Contacts of the helix formed by residues 394 - 403 (chain B) in PDB entry 5ODS
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 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B GLY 4.5 4.3 - - - +
391B ILE 3.8 18.3 + - - +
392B LEU* 3.2 6.6 + - - +
393B ARG* 1.3 79.0 - - - +
395B PRO* 1.3 75.4 - - + +
396B ASP* 3.9 18.5 - - - +
397B THR* 3.2 29.8 + - - -
398B ILE* 3.6 13.5 + - - +
417B TYR* 4.7 0.7 + - - -
431B GLU* 6.3 0.2 - - - -
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Residues in contact with PRO 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 1.3 89.9 - - + +
396B ASP* 1.3 59.9 + - - +
398B ILE* 3.1 16.9 + - + +
399B ARG* 2.8 65.9 + - - +
430B TYR* 4.0 24.9 - - + -
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 3.9 13.3 - - - +
395B PRO* 1.3 91.0 - - - +
397B THR* 1.3 62.1 + - - +
399B ARG* 3.5 25.0 + - - +
400B ARG* 3.2 25.7 + - - +
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Residues in contact with THR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B PHE* 3.7 32.3 - - + -
384B ALA* 4.4 0.7 - - + -
392B LEU* 2.7 35.6 + - + +
394B THR* 3.2 19.8 + - - -
395B PRO 3.1 0.4 - - - -
396B ASP* 1.3 76.5 - - - +
398B ILE* 1.3 65.4 + - - +
400B ARG* 3.1 17.0 + - - +
401B PHE* 3.2 17.1 + - + -
417B TYR* 3.8 21.8 - - + +
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Residues in contact with ILE 398 (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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394B THR 3.6 18.2 - - - +
395B PRO* 3.1 15.1 + - + +
397B THR* 1.3 75.3 - - - +
399B ARG* 1.3 57.8 + - + +
401B PHE* 3.3 7.7 + - - +
402B GLN* 2.9 41.2 + - - +
414B LEU* 3.8 20.6 - - + +
417B TYR* 3.9 20.2 - - + +
418B PHE* 4.2 11.7 - - + -
430B TYR* 4.3 20.9 - - + -
431B GLU* 4.6 22.2 - - + -
434B GLU* 4.2 14.6 - - + -
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PRO* 2.8 37.5 + - - +
396B ASP* 3.5 36.2 + - - +
397B THR 3.2 0.2 - - - -
398B ILE* 1.3 78.4 - - + +
400B ARG* 1.3 61.0 + - + +
402B GLN* 3.6 12.2 + - - +
403B SER* 3.3 20.4 + - - -
430B TYR* 4.3 12.7 + - - -
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Residues in contact with ARG 400 (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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368B PHE* 3.6 18.6 - - + -
369B ASN* 2.7 46.5 + - - +
372B PHE* 3.3 60.9 - - + +
396B ASP 3.2 14.7 + - - +
397B THR* 3.1 13.3 + - - +
399B ARG* 1.3 77.2 - - + +
401B PHE* 1.3 61.7 + - - +
403B SER* 3.2 20.7 - - - -
404B VAL* 3.8 1.0 - - - +
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Residues in contact with PHE 401 (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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368B PHE* 3.6 35.2 - + - -
372B PHE* 4.0 18.8 - + - -
377B TYR* 4.2 22.2 - - + -
380B ALA* 4.6 2.0 - - + -
381B ALA* 4.3 18.2 - - + -
397B THR* 3.2 22.0 + - + -
398B ILE 3.3 5.8 + - - +
400B ARG* 1.3 76.0 - - - +
402B GLN* 1.3 64.1 + - - +
404B VAL* 3.3 21.8 + - - +
413B PRO* 3.6 31.3 - - + +
414B LEU* 3.9 29.7 + - + +
417B TYR* 3.7 35.0 - + + -
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Residues in contact with GLN 402 (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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398B ILE* 2.9 26.9 + - - +
399B ARG* 3.8 12.4 - - - +
400B ARG 3.3 0.2 - - - -
401B PHE* 1.3 76.9 - - - +
403B SER* 1.3 60.9 + - - +
404B VAL 3.1 7.5 + - - +
414B LEU* 3.8 25.4 - - + +
434B GLU* 3.5 38.1 + - - +
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Residues in contact with SER 403 (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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372B PHE* 5.7 1.7 - - - -
399B ARG 3.3 11.0 + - - -
400B ARG* 3.2 17.0 + - - -
401B PHE 3.1 0.4 - - - -
402B GLN* 1.3 79.5 - - - +
404B VAL* 1.3 59.7 + - - +
405B PRO* 3.8 6.5 - - - +
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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