Contacts of the helix formed by residues 359 - 367 (chain A) in PDB entry 7CAL
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 ILE 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A LEU* 4.1 17.9 - - + -
356A PRO* 3.7 24.5 - - + -
357A LYS 4.5 0.2 - - - +
358A ALA* 1.3 77.6 - - - +
360A ARG* 1.3 63.6 + - - +
362A SER* 3.5 4.3 + - - -
363A ILE* 3.2 30.6 + - + +
329B ILE* 4.5 10.8 - - + +
332B GLN* 3.4 40.6 - - + +
333B MET* 3.7 34.1 - - + +
336B HIS* 5.4 4.5 - - + +
398B PHE* 5.9 1.8 - - + -
402B GLU* 5.0 9.0 - - + -
403B ASP 4.7 10.3 - - - +
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Residues in contact with ARG 360 (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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352A LEU* 3.3 44.4 + - + +
353A ASN* 4.5 19.0 + - - -
355A LEU* 2.7 34.5 + - + +
356A PRO 3.2 14.8 + - - -
357A LYS* 4.3 8.7 - - - +
358A ALA 3.3 1.0 - - - +
359A ILE* 1.3 81.5 - - - +
361A SER* 1.3 60.2 + - - +
363A ILE* 3.3 13.1 + - + +
364A ALA* 3.2 22.7 + - - +
390A VAL 5.7 5.2 - - - -
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Residues in contact with SER 361 (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 LYS 3.0 21.1 + - - -
358A ALA* 3.9 0.9 + - - -
359A ILE 3.4 0.2 - - - -
360A ARG* 1.3 78.9 - - - +
362A SER* 1.3 57.2 + - - +
363A ILE 3.5 0.2 - - - -
364A ALA* 4.1 4.8 - - - +
365A ASN* 3.1 30.7 + - - +
390A VAL* 3.6 30.9 - - - +
406B LEU* 3.9 21.2 - - - +
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Residues in contact with SER 362 (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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358A ALA 3.3 19.9 + - - -
359A ILE 3.5 0.6 + - - -
360A ARG 3.2 0.6 - - - -
361A SER* 1.3 74.8 - - - +
363A ILE* 1.3 64.5 + - - +
364A ALA 3.3 0.4 - - - -
365A ASN* 3.8 6.9 - - - +
366A TYR* 3.4 21.0 + - - +
329B ILE* 3.9 28.3 - - - +
332B GLN* 5.6 0.7 - - - -
403B ASP* 5.4 4.0 + - - -
406B LEU* 5.0 12.6 - - - +
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Residues in contact with ILE 363 (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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352A LEU* 5.5 4.3 - - + -
355A LEU* 3.8 26.5 - - + -
359A ILE* 3.2 22.1 + - + +
360A ARG* 3.3 10.5 + - + +
362A SER* 1.3 77.4 - - - +
364A ALA* 1.3 59.1 + - + +
365A ASN 3.1 0.6 + - - -
366A TYR* 3.4 3.3 + - - +
367A LEU* 3.0 40.6 + - + +
319B PHE* 3.9 31.0 - - + -
325B LEU* 4.4 20.6 - - + -
329B ILE* 4.5 11.4 - - + -
333B MET* 4.0 17.7 - - + -
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Residues in contact with ALA 364 (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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360A ARG 3.2 12.6 + - - +
361A SER* 4.1 5.1 - - - +
362A SER 3.3 0.4 - - - -
363A ILE* 1.3 79.4 - - + +
365A ASN* 1.3 64.5 + - - +
367A LEU* 2.9 19.9 - - - +
368A PHE* 4.0 17.8 - - + -
389A LEU* 3.3 35.0 - - - +
390A VAL* 4.7 7.2 - - - -
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Residues in contact with ASN 365 (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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361A SER* 3.1 20.3 + - - +
362A SER* 3.5 7.9 + - - +
363A ILE 3.1 0.8 - - - -
364A ALA* 1.3 85.2 + - - +
366A TYR* 1.3 64.3 + - - +
367A LEU 3.4 0.2 - - - -
369A PHE* 3.2 30.0 - - + +
370A PRO* 5.4 0.2 - - - +
387A PHE* 3.3 41.6 + - + -
389A LEU* 3.4 26.9 + - - +
390A VAL* 5.3 3.2 - - - +
406B LEU* 4.8 1.6 - - - +
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Residues in contact with TYR 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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362A SER 3.4 13.2 + - - +
363A ILE 4.1 2.5 - - - +
365A ASN* 1.3 79.9 - - - +
367A LEU* 1.3 78.5 + - + +
368A PHE 3.8 1.6 + - - -
369A PHE 4.5 2.3 + - - -
370A PRO* 4.9 5.9 - - - +
323B ASN 4.6 2.5 - - - -
324B GLN 3.8 18.6 + - - -
325B LEU* 3.8 8.1 - - + -
326B PRO* 3.7 42.5 - - + +
329B ILE* 5.7 2.2 - - + -
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Residues in contact with LEU 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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363A ILE* 3.0 27.8 + - + +
364A ALA 2.9 23.0 - - - +
366A TYR* 1.3 94.9 - - + +
368A PHE* 1.3 90.2 + - + +
369A PHE 3.0 4.1 + - - -
319B PHE* 4.8 1.8 - - + -
323B ASN* 3.4 45.1 - - + +
325B LEU* 3.8 16.4 - - + -
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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