Contacts of the helix formed by residues 386 - 393 (chain C) in PDB entry 5L26
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 ARG 386 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C ILE* 3.6 10.4 + - + +
166C ARG* 3.6 23.6 + - - +
167C ARG 4.4 0.4 - - - -
168C MET* 2.5 31.1 + - - +
169C THR 3.4 18.8 + - - -
170C GLU* 4.2 8.1 + - - +
173C LEU* 3.5 28.7 - - + +
383C ALA* 3.1 27.7 + - + +
384C PRO 3.1 0.8 - - - -
385C LYS* 1.3 85.6 - - + +
387C ARG* 1.3 62.9 + - - +
388C LYS 3.2 3.4 - - - -
389C ASP* 2.9 39.1 + - - +
390C VAL* 3.1 18.1 + - + +
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Residues in contact with ARG 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU* 5.3 12.7 - - - +
376C VAL* 3.7 29.1 - - + +
377C GLY* 5.8 3.0 - - - -
380C SER* 3.3 31.8 + - - +
383C ALA 3.7 2.7 + - - -
384C PRO 3.3 17.2 + - - +
385C LYS 3.4 0.2 - - - -
386C ARG* 1.3 78.0 - - - +
388C LYS* 1.3 62.5 + - - +
390C VAL* 3.4 8.2 + - - +
391C ALA* 3.2 23.9 + - + +
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Residues in contact with LYS 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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385C LYS 4.7 6.1 + - - +
386C ARG 3.2 1.0 - - - -
387C ARG* 1.3 78.8 - - - +
389C ASP* 1.3 67.7 + - - +
391C ALA* 3.8 4.0 + - - +
392C ARG* 3.2 27.5 + - - +
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Residues in contact with ASP 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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170C GLU* 4.2 7.2 - - - +
173C LEU* 3.9 17.0 - - + -
385C LYS 5.0 1.6 - - - +
386C ARG* 2.9 40.0 + - - +
388C LYS* 1.3 79.9 - - - +
390C VAL* 1.3 63.7 + - - +
392C ARG* 2.8 40.7 + - - +
393C LEU* 3.1 30.3 + - - +
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Residues in contact with VAL 390 (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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173C LEU* 4.1 11.9 - - + -
177C MET* 3.3 23.6 - - + +
372C ILE* 5.5 0.2 - - - +
375C LEU* 4.1 4.0 - - + +
376C VAL* 3.9 32.3 - - + +
379C LEU* 3.6 43.7 - - + -
380C SER 5.4 0.2 - - - +
386C ARG* 3.1 19.9 + - + +
387C ARG* 3.4 9.4 + - - +
389C ASP* 1.3 77.2 - - - +
391C ALA* 1.3 62.3 + - - +
393C LEU 3.3 0.9 + - - -
394C GLY* 3.3 17.3 + - - -
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Residues in contact with ALA 391 (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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243A THR* 6.1 2.9 - - + +
372C ILE* 5.0 4.1 - - + +
376C VAL* 3.8 25.5 - - + +
387C ARG* 3.2 14.0 + - + +
388C LYS* 4.2 4.3 - - - +
390C VAL* 1.3 79.9 - - - +
392C ARG* 1.3 62.7 + - - +
394C GLY* 3.3 11.6 + - - -
395C ILE* 5.0 1.0 + - - +
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Residues in contact with ARG 392 (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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170C GLU* 2.5 40.2 + - - -
388C LYS* 3.2 21.6 + - - +
389C ASP* 2.8 42.1 + - - +
390C VAL 3.2 0.8 - - - -
391C ALA* 1.3 82.0 - - - +
393C LEU* 1.3 64.2 + - + +
394C GLY 3.2 3.0 + - - -
395C ILE* 4.9 2.8 + - - +
396C LYS* 5.4 1.6 + - - +
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Residues in contact with LEU 393 (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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170C GLU* 3.4 39.7 - - + +
173C LEU* 4.8 4.5 - - + -
174C PHE* 3.7 41.3 - - + +
177C MET* 3.5 13.9 - - + +
221C VAL* 5.3 8.5 - - + -
389C ASP 3.1 20.8 + - - +
390C VAL 3.3 2.9 + - - -
391C ALA 3.3 0.4 - - - -
392C ARG* 1.3 88.0 - - + +
394C GLY* 1.3 63.1 + - - +
395C ILE 3.6 1.3 - - - -
396C LYS* 3.7 9.4 + - + -
397C ALA* 3.1 25.3 + - - +
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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