Contacts of the helix formed by residues 382 - 389 (chain C) in PDB entry 6CP3
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 VAL 382 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C PRO* 3.7 12.2 - - + +
149C GLN* 3.4 29.6 - - - +
380C ALA 3.9 0.2 + - - -
381C GLN* 1.3 77.7 - - - +
383C LYS* 1.3 66.3 + - - +
384C ALA* 3.8 7.0 - - + +
385C LEU* 3.0 18.7 + - + +
386C LYS* 3.0 10.0 + - - +
440C THR* 3.9 29.6 - - + +
489C GLY* 3.4 27.8 - - - +
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Residues in contact with LYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLN 3.4 4.4 + - - +
382C VAL* 1.3 74.7 - - - +
384C ALA* 1.3 57.1 + - - +
386C LYS* 3.0 25.6 + - + +
387C GLN* 2.9 56.2 + - + +
489C GLY 3.8 7.3 + - - +
490C GLU* 3.7 32.1 - - + +
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C VAL* 3.2 5.1 - - + -
383C LYS* 1.3 77.1 - - - +
385C LEU* 1.3 60.0 + - - +
387C GLN* 3.5 16.2 + - - +
388C VAL* 3.8 6.9 + - - +
440C THR* 5.4 0.4 - - + -
444C VAL* 3.7 27.0 - - + +
485C ILE* 5.0 7.2 - - + -
489C GLY* 3.0 29.7 + - - +
490C GLU* 3.8 17.9 - - - +
491C LEU* 4.1 10.6 - - + +
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Residues in contact with LEU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ASP* 3.3 42.8 - - + +
157C ALA* 4.1 7.2 - - + +
381C GLN* 3.4 14.7 + - + +
382C VAL* 3.0 21.1 + - + +
384C ALA* 1.3 77.4 - - - +
386C LYS* 1.3 64.0 + - - +
388C VAL* 3.4 13.6 - - + +
389C ALA* 3.3 21.1 + - + +
440C THR* 4.7 8.7 - - + +
443C GLN* 4.3 14.8 - - + +
444C VAL* 4.0 25.3 - - + +
447C ILE* 4.3 18.4 - - + -
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Residues in contact with LYS 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C SER* 3.4 45.9 + - - +
379C ALA* 5.0 2.4 - - - +
381C GLN* 4.3 15.6 - - - +
382C VAL 3.0 10.6 + - - +
383C LYS* 3.0 29.9 + - + +
385C LEU* 1.3 77.8 - - - +
387C GLN* 1.3 63.5 + - + +
389C ALA 4.9 3.8 - - - +
390C GLY* 3.1 31.0 + - - -
423D VAL* 6.3 0.4 - - - +
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Residues in contact with GLN 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C LYS* 2.9 53.5 + - + +
384C ALA* 3.9 6.7 - - - +
385C LEU 3.3 0.8 - - - -
386C LYS* 1.3 78.7 - - + +
388C VAL* 1.3 62.7 + - + +
390C GLY* 4.6 2.4 + - - -
490C GLU* 4.7 1.2 - - - +
491C LEU* 3.3 49.0 + - + +
496C LEU* 5.0 9.6 - - + +
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Residues in contact with VAL 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C ALA 3.8 9.4 + - - +
385C LEU* 3.4 20.0 - - + +
387C GLN* 1.3 80.1 - - + +
389C ALA* 1.3 56.5 + - - +
390C GLY 3.7 1.3 - - - -
444C VAL* 3.8 27.8 - - + +
447C ILE* 3.4 31.8 - - + +
448C TYR* 3.9 38.4 - - + +
451C VAL* 3.4 24.5 - - - +
491C LEU* 4.4 9.0 - - + -
496C LEU* 5.3 2.7 - - + -
499C LEU* 5.1 0.2 - - + -
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Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA* 4.2 17.7 - - + +
381C GLN* 5.2 3.9 + - - +
385C LEU* 3.3 13.9 + - + +
386C LYS* 3.2 8.9 + - - +
388C VAL* 1.3 79.4 - - - +
390C GLY* 1.3 63.5 + - - +
391C SER 3.3 3.5 + - - -
392C LEU* 3.6 32.0 + - + +
393C LYS 5.2 0.5 + - - -
447C ILE* 3.8 13.9 - - + -
451C VAL* 5.0 1.1 - - - -
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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