Contacts of the helix formed by residues 365 - 376 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A THR* 1.3 73.9 - - - +
366A GLU* 1.3 82.6 + - - +
368A ASP* 3.3 8.7 + - - +
369A GLU* 3.0 41.8 + - - +
414A ARG* 4.1 10.9 + - - +
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Residues in contact with GLU 366 (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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364A THR* 3.5 20.9 - - - +
365A ASP* 1.3 97.1 + - - +
367A GLU* 1.3 58.8 + - + +
369A GLU* 3.3 6.9 + - - +
370A PHE* 2.9 26.6 + - - +
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Residues in contact with GLU 367 (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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362A SER 3.6 3.0 - - - +
363A PHE* 3.5 9.2 - - + -
364A THR* 3.2 38.4 + - - +
366A GLU* 1.3 77.1 - - + +
368A ASP* 1.3 59.5 + - - +
370A PHE* 3.1 8.6 + - - +
371A ILE* 2.9 36.5 + - + +
395A VAL* 4.1 24.9 - - + +
397A ASN* 4.4 10.9 + - - +
398A HIS* 2.7 39.7 + - - -
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Residues in contact with ASP 368 (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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363A PHE* 3.5 11.7 - - - +
364A THR 3.1 17.7 + - - +
365A ASP* 3.6 11.0 - - - +
367A GLU* 1.3 75.5 - - - +
369A GLU* 1.3 58.3 + - - +
371A ILE* 3.4 1.0 + - - -
372A LEU* 3.0 33.6 + - - +
406A ARG* 2.8 43.5 + - - +
411A LEU* 3.4 32.2 - - + +
414A ARG* 3.4 20.4 + - - +
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Residues in contact with GLU 369 (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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365A ASP* 3.0 33.7 + - - +
366A GLU* 3.7 6.5 - - - +
368A ASP* 1.3 77.1 - - - +
370A PHE* 1.3 61.6 + - - +
372A LEU* 3.6 15.2 + - - +
373A ASP* 3.1 23.2 + - - +
376A ARG* 4.7 11.1 + - - -
414A ARG* 3.0 26.3 + - - -
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Residues in contact with PHE 370 (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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366A GLU 2.9 14.7 + - - +
367A GLU* 3.1 11.6 + - - +
369A GLU* 1.3 74.1 - - - +
371A ILE* 1.3 67.3 + - + +
373A ASP* 3.2 12.2 + - + +
374A VAL* 3.0 51.6 + - + +
391A ILE* 4.4 14.6 - - + -
394A TYR* 3.8 43.1 - + + -
395A VAL* 4.1 18.2 - - + -
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Residues in contact with ILE 371 (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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363A PHE* 4.0 28.9 - - + -
367A GLU* 2.9 23.3 + - + +
368A ASP* 3.4 4.5 + - - +
370A PHE* 1.3 75.9 - - + +
372A LEU* 1.3 63.6 + - - +
374A VAL* 3.2 3.5 + - - +
375A VAL* 3.1 22.9 + - - +
388A TYR* 4.7 2.5 - - + -
391A ILE* 4.1 23.1 - - + -
395A VAL* 5.3 4.0 - - + -
403A ILE* 3.9 32.5 - - + -
406A ARG* 4.5 3.1 - - + -
407A PHE* 4.1 23.6 - - + -
411A LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 372 (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 ASP 3.0 21.2 + - - +
369A GLU* 3.8 29.4 - - - +
371A ILE* 1.3 75.9 - - - +
373A ASP* 1.3 62.4 + - - +
375A VAL* 3.3 5.2 + - - +
376A ARG* 3.0 46.3 + - - +
407A PHE* 3.9 13.9 - - + -
411A LEU* 3.5 37.2 - - + +
414A ARG* 4.1 24.9 - - + +
415A LEU* 4.1 19.6 - - + +
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Residues in contact with ASP 373 (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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369A GLU 3.1 16.5 + - - +
370A PHE* 3.2 13.6 + - + +
372A LEU* 1.3 78.0 - - - +
374A VAL* 1.3 66.9 + - - +
376A ARG* 3.3 15.7 + - - +
377A LYS* 3.0 59.6 + - - +
419A TYR* 4.4 11.4 + - - -
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Residues in contact with VAL 374 (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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370A PHE* 3.0 50.4 + - + +
371A ILE 3.2 7.4 + - - +
373A ASP* 1.3 79.3 - - + +
375A VAL* 1.3 60.5 + - - +
377A LYS* 3.4 3.1 + - - +
378A ASN* 2.9 43.3 + - - +
387A LEU* 4.2 12.8 - - + -
391A ILE* 3.7 29.6 - - + -
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Residues in contact with VAL 375 (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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371A ILE* 3.1 17.4 + - + +
372A LEU 3.3 4.2 + - - +
374A VAL* 1.3 74.1 - - - +
376A ARG* 1.3 60.7 + - - +
378A ASN 3.1 0.7 - - - -
379A PRO* 2.9 30.9 - - + +
382A ARG* 3.9 23.3 - - + -
387A LEU* 3.9 11.4 - - + -
388A TYR* 3.5 33.4 - - + +
391A ILE* 4.8 1.6 - - + -
407A PHE* 3.7 33.9 - - + -
415A LEU* 4.4 11.4 - - + -
418A VAL* 4.4 0.8 - - + +
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Residues in contact with ARG 376 (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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369A GLU* 4.7 9.3 + - - -
372A LEU* 3.0 45.4 + - - +
373A ASP* 3.7 12.2 + - - +
374A VAL 3.3 0.2 - - - -
375A VAL* 1.3 77.1 - - - +
377A LYS* 1.3 57.4 + - - +
378A ASN 3.2 0.2 - - - -
379A PRO* 3.3 12.0 - - - +
414A ARG 3.2 13.9 + - - -
415A LEU* 2.9 39.6 + - + +
416A GLU* 5.0 1.2 - - - +
417A TYR* 3.0 58.9 + - - +
418A VAL* 3.8 11.4 - - - +
419A TYR* 3.0 42.0 + - + +
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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