Contacts of the helix formed by residues 374 - 381 (chain B) in PDB entry 3IAD
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 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B VAL* 1.3 77.3 - - - +
375B ASN* 1.3 63.5 + - - +
376B GLN* 3.5 9.8 + - - +
377B PHE* 3.1 18.2 + - - +
378B LEU* 3.1 23.2 + - - +
395B LEU* 4.2 4.5 - - - -
509B GLN* 3.0 24.0 + - - -
521B SER* 5.2 0.7 + - - -
901B 15X 3.2 30.7 - - - -
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Residues in contact with ASN 375 (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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374B SER* 1.3 73.4 - - - +
376B GLN* 1.3 52.6 + - - +
378B LEU* 3.2 7.8 + - - +
379B ILE* 2.7 48.8 + - + +
391B ASP 5.7 0.7 - - - +
393B SER* 4.4 4.8 - - - +
394B VAL* 3.6 15.4 - - + +
395B LEU* 2.9 42.0 + - - +
396B GLU* 3.1 25.1 + - - -
438B ASP* 4.4 7.3 + - - -
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Residues in contact with GLN 376 (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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424A GLN* 4.6 1.8 - - - +
374B SER* 3.2 9.6 + - - +
375B ASN* 1.3 79.4 - - - +
377B PHE* 1.3 57.0 + - - +
379B ILE* 3.9 24.2 - - - +
380B ASN* 2.6 75.3 + - - +
521B SER* 6.1 2.0 - - - +
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Residues in contact with PHE 377 (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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373B VAL* 4.0 19.7 - - + -
374B SER* 3.1 27.0 + - - +
375B ASN 3.2 0.2 - - - -
376B GLN* 1.3 76.1 - - - +
378B LEU* 1.3 62.5 + - + +
380B ASN* 3.4 6.1 + - - +
381B THR* 2.9 45.1 + - + +
509B GLN* 3.9 17.3 - - + +
512B ARG* 4.2 38.4 - - + -
513B GLU* 3.8 33.7 - - + +
516B ARG* 3.9 25.4 - - - -
518B MET* 4.3 14.8 - - + -
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Residues in contact with LEU 378 (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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371B PRO* 4.8 8.5 - - + -
373B VAL* 4.2 17.3 - - + -
374B SER 3.1 13.1 + - - +
375B ASN* 3.5 8.1 - - - +
377B PHE* 1.3 80.6 - - + +
379B ILE* 1.3 61.9 + - - +
381B THR* 3.2 7.4 + - - +
383B SER* 3.0 51.8 + - - +
385B LEU* 4.5 13.0 - - + -
386B ALA* 3.5 2.4 - - - +
394B VAL* 4.1 20.6 - - + -
395B LEU* 3.7 36.6 - - + -
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Residues in contact with ILE 379 (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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420A LYS* 4.5 0.5 + - - -
424A GLN* 4.7 5.7 + - - +
427A ARG* 5.5 1.2 + - - +
375B ASN* 2.7 35.6 + - + +
376B GLN* 3.7 27.8 - - - +
377B PHE 3.3 0.2 - - - -
378B LEU* 1.3 73.7 - - - +
380B ASN* 1.3 61.4 + - - +
382B ASN* 3.0 27.0 + - - +
386B ALA* 3.8 6.8 - - + +
391B ASP* 3.5 61.3 - - + +
394B VAL* 4.2 7.4 - - + -
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Residues in contact with ASN 380 (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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420A LYS* 3.5 21.0 + - - -
424A GLN* 2.7 31.5 + - - +
376B GLN* 2.6 60.6 + - - +
377B PHE* 3.9 3.6 - - - +
379B ILE* 1.3 71.0 - - - +
381B THR* 1.3 57.7 + - - +
382B ASN 3.3 1.3 - - - -
518B MET* 4.1 24.9 - - + +
410D GLU* 3.9 6.6 - - - +
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Residues in contact with THR 381 (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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377B PHE* 2.9 42.7 + - + +
378B LEU* 3.2 13.7 + - - +
380B ASN* 1.3 77.9 - - - +
382B ASN* 1.3 67.1 + - - +
383B SER* 3.4 7.8 + - - -
516B ARG* 3.9 21.3 - - - +
518B MET* 4.7 11.7 - - - -
409D GLU* 3.3 18.4 + - - +
410D GLU* 3.0 25.0 + - - -
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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