Contacts of the helix formed by residues 476 - 486 (chain C) in PDB entry 1R4N
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 ASP 476 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458C LYS* 2.6 38.9 + - - -
474C VAL 3.9 5.8 - - - +
475C LYS* 1.3 71.4 - - - +
477C ASP* 1.3 55.4 + - - +
479C VAL* 2.7 37.8 + - + +
480C HIS* 3.3 17.0 + - + +
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Residues in contact with ASP 477 (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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475C LYS* 3.0 24.2 - - + +
476C ASP* 1.3 78.0 - - - +
478C TYR* 1.3 58.9 + - - +
479C VAL 2.9 5.9 + - - -
480C HIS* 3.0 16.5 + - - +
481C GLU* 2.9 22.7 + - - +
29D PRO* 3.9 23.4 - - + +
30D PHE* 4.1 15.3 - - + -
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Residues in contact with TYR 478 (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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419C PRO 3.4 22.6 + - - -
420C ASP* 3.2 28.1 + - - +
424C VAL* 3.7 23.6 - - + -
425C LEU* 4.0 26.0 - - + -
428C MET* 3.6 22.6 - - + +
474C VAL* 4.2 1.1 - - + -
475C LYS* 3.1 39.2 + - + +
477C ASP* 1.3 75.4 - - - +
479C VAL* 1.3 61.4 + - - +
481C GLU* 4.0 6.7 - - + -
482C PHE* 3.3 29.1 + + - -
525C MET* 5.3 5.8 - - + -
30D PHE* 3.8 30.5 - + - -
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Residues in contact with VAL 479 (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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428C MET* 4.3 5.8 - - + -
454C ILE* 3.7 24.2 - - + +
457C LEU* 3.4 33.1 - - + +
458C LYS* 3.8 22.7 - - + +
461C LEU* 4.5 21.1 - - + -
474C VAL 4.9 0.9 - - - +
475C LYS 4.1 4.0 - - - +
476C ASP* 2.7 35.2 + - + +
478C TYR* 1.3 72.1 - - - +
480C HIS* 1.3 65.9 + - - +
482C PHE 3.6 1.0 + - - -
483C CYS* 3.2 21.4 + - - -
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Residues in contact with HIS 480 (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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450C VAL* 5.6 1.2 - - - +
454C ILE* 3.4 43.1 - - + +
476C ASP* 3.3 20.5 + - + +
477C ASP* 3.0 17.4 + - - +
479C VAL* 1.3 78.6 - - - +
481C GLU* 1.3 67.7 - - - +
483C CYS* 2.8 17.8 + - - +
484C ARG* 2.9 11.4 + - - +
29D PRO* 3.6 17.5 - - + -
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Residues in contact with GLU 481 (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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477C ASP 2.9 15.4 + - - +
478C TYR* 3.9 8.3 - - + +
480C HIS* 1.3 76.0 - - - +
482C PHE* 1.3 58.2 + - + +
484C ARG* 2.6 62.1 + - - +
485C TYR* 2.9 30.1 + - + +
525C MET* 3.0 28.6 - - + +
29D PRO* 3.8 8.7 - - + +
30D PHE* 3.0 22.4 + - + +
315D TYR* 3.4 22.1 + - - -
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Residues in contact with PHE 482 (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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156C TYR* 3.7 24.1 + + - -
159C VAL* 3.8 20.4 - - + -
425C LEU* 3.9 25.4 - - + -
428C MET* 3.5 37.2 - - + -
429C LEU* 3.5 26.7 - - + -
432C VAL* 3.7 24.9 - - + -
443C PRO* 3.8 6.2 - - - +
457C LEU* 4.4 2.7 - - + -
478C TYR* 3.3 23.1 + + - +
479C VAL 4.1 3.1 - - - +
480C HIS 3.4 0.6 - - - -
481C GLU* 1.3 81.8 - - + +
483C CYS* 1.3 61.8 + - - +
485C TYR* 3.4 34.9 + + - +
486C GLY 3.5 4.5 + - - -
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Residues in contact with CYS 483 (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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443C PRO* 3.2 29.7 - - - +
444C GLY* 3.5 3.5 - - - +
450C VAL* 4.5 12.5 - - + +
453C ASP* 4.1 6.3 - - - -
454C ILE* 3.6 44.6 - - + -
457C LEU* 3.6 16.4 - - - -
479C VAL 3.2 16.1 + - - -
480C HIS 2.8 10.1 + - - +
482C PHE* 1.3 77.2 - - - +
484C ARG* 1.3 58.9 + - - +
486C GLY 3.2 1.2 + - - -
26D ARG* 3.0 18.0 + - - -
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Residues in contact with ARG 484 (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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450C VAL* 5.0 5.8 - - + +
480C HIS 2.9 9.6 + - - +
481C GLU* 2.6 36.2 + - - +
483C CYS* 1.3 67.6 - - - +
485C TYR* 1.3 62.7 + - + +
486C GLY 3.0 1.6 - - - -
22D LYS* 3.9 19.8 + - - +
23D PHE* 2.9 33.2 + - + +
26D ARG* 2.7 47.4 + - + +
27D SER 3.3 24.8 + - - +
28D GLY* 3.9 15.3 - - - -
29D PRO* 5.6 0.4 - - + -
31D THR* 4.5 7.5 + - - +
35D PHE* 4.6 3.6 - - - -
314D ALA* 3.6 17.8 + - - +
315D TYR* 2.9 38.3 + - - -
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Residues in contact with TYR 485 (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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156C TYR* 4.0 10.8 - + + -
157C GLY* 3.4 27.8 - - - +
158C LEU* 3.7 21.6 - - + +
159C VAL* 4.1 9.9 - - + +
481C GLU* 2.9 24.2 + - + +
482C PHE* 3.4 44.9 - + - +
484C ARG* 1.3 77.2 - - + +
486C GLY* 1.3 65.0 + - - +
487C ALA 4.2 3.6 - - - +
488C ALA* 2.8 26.3 + - - +
525C MET* 2.8 38.6 - - - +
22D LYS* 3.8 4.5 - - - +
23D PHE* 4.3 13.7 - + - -
315D TYR* 3.5 22.9 - - - -
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Residues in contact with GLY 486 (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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443C PRO 3.7 9.6 - - - -
444C GLY 3.3 26.5 - - - -
445C VAL* 4.1 12.7 - - - +
482C PHE 3.5 2.8 + - - -
483C CYS 3.2 4.0 + - - -
484C ARG 2.9 6.0 + - - -
485C TYR* 1.3 79.0 - - - +
487C ALA* 1.3 69.4 + - - +
488C ALA 2.9 1.6 + - - -
22D LYS* 3.7 18.6 + - - -
26D ARG* 4.0 1.1 - - - -
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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