Contacts of the helix formed by residues 401 - 408 (chain C) in PDB entry 3SWD
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 401 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LYS* 4.7 7.0 + - - +
399C TYR 3.3 5.3 + - - -
400C GLU* 1.3 102.0 + - + +
402C ILE* 1.3 64.6 - - - +
403C GLU* 3.2 13.2 - - - +
404C ASP* 3.0 51.6 + - - +
405C LYS* 3.4 23.5 + - - +
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Residues in contact with ILE 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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4C PHE* 4.0 26.5 - - + -
234C GLU* 6.1 1.1 - - - +
237C THR* 5.1 3.4 - - + -
238C PHE* 4.3 17.9 - - + -
374C ALA* 4.4 19.1 - - + -
377C VAL* 5.2 6.3 - - + -
378C LEU* 5.1 7.6 - - + -
395C ILE* 4.1 14.6 - - + -
396C ASP* 6.0 0.7 - - - +
399C TYR* 4.0 37.5 + - + +
400C GLU 3.3 4.0 + - - -
401C ARG* 1.3 76.0 - - - +
403C GLU* 1.3 67.4 + - - +
405C LYS* 3.5 4.6 + - - +
406C LEU* 3.1 42.0 + - + +
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Residues in contact with GLU 403 (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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4C PHE* 3.6 29.9 - - + -
396C ASP* 5.3 1.2 - - - +
401C ARG* 3.7 11.0 - - - -
402C ILE* 1.3 85.0 + - - +
404C ASP* 1.3 70.5 + - - +
407C ARG* 2.9 45.1 + - - +
413C ILE* 3.7 28.3 - - + +
415C ARG* 3.1 40.3 + - + +
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Residues in contact with ASP 404 (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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401C ARG* 3.0 54.3 + - - +
403C GLU* 1.3 82.9 - - - +
405C LYS* 1.3 62.5 + - + +
407C ARG* 2.8 35.6 + - - +
408C ALA* 3.0 24.0 + - - +
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Residues in contact with LYS 405 (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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15C GLU 5.2 0.3 - - - +
16C VAL* 3.8 24.9 - - + +
17C THR 3.2 19.7 + - - +
19C SER* 2.9 28.4 + - - -
234C GLU* 3.1 25.5 + - - +
238C PHE* 3.7 23.3 - - + -
400C GLU* 3.7 21.2 + - - +
401C ARG* 3.4 17.3 + - - +
402C ILE* 4.2 2.5 - - - +
403C GLU 3.4 0.4 - - - -
404C ASP* 1.3 76.8 - - + +
406C LEU* 1.3 62.6 + - - +
408C ALA* 3.3 15.4 + - - +
409C LEU* 3.4 18.0 + - - +
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Residues in contact with LEU 406 (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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12C LEU* 4.0 26.6 - - + +
238C PHE* 3.9 24.9 - - + -
241C ALA* 4.7 1.1 - - + -
377C VAL* 3.6 30.3 - - + -
378C LEU* 4.5 14.4 - - + -
381C CYS* 4.4 9.9 - - - -
402C ILE* 3.1 33.4 + - + +
403C GLU 4.0 3.1 - - - +
405C LYS* 1.3 73.6 - - - +
407C ARG* 1.3 60.7 + - - +
409C LEU* 2.9 22.9 + - + +
410C GLY 3.3 0.3 + - - -
411C ALA* 3.0 29.1 + - + +
413C ILE* 4.4 9.4 - - + -
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Residues in contact with ARG 407 (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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403C GLU* 2.9 31.6 + - - +
404C ASP* 2.8 33.7 + - - +
405C LYS 3.3 0.2 - - - -
406C LEU* 1.3 72.2 - - - +
408C ALA* 1.3 56.5 + - - +
409C LEU 3.0 4.5 - - - -
410C GLY* 3.0 18.5 + - - -
411C ALA* 3.8 20.4 + - - +
413C ILE* 2.7 41.1 + - + +
414C GLU* 4.4 7.3 - - - +
415C ARG 5.2 1.4 - - - +
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Residues in contact with ALA 408 (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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13C GLN 4.2 3.5 - - - +
14C GLY* 5.2 0.7 - - - -
15C GLU 4.8 11.7 + - - +
404C ASP 3.0 16.1 + - - +
405C LYS* 3.6 9.2 - - - +
406C LEU 3.2 0.2 - - - -
407C ARG* 1.3 75.2 - - - +
409C LEU* 1.3 63.0 + - - +
410C GLY 3.4 0.2 - - - -
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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