Contacts of the helix formed by residues 476 - 486 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A LYS* 2.6 37.8 + - + -
474A VAL 3.8 6.4 - - - +
475A LYS* 1.3 71.4 - - - +
477A ASP* 1.3 55.6 + - - +
479A VAL* 2.7 38.4 + - + +
480A HIS* 3.3 16.8 + - + +
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Residues in contact with ASP 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A LYS* 4.0 23.7 - - + +
476A ASP* 1.3 78.6 - - - +
478A TYR* 1.3 58.6 + - - +
479A VAL 2.9 0.7 + - - -
480A HIS* 3.0 13.3 + - - +
481A GLU* 2.9 27.9 + - - +
29B PRO* 3.6 26.4 - - + +
30B PHE* 3.9 15.3 - - + -
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Residues in contact with TYR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A PRO 3.4 22.6 + - - -
420A ASP* 3.2 28.3 + - - +
424A VAL* 3.7 23.1 - - + -
425A LEU* 4.0 26.5 - - + -
428A MET* 3.7 22.5 - - + +
474A VAL* 4.3 1.6 - - + -
475A LYS* 3.1 38.7 + - + +
477A ASP* 1.3 76.1 - - - +
479A VAL* 1.3 59.6 + - - +
481A GLU* 4.0 7.6 - - + -
482A PHE* 3.3 29.6 + + - -
525A MET* 5.2 5.2 - - + -
30B PHE* 3.6 32.0 - + - -
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A MET* 4.3 5.2 - - + -
454A ILE* 3.7 26.0 - - + +
457A LEU* 3.4 36.7 - - + +
458A LYS* 3.8 22.9 - - + +
461A LEU* 4.4 21.5 - - + -
474A VAL 4.9 0.9 - - - +
475A LYS 4.1 4.0 - - - +
476A ASP* 2.7 28.5 + - + +
478A TYR* 1.3 78.9 - - - +
480A HIS* 1.3 67.6 + - - +
482A PHE 3.5 0.9 + - - -
483A CYS* 3.2 16.9 + - - -
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Residues in contact with HIS 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A VAL* 5.6 1.0 - - - +
454A ILE* 3.3 44.4 - - + +
476A ASP* 3.3 20.3 + - + +
477A ASP* 3.0 14.6 + - - +
479A VAL* 1.3 76.8 - - - +
481A GLU* 1.3 68.3 + - - +
483A CYS* 2.8 16.9 + - - +
484A ARG* 2.9 11.5 + - - +
29B PRO* 3.3 23.3 - - + -
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A ASP 2.9 16.0 + - - +
478A TYR* 3.9 7.6 - - + +
480A HIS* 1.3 75.5 - - - +
482A PHE* 1.3 58.5 + - + +
484A ARG* 2.5 61.5 + - - +
485A TYR* 3.0 29.0 + - + +
525A MET* 3.0 27.2 - - + +
29B PRO* 3.7 7.4 - - + +
30B PHE* 3.0 22.6 + - + +
315B TYR* 3.2 24.4 + - - -
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TYR* 3.7 23.4 + + - -
159A VAL* 3.8 20.2 - - + -
425A LEU* 3.9 25.4 - - + -
428A MET* 3.4 37.2 - - + -
429A LEU* 3.6 26.7 - - + -
432A VAL* 3.6 25.4 - - + -
443A PRO* 3.9 6.0 - - - +
457A LEU* 4.4 2.2 - - + -
478A TYR* 3.3 24.8 + + - +
479A VAL 4.1 3.4 - - - +
480A HIS 3.4 0.2 - - - -
481A GLU* 1.3 81.2 - - + +
483A CYS* 1.3 61.2 + - - +
485A TYR* 3.3 35.5 + + - +
486A GLY 3.5 4.5 + - - -
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Residues in contact with CYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PRO* 3.2 27.3 - - - +
444A GLY* 3.5 2.4 - - - +
450A VAL* 4.5 11.7 - - + +
453A ASP* 4.1 6.5 - - - -
454A ILE* 3.6 41.5 - - + -
457A LEU* 3.6 18.4 - - - -
479A VAL 3.2 15.6 + - - +
480A HIS 2.8 13.7 + - - +
482A PHE* 1.3 73.4 - - - +
484A ARG* 1.3 60.0 + - - +
486A GLY 3.2 5.9 + - - -
26B ARG* 2.9 19.6 + - - -
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A VAL* 5.0 5.1 - - + +
480A HIS 2.9 9.7 + - - +
481A GLU* 2.5 34.7 + - - +
483A CYS* 1.3 68.4 - - - +
485A TYR* 1.3 61.4 + - + +
22B LYS* 3.9 20.2 + - - +
23B PHE* 2.8 35.6 + - + +
26B ARG* 2.7 48.8 + - + +
27B SER 3.2 22.9 - - - +
28B GLY* 3.9 14.2 - - - -
29B PRO* 5.4 0.2 - - + -
31B THR* 4.4 8.2 + - - +
35B PHE* 4.4 3.8 - - - -
314B ALA* 3.5 22.0 + - - +
315B TYR* 3.1 34.7 + - - -
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Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TYR* 4.0 10.8 - + + -
157A GLY* 3.4 29.2 - - - +
158A LEU* 3.7 20.1 - - + +
159A VAL* 4.1 9.5 - - + +
481A GLU* 3.0 23.1 + - + +
482A PHE* 3.4 44.7 - + - +
484A ARG* 1.3 77.7 - - + +
486A GLY* 1.3 66.8 + - - +
487A ALA 4.2 3.6 - - - +
488A ALA* 2.8 24.9 + - - +
525A MET* 2.8 38.6 - - - +
22B LYS* 3.7 3.5 - - - +
23B PHE* 4.1 13.7 - + - -
315B TYR* 3.2 25.4 - + - -
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Residues in contact with GLY 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PRO 3.7 8.7 - - - -
444A GLY 3.3 27.1 - - - -
445A VAL* 4.1 11.2 - - - +
482A PHE 3.5 3.0 + - - -
483A CYS 3.2 3.6 + - - -
484A ARG 2.9 6.6 + - - -
485A TYR* 1.3 77.7 - - - +
487A ALA* 1.3 69.8 + - - +
488A ALA 2.9 1.4 + - - -
22B LYS* 3.6 19.4 + - - -
26B ARG* 3.8 2.0 - - - -
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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