Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 3C98
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 PRO 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.8 15.7 - - + +
383A ILE* 4.1 21.8 - - + +
384A LYS 3.8 0.9 - - - -
385A ASP* 1.3 88.0 - - - +
387A MET* 1.3 66.4 + - - +
388A ARG 2.9 1.9 + - - -
389A ALA* 3.2 14.6 + - - +
390A ILE* 3.6 12.8 + - - +
411A TYR* 3.8 24.5 - - + -
414A LEU* 4.2 22.9 - - + -
415A LYS* 4.7 16.2 - - - +
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Residues in contact with MET 387 (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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385A ASP* 3.2 15.8 + - - +
386A PRO* 1.3 78.5 - - - +
388A ARG* 1.3 63.8 + - - +
390A ILE* 3.8 8.7 - - - -
391A VAL* 3.1 46.8 + - + +
411A TYR* 3.2 37.7 - - + +
422A ASN* 4.5 15.3 - - + +
426A LEU* 3.7 28.9 - - + -
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Residues in contact with ARG 388 (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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384A LYS 5.4 0.7 - - - +
385A ASP* 3.5 29.6 + - + +
386A PRO 2.9 1.2 + - - -
387A MET* 1.3 78.6 - - - +
389A ALA* 1.3 56.9 + - + +
391A VAL* 4.6 1.2 - - - +
392A PRO* 2.9 24.8 - - - +
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Residues in contact with ALA 389 (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 VAL* 4.2 24.6 - - + +
386A PRO 3.2 7.7 + - - +
388A ARG* 1.3 78.6 - - + +
390A ILE* 1.3 64.7 + - - +
392A PRO* 3.4 12.0 - - - +
393A ILE* 3.6 19.6 + - - +
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Residues in contact with ILE 390 (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 VAL* 4.3 13.2 - - + -
372A LEU* 3.9 15.5 - - + -
386A PRO 3.8 11.7 - - - +
387A MET* 3.2 10.9 + - - +
389A ALA* 1.3 78.4 - - - +
391A VAL* 1.3 65.9 + - - +
393A ILE* 3.0 9.1 + - - +
394A LEU* 3.0 41.9 + - + +
407A ILE* 3.8 24.0 - - + +
408A ILE* 5.5 2.0 - - + -
411A TYR* 3.3 47.1 - - + -
426A LEU* 4.7 10.1 - - + -
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Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 3.1 38.7 + - + +
388A ARG* 4.6 1.1 - - - +
390A ILE* 1.3 77.9 - - + +
392A PRO* 1.3 69.9 - - + +
393A ILE 3.2 0.2 + - - -
394A LEU* 3.3 8.8 + - + +
395A LEU* 3.2 35.2 + - + +
426A LEU* 5.6 2.9 - - + -
429A HIS* 3.7 31.6 - - + +
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Residues in contact with PRO 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LYS* 5.9 1.2 + - - -
388A ARG 2.9 29.4 - - - +
389A ALA* 3.4 12.6 - - - +
391A VAL* 1.3 91.4 - - + +
393A ILE* 1.3 59.8 + - + +
395A LEU* 3.4 9.4 + - + +
396A ASP* 3.3 20.4 + - - +
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Residues in contact with ILE 393 (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 LYS* 3.9 32.3 - - + +
365A LEU* 4.3 24.9 - - + -
368A VAL* 3.6 37.5 - - + -
389A ALA 3.6 10.1 - - - +
390A ILE* 3.0 11.1 + - - +
392A PRO* 1.3 77.0 - - + +
394A LEU* 1.3 71.1 + - + +
395A LEU 3.1 1.8 - - - -
396A ASP* 3.1 24.3 + - - +
399A VAL* 4.0 13.0 - - + +
404A LYS* 3.9 4.4 - - + -
407A ILE* 4.3 17.9 - - + -
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE* 3.0 37.9 + - + +
391A VAL* 3.3 7.6 + - + +
393A ILE* 1.3 77.8 - - + +
395A LEU* 1.3 58.1 + - - +
404A LYS* 2.9 63.7 + - + +
407A ILE* 4.6 6.5 - - + -
408A ILE* 4.0 12.3 - - + -
426A LEU* 3.7 37.0 - - + +
429A HIS* 3.5 11.4 - - + +
430A ALA* 3.3 25.2 - - + +
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Residues in contact with LEU 395 (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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391A VAL* 3.2 32.8 + - + +
392A PRO* 3.8 7.9 - - + +
393A ILE 3.1 0.8 - - - -
394A LEU* 1.3 77.1 - - - +
396A ASP* 1.3 63.5 + - - +
397A ALA* 3.4 5.4 + - - +
404A LYS* 4.6 0.9 - - - -
429A HIS* 3.4 38.4 - - + +
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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