Contacts of the helix formed by residues 395 - 399 (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 ASP 395 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ASN* 4.9 0.2 - - - -
236B ASP* 3.5 9.9 - - - +
238B THR* 5.1 0.2 + - - -
393C PRO 3.1 7.2 + - - +
394C TYR* 1.3 77.9 - - - +
396C GLN* 1.3 59.2 + - - +
397C TYR* 3.0 40.6 + - - +
398C LEU* 3.0 41.1 + - + +
399C TRP 3.9 0.5 + - - -
436C ALA* 4.0 3.3 - - - +
437C GLY 4.3 0.6 + - - -
460C ILE 5.4 0.9 - - - +
461C GLY* 5.8 2.0 - - - -
462C ALA* 4.5 11.8 - - - +
476C PHE* 3.7 3.0 - - - -
534C LEU* 3.5 29.7 - - - +
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Residues in contact with GLN 396 (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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234B ASN* 2.9 30.8 + - - +
236B ASP* 2.8 21.6 + - + +
238B THR* 3.9 17.9 - - + -
239B HIS* 3.5 45.2 + - + +
395C ASP* 1.3 71.6 + - - +
397C TYR* 1.3 61.8 + - - +
399C TRP* 3.2 46.5 + - - +
436C ALA* 4.2 8.8 - - - +
439C ASN* 4.1 5.5 - - - +
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Residues in contact with TYR 397 (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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238B THR* 3.3 35.4 - - + -
242B GLU* 2.6 34.7 + - + -
214C MET 4.5 0.9 - - - +
217C GLU* 3.3 30.9 - - - +
218C ALA* 3.3 36.9 + - - +
220C LYS* 3.8 19.3 - - + -
221C PRO* 3.5 28.1 - - + +
225C ARG* 4.5 0.5 + - - -
395C ASP* 3.0 21.4 + - - +
396C GLN* 1.3 77.9 - - - +
398C LEU* 1.3 55.2 + - - +
399C TRP* 3.2 5.7 + - - -
400C ARG 4.7 0.5 + - - -
466C GLN* 4.6 9.0 - - + -
467C ASN* 2.9 22.1 + - - -
534C LEU* 4.6 3.4 - - + -
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Residues in contact with LEU 398 (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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214C MET* 4.9 2.9 - - - -
218C ALA* 3.8 14.4 - - + -
393C PRO* 3.5 31.7 - - + +
395C ASP* 3.0 23.5 + - + +
397C TYR* 1.3 76.2 - - - +
399C TRP* 1.3 56.8 + - - +
400C ARG 3.1 3.8 - - - +
401C LEU* 3.0 46.1 + - + +
402C PRO* 3.7 0.2 - - - +
460C ILE* 4.3 15.9 - - + -
531C ILE* 6.1 1.1 - - + -
534C LEU* 3.7 26.5 - - + -
539C LEU* 3.8 28.9 - - + -
542C ILE* 5.0 3.1 - - + -
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Residues in contact with TRP 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B TRP* 3.7 37.5 - + - -
400B ARG* 4.7 14.4 - - - -
213C VAL* 5.8 1.1 - - + -
217C GLU* 2.8 36.3 + - + +
396C GLN* 3.2 43.3 + - + +
397C TYR* 3.2 10.2 - - - -
398C LEU* 1.3 75.9 - - - +
400C ARG* 1.3 98.9 + - + +
401C LEU 3.4 0.7 - - - -
402C PRO* 3.6 11.6 - - - +
403C ALA 5.4 0.2 + - - -
435C GLU* 4.6 12.1 - - - +
436C ALA* 4.2 19.9 + - + +
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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