 - - - -
476C PHE* 3.7 24.2 - - + -
479C ASN* 3.8 24.5 - - + +
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Residues in contact with ASN 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 4.0 17.7 - - + +
206B GLY* 5.1 2.5 - - - +
209B ASP* 4.2 8.1 + - - -
210B LEU* 5.7 4.7 - - + +
233B SER* 2.8 36.2 + - - -
234B ASN* 3.4 30.0 + - - +
239B HIS* 5.1 0.2 - - - -
396C GLN* 4.1 4.6 - - - +
435C GLU* 5.5 4.3 - - + -
436C ALA 3.2 12.7 + - - +
438C THR* 1.3 77.3 - - - +
440C GLY* 1.3 63.5 + - - +
442C HIS* 3.0 16.5 + - - +
443C ALA* 3.4 12.0 + - - +
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Residues in contact with GLY 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C GLU* 5.1 4.4 - - - +
436C ALA 3.7 6.6 + - - -
437C GLY* 4.6 1.0 - - - -
438C THR 3.3 1.2 - - - -
439C ASN* 1.3 79.4 - - - +
441C GLN* 1.3 56.4 + - - +
443C ALA* 3.0 4.7 + - - -
444C PHE* 3.0 49.0 + - - -
445C TYR* 3.0 27.3 + - - -
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Residues in contact with GLN 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B GLU* 4.0 6.1 + - - -
411B GLU* 4.5 0.3 - - - +
567B VAL* 3.3 28.6 - - - +
570B GLY 6.0 0.2 - - - -
571B LYS* 5.8 4.6 - - - +
394C TYR* 2.7 23.6 + - - +
438C THR* 3.3 21.6 - - - +
439C ASN 3.1 0.2 - - - -
440C GLY* 1.3 76.1 - - - +
442C HIS* 1.3 65.9 + - + +
443C ALA 3.4 0.6 + - - -
445C TYR* 3.4 36.4 + - + +
479C ASN* 3.0 41.8 + - - +
483C GLN* 3.5 22.5 - - - +
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Residues in contact with HIS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 3.7 15.4 - - + +
206B GLY* 3.7 17.6 - - - +
263B THR* 3.8 15.5 - - + -
265B GLU* 2.7 36.1 + - - -
407B GLN* 2.8 32.9 + - - -
411B GLU* 3.3 10.8 - - - +
567B VAL* 5.2 2.1 - - - +
571B LYS* 4.3 20.7 - - - -
5002B G6Q 2.7 33.1 + - - +
438C THR 3.4 18.6 - - - -
439C ASN 3.0 5.8 + - - +
441C GLN* 1.3 85.2 + - + +
443C ALA* 1.3 51.5 + - - +
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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