Contacts of the helix formed by residues 367 - 377 (chain A) in PDB entry 1ISR
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 TRP 367 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 3.1 49.0 - - - -
38A VAL* 4.5 0.4 - - - -
39A ALA* 4.0 12.6 - - + -
53A VAL* 3.8 28.9 - - + -
54A HIS* 4.2 19.2 - + - -
70A ILE* 4.4 4.2 - - + +
76A ILE* 3.9 12.7 - - + +
79A VAL* 3.8 35.4 - - + -
105A ILE* 3.9 24.7 - - + -
107A ASP* 4.2 22.6 - - + +
365A ASN* 3.1 11.9 + - - +
366A PRO* 1.3 82.1 - - + +
368A PHE* 1.3 62.5 + - - +
369A PRO 3.5 1.1 - - - -
370A GLU* 3.5 16.2 + - - +
371A PHE* 3.1 22.0 + - - +
385A LEU* 5.5 2.7 - - + -
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Residues in contact with PHE 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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76A ILE* 4.3 14.1 - - + -
80A GLU* 4.5 2.2 - - - -
354A PHE* 5.1 1.8 - + - -
357A LEU* 4.1 27.1 - - + -
358A ARG 3.8 14.6 - - - -
359A LEU* 3.9 15.0 - - + -
362A ASN* 3.8 33.4 - - + +
365A ASN* 2.9 21.3 + - - +
367A TRP* 1.3 74.9 - - - +
369A PRO* 1.3 68.5 - - + +
371A PHE* 2.9 29.2 + + - +
372A TRP* 2.8 64.2 + + - +
400A LEU* 4.7 5.2 - - + -
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Residues in contact with PRO 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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359A LEU* 3.9 19.3 - - + +
362A ASN 5.8 1.8 - - - +
365A ASN 4.1 1.8 - - - +
366A PRO* 3.1 18.4 - - + +
368A PHE* 1.3 95.2 - - + +
370A GLU* 1.3 62.7 + - - +
372A TRP* 3.4 1.9 + - - +
373A GLN* 3.3 29.5 + - - +
380A LEU* 3.9 11.4 - - + +
383A HIS* 3.6 33.4 - - + +
385A LEU* 4.5 3.1 - - + -
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Residues in contact with GLU 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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54A HIS* 3.3 36.4 + - - -
69A GLU* 5.4 0.9 - - - -
70A ILE* 4.2 20.2 + - + +
367A TRP* 3.5 16.6 + - - +
368A PHE 3.2 0.4 - - - -
369A PRO* 1.3 80.6 - - - +
371A PHE* 1.3 64.3 + - - +
373A GLN* 3.6 10.5 + - - +
374A HIS* 3.4 20.5 + - + +
385A LEU* 4.1 32.3 - - + +
387A ASN* 5.5 4.6 + - - +
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Residues in contact with PHE 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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70A ILE* 4.0 19.3 - - + +
71A ARG 4.5 0.9 - - - -
72A GLU* 3.6 39.9 - - + -
76A ILE* 3.5 40.6 - - + -
354A PHE* 4.2 9.0 - + - -
367A TRP 3.1 14.9 + - - +
368A PHE* 2.9 24.5 + + - +
370A GLU* 1.3 74.4 - - - +
372A TRP* 1.3 58.7 + - - +
373A GLN 3.2 0.3 + - - -
374A HIS* 3.2 3.0 + - - +
375A ARG* 2.7 67.1 + - + +
400A LEU* 4.1 20.4 - - + -
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Residues in contact with TRP 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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357A LEU 4.3 6.5 - - - -
358A ARG* 4.0 11.2 - - + -
359A LEU* 3.3 56.2 - - + +
368A PHE* 2.8 47.1 + + - +
369A PRO 3.4 4.9 + - - +
371A PHE* 1.3 75.3 - + - +
373A GLN* 1.3 63.9 + - + +
375A ARG* 3.9 5.8 - - - -
376A PHE* 3.1 39.3 + + - +
378A CYS* 4.2 12.1 - - - -
394A CYS* 4.4 3.1 - - - +
396A GLY* 4.1 14.3 - - - -
398A GLU* 3.6 55.0 + - - -
400A LEU* 4.6 12.6 - - + -
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Residues in contact with GLN 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 PRO 3.3 14.1 + - - +
370A GLU* 3.8 7.9 - - - +
371A PHE 3.2 0.8 - - - -
372A TRP* 1.3 76.7 - - - +
374A HIS* 1.3 52.9 + - - +
375A ARG 3.2 0.2 + - - -
377A GLN* 2.8 32.1 + - - -
378A CYS* 3.1 28.0 + - - +
379A ARG* 3.2 3.5 - - - -
380A LEU* 3.2 54.1 + - + +
385A LEU* 2.9 28.9 + - - +
387A ASN* 2.9 35.6 + - + +
390A PHE* 4.0 2.0 - - - -
394A CYS* 4.1 2.9 - - - -
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Residues in contact with HIS 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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69A GLU* 3.5 33.5 + - + -
70A ILE* 3.6 37.7 - - + +
370A GLU* 3.4 7.3 + - + +
371A PHE* 3.2 2.3 + - - +
373A GLN* 1.3 79.2 - - - +
375A ARG* 1.3 63.7 + - - +
377A GLN* 3.9 11.7 + - - +
387A ASN* 4.9 9.2 - - - +
390A PHE* 4.1 22.8 - + + -
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Residues in contact with ARG 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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72A GLU* 3.2 34.5 + - - -
371A PHE* 2.7 43.8 + - + +
372A TRP* 3.4 9.0 - - - +
373A GLN 3.1 0.4 - - - -
374A HIS* 1.3 81.1 - - - +
376A PHE* 1.3 89.5 + - + +
377A GLN* 3.6 2.6 + - - +
400A LEU* 2.8 39.4 + - + +
402A GLU* 3.1 24.4 + - - +
403A ASN* 4.3 11.5 + - - +
404A TYR* 4.3 2.8 - - - +
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Residues in contact with PHE 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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372A TRP* 3.1 49.5 + + - +
375A ARG* 1.3 97.2 - - + +
377A GLN* 1.3 74.8 + - - +
378A CYS* 3.5 6.3 - - - +
398A GLU* 3.5 36.1 - - + +
399A SER 3.1 32.3 - - - -
400A LEU* 3.5 24.9 - - + -
402A GLU* 3.3 24.5 - - - -
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Residues in contact with GLN 377 (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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373A GLN 2.8 10.7 + - - -
374A HIS 3.9 7.1 + - - +
375A ARG 3.6 2.5 + - - +
376A PHE* 1.3 82.6 - - - +
378A CYS* 1.3 56.4 + - - +
390A PHE* 3.4 45.2 - - + +
392A LYS* 4.6 8.5 - - - +
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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