Contacts of the helix formed by residues 374 - 381 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373C VAL* 1.3 75.1 - - - +
375C ASN* 1.3 65.5 - - - +
376C GLN* 3.7 9.2 + - - +
377C PHE* 3.2 18.8 + - - +
378C LEU* 3.1 23.4 + - - +
395C LEU* 4.1 3.6 - - - -
509C GLN* 3.0 20.9 + - - -
521C SER* 5.6 0.3 + - - -
901C 15X 3.5 18.4 - - - -
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Residues in contact with ASN 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C SER* 1.3 72.3 - - - +
376C GLN* 1.3 58.0 + - - +
378C LEU* 2.9 8.8 + - - +
379C ILE* 2.8 42.6 + - + +
391C ASP 5.8 0.7 - - - +
393C SER* 4.2 4.8 - - - +
394C VAL* 3.6 15.3 - - + +
395C LEU* 2.8 41.5 + - - +
396C GLU* 3.2 26.7 + - - -
438C ASP* 4.2 9.9 + - - -
901C 15X 4.8 0.4 + - - -
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Residues in contact with GLN 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C SER* 3.3 8.7 + - - +
375C ASN* 1.3 78.9 - - - +
377C PHE* 1.3 55.6 + - - +
379C ILE* 4.2 24.3 - - - +
380C ASN* 2.9 69.9 + - - +
424D GLN* 4.4 3.6 - - - +
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Residues in contact with PHE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C VAL* 3.9 26.5 - - + -
374C SER* 3.2 25.8 + - - +
375C ASN 3.2 0.4 - - - -
376C GLN* 1.3 78.6 - - - +
378C LEU* 1.3 62.3 + - + +
380C ASN* 3.6 5.0 + - - +
381C THR* 3.2 46.9 + - + +
509C GLN* 3.8 28.0 - - + +
512C ARG* 4.4 25.8 - - + -
513C GLU* 3.9 25.6 - - + -
516C ARG* 3.9 27.4 - - - -
518C MET* 4.3 14.6 - - + -
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C PRO* 4.8 6.3 - - + -
373C VAL* 3.8 20.4 - - + -
374C SER 3.1 12.9 + - - +
375C ASN* 2.9 8.1 + - - +
377C PHE* 1.3 78.5 - - + +
379C ILE* 1.3 64.2 + - - +
381C THR* 3.6 4.7 + - - +
382C ASN 3.5 1.9 + - - -
383C SER* 3.1 50.1 + - - +
385C LEU* 5.1 9.9 - - + -
386C ALA* 3.5 3.2 - - - +
394C VAL* 4.3 19.7 - - + -
395C LEU* 3.4 41.1 - - + -
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Residues in contact with ILE 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C ASN* 2.8 31.8 + - + +
376C GLN* 3.8 28.3 - - - +
378C LEU* 1.3 77.4 - - - +
380C ASN* 1.3 63.2 + - - +
382C ASN* 3.0 22.2 + - - +
386C ALA* 3.9 10.4 - - + +
391C ASP* 3.4 60.5 - - + +
394C VAL* 4.4 3.6 - - + -
420D LYS* 4.7 0.9 + - - -
424D GLN* 4.8 7.0 + - + +
427D ARG* 5.5 1.3 - - - +
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Residues in contact with ASN 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A GLU* 3.7 5.5 - - - +
376C GLN* 2.9 49.4 + - - +
377C PHE* 4.0 1.7 - - - +
379C ILE* 1.3 77.9 - - - +
381C THR* 1.3 58.6 + - - +
382C ASN 3.2 0.4 - - - -
518C MET* 4.0 28.1 - - + +
420D LYS* 2.8 29.3 + - - +
424D GLN* 2.6 33.6 + - - +
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Residues in contact with THR 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A GLU* 3.3 23.2 + - - +
410A GLU* 3.0 28.9 + - + -
377C PHE* 3.2 44.0 + - + +
378C LEU* 3.6 12.1 + - - +
379C ILE 3.3 0.2 - - - -
380C ASN* 1.3 76.2 - - - +
382C ASN* 1.3 63.9 + - - +
383C SER* 4.1 6.1 + - - -
516C ARG* 4.1 17.3 - - - +
518C MET* 4.5 14.1 - - + -
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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
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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