Contacts of the helix formed by residues 396 - 402 (chain C) in PDB entry 6IWQ
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 396 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C ALA 3.2 21.0 + - - -
289C GLN* 3.9 12.3 + - - +
291C ALA 3.1 23.5 + - - -
292C LYS* 4.2 21.7 + - - +
294C GLY 3.9 14.8 - - - +
295C GLN 2.8 23.7 + - - +
297C LEU* 3.9 29.2 - - + -
394C ILE 3.4 1.6 + - - -
395C GLU* 1.3 72.4 - - - +
397C GLU* 1.3 64.3 + - - +
399C PHE* 3.3 4.4 + - - +
400C PHE* 3.1 54.3 + - + -
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Residues in contact with GLU 397 (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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116C LYS* 2.4 44.9 - - + +
295C GLN 4.6 0.2 + - - -
322C ARG* 3.7 10.6 + - - +
395C GLU* 3.4 15.4 + - - +
396C ARG* 1.3 78.6 - - - +
398C PHE* 1.3 57.8 + - - +
400C PHE* 2.8 14.1 + - + +
401C GLU* 2.8 31.2 + - + +
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Residues in contact with PHE 398 (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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115C PHE* 4.0 17.3 - + - -
322C ARG* 3.3 35.6 - - - +
323C THR* 3.5 50.3 - - + -
394C ILE* 3.8 24.2 - - + -
395C GLU* 3.1 13.2 + - + +
397C GLU* 1.3 78.9 - - - +
399C PHE* 1.3 61.2 + - - +
401C GLU* 3.2 13.7 + - - +
402C LEU* 3.1 57.3 + - + +
423C ILE* 4.4 13.5 - - + -
428C GLY* 4.8 3.8 - - - -
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Residues in contact with PHE 399 (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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284C ARG 5.3 1.1 - - - -
285C SER* 5.6 0.9 - - - -
297C LEU* 4.1 12.8 - - + -
299C TYR* 3.4 30.3 - + - -
392C PHE* 4.7 2.7 - + - -
394C ILE* 3.2 32.7 - - + +
395C GLU 3.0 10.1 + - - +
396C ARG* 3.6 11.2 - - - +
397C GLU 3.2 0.2 - - - -
398C PHE* 1.3 77.2 - - - +
400C PHE* 1.3 60.9 - - - +
402C LEU* 3.1 10.8 + - + -
404C LEU* 3.0 65.0 + - + -
405C TYR* 4.3 24.0 - + - -
419C ILE* 3.3 29.2 - - + -
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Residues in contact with PHE 400 (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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288C ALA* 3.7 31.0 - - + -
289C GLN* 4.1 15.3 - - + -
297C LEU* 5.2 0.4 - - + -
396C ARG* 3.1 60.2 + - + -
397C GLU* 2.8 14.1 + - + +
399C PHE* 1.3 74.9 - - + +
401C GLU* 1.3 56.0 + - - +
403C GLY* 2.6 26.8 + - - +
404C LEU* 3.6 31.9 - - + +
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Residues in contact with GLU 401 (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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114C THR 4.3 3.0 - - - +
115C PHE* 3.3 29.1 - - + -
116C LYS* 2.7 38.4 + - + +
322C ARG* 2.4 38.0 + - - -
397C GLU* 2.8 19.3 + - + +
398C PHE* 3.2 14.2 + - - +
400C PHE* 1.3 71.3 - - - +
402C LEU* 1.3 58.0 + - - +
403C GLY 3.4 0.7 + - - -
501C PHE* 3.4 18.9 - - - -
505C HIS* 4.4 4.0 - - + -
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Residues in contact with LEU 402 (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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115C PHE* 3.5 30.3 - - + -
394C ILE* 5.3 0.9 - - + -
398C PHE* 3.1 34.8 + - + +
399C PHE* 3.6 10.1 - - + +
400C PHE 3.1 1.2 - - - -
401C GLU* 1.3 74.8 - - - +
403C GLY* 1.3 58.6 + - - +
404C LEU 3.2 1.2 + - - +
419C ILE* 4.2 15.9 - - + -
422C LYS* 2.9 55.0 + - + +
423C ILE* 3.5 32.8 - - + -
426C CYS* 4.8 1.3 - - + -
501C PHE* 3.9 19.1 - - + -
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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