Contacts of the helix formed by residues 394 - 403 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A GLY 4.5 4.3 - - - +
391A ILE 3.8 18.7 + - - +
392A LEU* 3.2 6.1 + - - +
393A ARG* 1.3 80.1 - - - +
395A PRO* 1.3 76.3 - - + +
396A ASP* 3.3 23.5 + - - +
397A THR* 3.2 29.1 + - - -
398A ILE* 3.6 13.1 + - - +
417A TYR* 4.7 0.7 + - - -
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Residues in contact with PRO 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A THR* 1.3 87.8 - - + +
396A ASP* 1.3 67.1 + - - +
398A ILE* 3.1 16.0 + - + +
399A ARG* 2.9 56.4 + - - +
430A TYR* 3.7 25.0 - - + -
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A THR* 3.3 19.8 + - - +
395A PRO* 1.3 84.6 - - - +
397A THR* 1.3 60.5 + - - +
399A ARG* 3.4 23.7 + - - +
400A ARG* 3.1 27.5 + - + +
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Residues in contact with THR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A PHE* 3.9 18.8 - - + -
384A ALA* 4.4 2.0 - - + -
392A LEU* 2.6 35.8 + - + +
394A THR* 3.2 20.0 + - - -
395A PRO 3.1 0.2 - - - -
396A ASP* 1.3 79.2 - - - +
398A ILE* 1.3 61.9 + - - +
400A ARG* 3.1 8.2 + - - +
401A PHE* 3.1 41.9 + - + -
417A TYR* 3.8 16.6 - - + +
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A THR 3.6 17.9 - - - +
395A PRO* 3.1 5.7 + - + +
397A THR* 1.3 75.1 - - - +
399A ARG* 1.3 53.4 + - + +
401A PHE* 3.2 8.8 + - + +
402A GLN* 2.7 53.6 + - + +
414A LEU* 5.8 2.5 - - + -
417A TYR* 4.0 21.1 - - + +
418A PHE* 4.1 23.3 - - + -
430A TYR* 3.6 33.0 - - + -
431A GLU* 4.1 23.3 - - + -
434A GLU* 4.5 9.4 - - + -
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PRO* 2.9 37.6 + - - +
396A ASP* 3.5 32.3 + - - +
397A THR 3.2 0.2 - - - -
398A ILE* 1.3 77.3 - - + +
400A ARG* 1.3 60.2 + - + +
402A GLN* 3.5 11.8 + - - +
403A SER* 2.9 27.0 + - - -
430A TYR* 4.3 17.8 + - - +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A PHE* 3.3 29.9 - - + -
369A ASN* 2.7 42.9 + - - +
372A PHE* 3.3 56.6 - - + +
396A ASP 3.1 16.4 + - - +
397A THR* 3.1 11.9 + - - +
399A ARG* 1.3 77.9 - - + +
401A PHE* 1.3 60.7 + - - +
403A SER* 3.3 22.0 + - - -
404A VAL 3.9 1.2 + - - -
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A PHE* 3.7 35.4 - + - -
372A PHE* 4.2 14.1 - + - -
377A TYR* 4.1 16.4 - + - -
380A ALA* 4.6 1.8 - - + -
381A ALA* 4.2 15.9 - - - -
397A THR* 3.1 25.8 + - + -
398A ILE* 3.7 7.9 - - - +
400A ARG* 1.3 73.5 - - - +
402A GLN* 1.3 62.4 + - - +
404A VAL* 3.0 23.1 - - - +
413A PRO* 3.4 38.6 - - + -
414A LEU* 3.3 27.5 - - + +
417A TYR* 3.7 37.9 - + + -
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ILE* 2.7 36.4 + - - +
399A ARG* 3.7 11.9 - - - +
400A ARG 3.2 0.2 - - - -
401A PHE* 1.3 72.5 - - - +
403A SER* 1.3 60.4 + - - +
404A VAL 3.2 11.1 + - - +
414A LEU* 4.3 23.6 - - + +
418A PHE* 6.2 0.2 - - - -
434A GLU* 3.1 31.3 + - - +
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Residues in contact with SER 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PHE* 5.7 1.1 - - - -
399A ARG 2.9 17.8 + - - -
400A ARG* 3.3 15.9 + - - -
401A PHE 3.2 0.6 - - - -
402A GLN* 1.3 76.7 - - - +
404A VAL* 1.3 61.0 + - - +
405A PRO* 4.1 1.9 - - - +
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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