Contacts of the helix formed by residues 395 - 405 (chain C) in PDB entry 1Y9D
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 GLY 395 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C VAL* 1.3 76.0 - - - +
396C ASP* 1.3 67.8 + - - -
397C ILE* 2.9 5.4 + - - +
398C ASN* 2.9 23.6 + - - +
399C LEU 4.1 0.9 + - - -
479C PHE* 3.9 14.7 - - - -
2802C TPP 3.7 28.7 - - - -
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Residues in contact with ASP 396 (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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395C GLY* 1.3 70.1 - - - -
397C ILE* 1.3 61.8 + - - +
398C ASN 3.2 0.9 + - - -
399C LEU* 3.2 11.6 + - - +
400C ASN* 3.0 34.5 + - - +
474C ASN* 4.5 5.8 + - - +
478C GLY* 3.9 8.1 - - - -
479C PHE* 3.3 35.0 + - - +
482C ASP* 4.2 6.2 - - - +
547C ASP 5.2 1.6 - - - +
549C PRO* 3.8 25.7 - - + +
2802C TPP 2.8 32.4 + - - +
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Residues in contact with ILE 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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377C LEU* 4.4 6.3 - - + -
392C ILE* 3.8 10.3 - - + -
393C ASP* 3.7 30.1 - - - +
394C VAL 4.1 3.8 - - - +
395C GLY* 2.9 5.3 + - - +
396C ASP* 1.3 77.8 - - - +
398C ASN* 1.3 58.2 + - - +
400C ASN* 3.8 5.8 - - + +
401C ALA* 2.8 34.9 + - + +
444C LEU* 3.8 34.3 - - + +
445C ALA 4.5 0.9 - - - +
446C GLY* 4.3 16.4 - - - +
472C PHE* 3.6 42.2 - - + -
2802C TPP 4.2 4.8 + - - +
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Residues in contact with ASN 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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245C TYR* 3.3 39.0 + - + -
265C ALA* 4.2 7.4 - - + -
392C ILE* 3.8 1.8 - - - +
393C ASP 2.8 23.1 + - - -
394C VAL* 3.3 11.3 - - - +
395C GLY 2.9 32.0 + - - +
397C ILE* 1.3 74.6 - - - +
399C LEU* 1.3 59.9 + - - +
401C ALA* 4.2 0.2 - - - +
402C ASN* 2.9 32.9 + - - +
415C THR* 3.6 11.7 + - - +
416C SER 5.8 0.4 + - - -
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Residues in contact with LEU 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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265C ALA* 4.0 25.4 - - + +
395C GLY 4.1 0.9 + - - +
396C ASP* 3.2 14.7 + - - +
398C ASN* 1.3 79.6 - - - +
400C ASN* 1.3 69.0 + - - +
402C ASN* 3.4 3.1 + - - +
403C ARG* 3.2 68.3 + - - +
479C PHE* 4.7 20.6 - - + -
549C PRO* 3.5 31.4 - - + +
550C LEU 4.6 3.4 - - - +
551C PRO* 5.8 3.1 - - + -
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Residues in contact with ASN 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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373C ALA* 3.5 26.8 - - + +
374C TYR* 4.1 13.2 - - - -
377C LEU* 3.5 19.5 - - + -
396C ASP* 3.0 27.9 + - - +
397C ILE* 4.1 7.0 - - + +
399C LEU* 1.3 91.0 - - - +
401C ALA* 1.3 57.8 + - - +
403C ARG* 3.2 2.8 + - - -
404C HIS* 2.8 41.2 + - + +
472C PHE* 5.7 1.4 - - - -
544C ILE* 5.9 0.2 - - - +
549C PRO* 3.8 20.9 - - - +
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Residues in contact with ALA 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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245C TYR* 5.0 0.4 - - - +
248C LYS* 3.6 4.1 - - - -
377C LEU* 3.9 8.2 - - + +
392C ILE* 3.8 28.9 - - + -
397C ILE* 2.8 33.2 + - + +
398C ASN* 4.2 1.6 - - - +
400C ASN* 1.3 69.9 - - - +
402C ASN* 1.3 65.9 + - - +
404C HIS 4.3 0.4 - - - +
405C LEU* 3.1 41.5 + - + +
444C LEU* 4.6 0.9 - - + -
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Residues in contact with ASN 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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245C TYR* 4.0 20.4 - - + +
248C LYS* 2.7 52.2 + - - +
258C TYR* 5.2 2.1 + - - -
261C SER* 2.7 31.5 + - - -
265C ALA* 2.8 23.7 + - - +
267C GLN* 3.4 23.6 - - + +
398C ASN 2.9 20.5 + - - +
399C LEU 3.4 5.6 - - - +
401C ALA* 1.3 74.4 - - - +
403C ARG* 1.3 59.1 + - - +
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Residues in contact with ARG 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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248C LYS* 4.9 0.5 + - - -
265C ALA 5.1 0.8 + - - -
266C ALA 2.9 27.3 + - - -
267C GLN* 4.1 19.1 + - + +
356C TRP* 3.7 37.5 - - + -
359C TYR* 5.7 0.8 - - - -
360C LEU* 3.8 27.1 - - + +
364C GLU* 5.0 0.7 - - - +
374C TYR* 6.4 0.2 - - - -
399C LEU* 3.2 42.0 + - - +
400C ASN* 3.2 9.2 + - - +
402C ASN* 1.3 78.9 - - + +
404C HIS* 1.3 75.1 + - + +
405C LEU 4.4 2.8 - - - +
549C PRO* 4.4 0.8 - - - +
550C LEU* 2.8 41.6 + - - +
552C ALA* 4.1 9.5 - - - +
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Residues in contact with HIS 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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360C LEU* 4.0 27.4 - - + +
363C LEU* 4.6 1.8 - - + -
364C GLU* 3.0 43.7 + - + +
374C TYR* 3.4 36.5 + + + -
377C LEU* 3.6 30.3 - - + -
381C ASN* 2.9 21.5 + - - +
400C ASN* 2.8 36.4 + - - +
403C ARG* 1.3 85.5 - - + +
405C LEU* 1.3 68.6 + - - +
406C LYS* 3.6 6.2 + - - +
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Residues in contact with LEU 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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248C LYS* 3.1 25.2 + - - -
253C ASP* 3.5 2.6 - - - +
377C LEU* 3.9 20.2 - - + +
380C VAL* 3.9 20.9 - - + -
381C ASN* 3.7 15.0 - - - +
390C TYR* 3.7 34.1 - - + -
392C ILE* 4.1 12.1 - - + -
401C ALA* 3.1 38.0 + - + +
403C ARG 4.4 2.3 - - - +
404C HIS* 1.3 79.4 - - - +
406C LYS* 1.3 60.8 + - - +
407C LEU* 3.8 20.2 - - + -
413C HIS* 5.7 0.4 - - + -
444C LEU* 4.2 3.4 - - + -
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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