Contacts of the helix formed by residues 393 - 397 (chain D) in PDB entry 2O1S
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 SER 393 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392D TYR* 1.3 71.8 - - - +
394D THR* 1.3 64.0 + - - +
396D LEU* 3.3 5.2 + - - -
397D GLN* 3.5 4.1 + - - +
418D ILE* 3.3 23.8 - - - +
419D ASP 3.0 10.4 + - - -
420D ARG 4.1 6.9 + - - -
421D ALA* 4.1 3.6 - - - -
433D GLY* 3.5 22.1 - - - -
435D PHE 4.5 0.5 + - - -
436D ASP* 2.6 35.1 + - - +
439D TYR* 2.9 23.5 + - - -
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Residues in contact with THR 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ASP* 3.6 0.2 - - - +
122D HIS* 2.7 30.0 + - - +
392D TYR* 4.0 13.0 - - + -
393D SER* 1.3 79.7 - - - +
395D PHE* 1.3 85.0 + - + +
397D GLN* 3.1 43.3 + - - +
420D ARG* 5.2 0.9 + - + -
430D THR 3.1 9.9 + - - -
431D HIS* 3.6 28.9 - - + +
432D GLN 3.7 11.0 + - - -
433D GLY* 4.1 2.0 - - - -
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Residues in contact with PHE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D HIS* 3.5 39.5 - + + -
123D SER 5.7 0.7 - - - -
346D MSE 4.7 20.6 - - + -
370D GLU* 3.3 32.7 - - + +
391D ILE* 3.8 7.0 - - + -
392D TYR* 3.1 45.8 + + + +
394D THR* 1.3 83.5 - - + +
396D LEU* 1.3 63.7 + - - +
397D GLN 3.0 5.6 - - - -
398D ARG* 2.9 23.7 + - - +
431D HIS* 3.7 27.6 - + - -
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Residues in contact with LEU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D VAL* 5.9 0.9 - - + -
389D VAL* 6.0 0.2 - - + -
391D ILE* 3.3 31.1 - - + +
392D TYR 2.9 17.1 + - - +
393D SER* 3.3 6.2 + - - +
395D PHE* 1.3 77.1 - - - +
397D GLN* 1.3 57.5 + - - +
399D ALA* 2.8 24.0 + - + +
400D TYR* 3.3 8.9 + - + -
403D VAL* 3.6 27.6 - - + -
416D PHE* 4.3 13.7 - - + -
418D ILE* 3.8 30.7 - - + -
439D TYR* 3.6 24.6 - - + +
440D LEU* 4.4 10.8 - - + -
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Residues in contact with GLN 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C TYR* 3.7 17.7 + - + +
401C ASP* 2.9 37.3 + - + +
404C LEU* 3.9 28.2 - - - +
122D HIS* 3.8 6.3 - - - -
393D SER* 3.5 10.2 + - - +
394D THR* 3.1 31.2 + - - +
395D PHE 3.0 0.2 - - - -
396D LEU* 1.3 79.6 - - - +
398D ARG* 1.3 58.9 + - - +
399D ALA 3.5 0.3 + - - -
400D TYR* 3.6 16.8 + - - +
432D GLN 4.1 5.5 - - - +
435D PHE* 3.6 21.7 + - - +
439D TYR* 3.7 23.1 + - + -
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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
------------------------------------------------------------
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