Contacts of the helix formed by residues 365 - 376 (chain B) in PDB entry 1IGN
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 ASP 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B THR* 1.3 73.3 - - - +
366B GLU* 1.3 66.5 + - - +
368B ASP* 3.3 8.4 + - - +
369B GLU* 3.0 37.7 + - - +
414B ARG* 3.5 27.4 + - - -
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Residues in contact with GLU 366 (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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364B THR* 3.2 19.4 + - - +
365B ASP* 1.3 86.4 + - - +
367B GLU* 1.3 65.6 + - + +
369B GLU* 3.7 6.1 + - - +
370B PHE* 3.1 22.9 + - - +
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Residues in contact with GLU 367 (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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362B SER 3.5 3.0 - - - +
363B PHE* 3.4 12.1 - - + -
364B THR* 3.0 40.1 + - - +
366B GLU* 1.3 76.9 - - + +
368B ASP* 1.3 58.9 + - - +
370B PHE* 3.2 7.2 + - - +
371B ILE* 2.9 37.4 + - + +
395B VAL* 4.1 23.6 - - + +
397B ASN* 4.4 12.0 + - - +
398B HIS* 2.8 34.8 + - - +
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Residues in contact with ASP 368 (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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363B PHE* 3.6 10.6 - - - +
364B THR 3.1 15.0 + - - +
365B ASP* 3.4 11.7 - - - +
367B GLU* 1.3 78.0 - - - +
369B GLU* 1.3 57.3 + - - +
371B ILE* 3.5 2.9 + - - +
372B LEU* 3.1 33.7 + - - +
406B ARG* 2.8 42.6 + - - +
411B LEU* 3.5 24.2 - - + +
414B ARG* 3.1 27.4 + - - +
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Residues in contact with GLU 369 (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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365B ASP* 3.0 30.7 + - - +
366B GLU* 4.0 6.5 - - - +
368B ASP* 1.3 73.4 - - - +
370B PHE* 1.3 62.2 + - - +
372B LEU* 3.6 11.9 - - - +
373B ASP* 2.9 29.6 + - - +
376B ARG* 4.6 12.5 + - - -
414B ARG* 2.6 30.0 + - - +
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Residues in contact with PHE 370 (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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366B GLU 3.1 16.9 + - - +
367B GLU* 3.4 7.0 - - - +
369B GLU* 1.3 77.0 - - - +
371B ILE* 1.3 66.5 + - + +
373B ASP* 3.2 8.9 + - + +
374B VAL* 2.9 49.1 + - + +
391B ILE* 4.0 15.7 - - + -
394B TYR* 3.5 50.0 - + + -
395B VAL* 4.1 17.0 - - + -
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Residues in contact with ILE 371 (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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363B PHE* 4.1 22.7 - - + -
367B GLU* 2.9 28.9 + - + +
368B ASP* 3.6 4.5 - - - +
370B PHE* 1.3 77.0 - - + +
372B LEU* 1.3 64.2 + - - +
374B VAL* 3.2 2.8 + - - +
375B VAL* 3.0 29.0 + - + +
388B TYR* 4.5 0.4 - - + -
391B ILE* 4.1 22.8 - - + +
395B VAL* 5.2 3.6 - - + -
403B ILE* 3.7 33.2 - - + -
406B ARG* 4.6 2.5 - - + -
407B PHE* 4.1 29.6 - - + -
411B LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 372 (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 ASP 3.1 21.7 + - - +
369B GLU* 3.6 13.2 - - - +
371B ILE* 1.3 77.1 - - - +
373B ASP* 1.3 63.8 + - - +
375B VAL* 3.2 4.7 + - - +
376B ARG* 2.9 49.9 + - - +
407B PHE* 3.9 15.3 - - + -
411B LEU* 3.6 36.6 - - + +
414B ARG* 3.8 37.5 - - + +
415B LEU* 4.1 18.4 - - + -
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Residues in contact with ASP 373 (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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369B GLU 2.9 19.1 + - - +
370B PHE* 3.2 10.4 + - + +
372B LEU* 1.3 75.5 - - - +
374B VAL* 1.3 65.3 + - - +
376B ARG* 3.5 15.8 + - - +
377B LYS* 2.8 61.5 + - - +
419B TYR* 4.0 13.0 + - - -
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Residues in contact with VAL 374 (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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370B PHE* 2.9 52.6 + - + +
371B ILE 3.6 4.5 - - - +
373B ASP* 1.3 79.7 - - - +
375B VAL* 1.3 60.1 + - - +
377B LYS* 3.3 4.0 + - - -
378B ASN* 3.0 47.2 + - - +
387B LEU* 4.1 11.0 - - + -
391B ILE* 3.7 28.5 - - + -
394B TYR* 6.0 1.6 - - + -
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Residues in contact with VAL 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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371B ILE* 3.0 17.8 + - + +
372B LEU 3.8 3.6 - - - +
374B VAL* 1.3 72.9 - - - +
376B ARG* 1.3 66.8 + - - +
378B ASN 3.1 1.6 - - - -
379B PRO* 3.0 24.9 - - + +
382B ARG* 4.0 18.4 - - + -
387B LEU* 4.1 12.6 - - + -
388B TYR* 3.5 37.7 - - + +
391B ILE* 4.5 2.2 - - + -
407B PHE* 3.7 36.1 - - + -
415B LEU* 5.0 7.6 - - + -
418B VAL* 4.6 1.9 - - + +
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Residues in contact with ARG 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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369B GLU* 4.6 11.7 + - - -
372B LEU* 2.9 46.4 + - - +
373B ASP* 3.7 19.7 + - - +
375B VAL* 1.3 76.5 - - - +
377B LYS* 1.3 58.1 + - - +
379B PRO* 3.2 13.0 - - - +
414B ARG 3.8 11.5 + - - -
415B LEU* 3.2 28.2 + - + +
416B GLU* 5.1 3.0 + - - -
417B TYR* 3.1 64.3 + - - +
418B VAL* 3.7 11.8 - - - +
419B TYR* 3.0 38.8 + - + +
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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