Contacts of the helix formed by residues 399 - 407 (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 ALA 399 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D GLU* 3.6 36.1 - - + +
371D GLN* 4.5 0.4 - - - +
374D VAL* 3.6 13.5 - - + -
391D ILE* 5.1 1.3 - - + -
395D PHE 4.0 0.2 + - - -
396D LEU* 2.8 19.8 + - + +
398D ARG* 1.3 77.5 - - - +
400D TYR* 1.3 65.9 + - - +
401D ASP 3.2 2.7 - - - -
402D GLN* 3.1 12.6 + - - +
403D VAL* 3.1 23.0 + - - +
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Residues in contact with TYR 400 (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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397C GLN* 3.6 26.2 + - + +
398C ARG* 6.1 0.2 - - - +
400C TYR* 4.1 15.7 - + + -
435C PHE* 4.8 0.2 - - - +
439C TYR* 3.7 32.5 - + + +
396D LEU* 3.3 6.3 + - + +
397D GLN* 3.7 14.4 - - - +
398D ARG 3.5 2.4 - - - -
399D ALA* 1.3 75.6 - - - +
401D ASP* 1.3 57.9 + - - +
403D VAL* 3.3 8.7 + - + +
404D LEU* 3.0 44.5 + - + +
439D TYR* 2.6 61.7 + + + -
440D LEU* 5.1 1.6 - - + -
442D CYS* 3.2 19.6 - - - -
443D ILE* 3.5 21.3 - - + +
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Residues in contact with ASP 401 (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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122C HIS* 2.8 42.6 + - - -
397C GLN* 3.3 19.7 + - - +
398C ARG* 2.8 60.6 + - + +
398D ARG 5.4 0.2 + - - -
399D ALA 3.2 0.8 - - - -
400D TYR* 1.3 80.0 - - - +
402D GLN* 1.3 60.4 + - - +
404D LEU* 4.5 1.6 - - - -
405D HIS* 2.7 39.4 + - - +
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Residues in contact with GLN 402 (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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159C MSE 3.4 27.1 - - + +
398C ARG* 3.8 14.6 - - - +
371D GLN* 3.3 39.0 + - - +
374D VAL* 3.1 23.8 - - + -
375D THR* 2.8 25.8 - - - +
398D ARG 4.2 0.9 - - - +
399D ALA* 3.1 24.0 + - - +
401D ASP* 1.3 76.2 + - - +
403D VAL* 1.3 61.1 + - - +
406D ASP* 2.8 40.2 + - - +
407D VAL* 3.2 5.5 + - - +
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Residues in contact with VAL 403 (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* 4.1 10.5 - - + -
396D LEU* 3.6 29.2 - - + -
399D ALA 3.1 15.7 + - - +
400D TYR* 3.5 9.6 - - + +
402D GLN* 1.3 76.3 - - - +
404D LEU* 1.3 58.3 + - - +
407D VAL* 3.3 5.7 - - - +
408D ALA* 3.0 27.0 + - - +
416D PHE* 3.8 24.5 - - + -
440D LEU* 4.4 15.7 - - + -
443D ILE* 4.5 5.4 - - + -
446D MSE 3.6 26.5 - - + -
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Residues in contact with LEU 404 (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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397C GLN* 3.4 38.4 - - + +
435C PHE* 3.8 22.9 - - + -
591C PHE* 3.9 20.3 - - + -
400D TYR* 3.0 36.0 + - + +
401D ASP 3.9 2.0 - - - +
403D VAL* 1.3 79.8 - - - +
405D HIS* 1.3 58.8 + - - +
408D ALA* 3.5 4.8 - - - +
409D ILE* 3.1 33.5 + - + +
443D ILE* 3.3 38.6 - - + -
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Residues in contact with HIS 405 (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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119C SER 3.9 12.5 + - - +
120C VAL* 4.1 4.5 - - - -
121C GLY* 3.5 16.5 + - - -
122C HIS* 3.1 57.3 + + + +
125C THR* 4.4 5.7 + - + +
397C GLN* 5.3 0.9 - - - +
398C ARG* 5.5 0.7 - - - -
430C THR* 3.8 12.6 + - - -
401D ASP* 2.7 31.2 + - - +
404D LEU* 1.3 75.2 - - + +
406D ASP* 1.3 85.6 + - - +
409D ILE* 3.3 39.6 - - + +
410D GLN* 4.0 6.1 + - - +
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Residues in contact with ASP 406 (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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118C LEU* 5.1 3.1 - - + +
125C THR* 3.3 24.7 + - - +
398C ARG* 5.3 0.9 + - - -
375D THR* 2.7 38.3 + - + +
378D ALA* 3.6 5.6 - - + +
402D GLN* 2.8 33.3 + - + +
405D HIS* 1.3 97.5 - - - +
407D VAL* 1.3 62.0 + - + +
410D GLN* 3.4 26.7 + - - +
412D LEU* 3.5 13.5 - - - +
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D VAL* 3.7 34.8 - - + +
378D ALA* 4.3 4.5 - - + -
402D GLN 3.2 3.0 + - - +
403D VAL* 3.3 9.6 + - - +
405D HIS 3.5 0.6 - - - -
406D ASP* 1.3 85.3 - - + +
408D ALA* 1.3 62.5 + - - +
409D ILE 3.4 0.4 - - - -
410D GLN 3.4 2.1 + - - -
411D LYS 2.9 22.9 + - - -
412D LEU* 2.9 36.3 + - + +
414D VAL* 3.9 26.7 - - + -
416D PHE* 4.3 7.0 - - + -
446D MSE 5.5 0.2 - - + -
471D PRO* 3.4 20.2 - - + -
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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