Contacts of the helix formed by residues 402 - 415 (chain C) in PDB entry 3A4Y
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 GLU 402 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ARG 3.9 6.7 - - - -
11C GLU* 4.7 2.2 - - - +
12C VAL* 4.3 9.4 - - + +
401C GLY* 1.3 73.3 - - - +
403C GLU* 1.3 67.5 + - - +
404C GLU* 4.2 20.8 - - - +
405C LYS* 2.8 50.8 + - + +
406C LEU* 3.0 20.5 + - - +
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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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10C ARG* 3.0 46.3 + - + +
401C GLY 3.6 1.9 + - - -
402C GLU* 1.3 72.3 - - - +
404C GLU* 1.3 75.6 + - - +
406C LEU* 3.2 0.3 + - - -
407C LEU* 2.7 48.8 + - + +
422C LEU* 4.2 11.4 - - + +
445C FLC 3.6 19.8 - - - +
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Residues in contact with GLU 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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191C ASP* 5.6 0.7 - - - -
402C GLU* 4.2 18.9 - - + +
403C GLU* 1.3 93.4 + - - +
405C LYS* 1.3 71.6 + - + +
407C LEU* 3.5 6.6 + - - +
408C ALA* 3.4 15.9 + - - +
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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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187C GLY 3.9 15.9 - - - +
188C THR* 3.7 18.9 + - - +
189C TYR* 5.6 0.8 - - - -
190C GLY 3.7 7.9 - - - +
191C ASP* 3.0 40.1 + - + +
192C ARG* 4.6 2.9 - - - +
341C TYR* 4.0 21.5 + - - -
402C GLU* 2.8 50.1 + - + +
404C GLU* 1.3 80.5 - - + +
406C LEU* 1.3 65.1 + - - +
408C ALA* 3.0 20.6 + - - +
409C LEU 3.4 3.5 + - - -
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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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10C ARG* 4.6 9.9 - - - +
187C GLY* 3.9 15.3 - - - +
398C LEU* 3.8 46.6 - - + +
399C VAL* 4.2 7.9 - - - +
400C HIS 4.2 2.7 - - - +
401C GLY* 3.1 44.9 - - - +
402C GLU 3.0 11.7 + - - +
403C GLU 3.8 0.2 - - - +
405C LYS* 1.3 75.4 - - - +
407C LEU* 1.3 52.0 + - - +
409C LEU* 3.2 7.0 + - - +
410C GLY* 2.7 33.8 + - - -
422C LEU* 3.7 30.7 - - + +
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Residues in contact with LEU 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* 2.7 54.9 + - + +
404C GLU* 3.7 7.0 - - - +
406C LEU* 1.3 75.9 - - - +
408C ALA* 1.3 64.1 + - - +
410C GLY* 3.1 3.9 + - - +
411C LYS* 2.8 23.0 + - - +
422C LEU* 3.4 29.4 - - + -
445C FLC 5.7 5.8 - - - +
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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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190C GLY 3.6 9.2 - - - +
191C ASP* 3.7 18.4 - - + +
383C GLN* 4.8 1.3 - - - +
404C GLU 3.4 8.7 + - - +
405C LYS 3.0 12.1 + - - +
407C LEU* 1.3 76.7 - - - +
409C LEU* 1.3 65.9 + - - +
411C LYS* 2.8 26.7 + - - +
412C LEU* 3.3 10.2 + - - +
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Residues in contact with LEU 409 (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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186C GLU 4.5 2.5 - - - +
187C GLY* 4.3 7.0 - - - -
190C GLY* 2.8 34.1 + - - +
383C GLN* 4.7 6.1 - - + +
386C LEU* 3.3 43.5 - - + -
387C LEU* 5.0 8.7 - - + -
390C LEU* 5.9 4.5 - - + -
398C LEU* 3.7 16.6 - - + -
405C LYS 3.4 1.0 + - - +
406C LEU* 3.2 7.7 + - - +
408C ALA* 1.3 74.1 - - - +
410C GLY* 1.3 66.2 + - - +
411C LYS 3.0 1.0 + - - -
412C LEU* 3.1 15.8 + - - +
413C LEU* 3.2 41.7 + - + +
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Residues in contact with GLY 410 (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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398C LEU* 4.3 6.3 - - - -
406C LEU 2.7 19.7 + - - -
407C LEU* 3.5 6.3 - - - -
408C ALA 3.1 0.2 - - - -
409C LEU* 1.3 77.3 - - - +
411C LYS* 1.3 64.0 + - - +
413C LEU* 3.6 5.9 + - - +
414C ALA* 3.6 8.3 + - - +
420C VAL* 3.6 33.6 - - - +
422C LEU* 6.1 2.2 - - - -
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Residues in contact with LYS 411 (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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407C LEU 2.8 10.9 + - - +
408C ALA* 2.8 15.9 + - - +
410C GLY* 1.3 76.5 - - - +
412C LEU* 1.3 70.1 + - + +
414C ALA* 3.0 22.4 + - - +
415C LEU* 3.5 20.7 - - + +
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Residues in contact with LEU 412 (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 GLN* 3.1 47.8 - - + +
387C LEU* 3.9 21.0 - - + +
408C ALA 3.8 11.2 - - - +
409C LEU* 3.1 7.1 + - - +
411C LYS* 1.3 83.4 - - + +
413C LEU* 1.3 62.2 + - - +
415C LEU* 3.3 37.4 - - + +
416C ARG* 3.9 11.4 + - - +
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Residues in contact with LEU 413 (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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387C LEU* 4.0 14.6 - - + -
390C LEU* 4.5 14.4 - - + -
396C VAL* 4.4 21.3 - - + -
398C LEU* 4.5 2.0 - - + -
409C LEU* 3.2 36.2 + - + +
410C GLY* 3.9 2.0 - - - +
411C LYS 3.0 1.0 + - - -
412C LEU* 1.3 75.6 - - - +
414C ALA* 1.3 62.6 + - - +
416C ARG* 3.3 23.8 + - - +
418C GLN* 3.0 53.3 + - + +
420C VAL* 3.4 32.3 - - + -
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Residues in contact with ALA 414 (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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410C GLY 3.6 8.1 + - - +
411C LYS* 3.0 11.6 + - - +
413C LEU* 1.3 73.4 - - - +
415C LEU* 1.3 60.0 + - + +
416C ARG 3.0 5.6 - - - -
417C GLY* 2.8 20.0 + - - -
418C GLN 3.5 14.3 + - - +
420C VAL* 5.7 2.7 - - + -
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Residues in contact with LEU 415 (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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411C LYS* 3.5 22.7 - - + +
412C LEU* 3.3 42.0 - - + +
413C LEU 3.2 0.2 - - - -
414C ALA* 1.3 79.6 - - + +
416C ARG* 1.3 61.6 + - + +
417C GLY 3.3 0.6 + - - -
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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