Contacts of the helix formed by residues 472 - 485 (chain A) in PDB entry 4IQJ
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 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A GLY 3.9 16.1 - - - +
418A VAL* 3.7 33.6 - - + +
469A SER* 3.1 19.6 + - - +
471A ARG* 1.3 90.6 - - + +
473A ARG* 1.3 63.0 + - - +
474A ASP 3.2 3.4 + - - -
475A ARG* 2.8 51.5 + - - +
476A VAL* 3.7 4.2 + - - +
629A ASP* 5.5 3.1 - - - +
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Residues in contact with ARG 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PHE* 4.5 12.3 - - + -
469A SER 2.9 15.4 + - - +
470A ASP* 3.9 10.8 + - - +
471A ARG 3.3 2.4 - - - -
472A GLU* 1.3 78.5 - - - +
474A ASP* 1.3 81.2 + - - +
476A VAL* 3.4 14.9 + - - +
477A ILE* 3.3 36.6 + - - +
491A GLN* 4.4 4.8 - - - +
576A ALA* 2.9 28.7 + - - +
577A ALA* 4.3 3.0 - - - +
599A ARG* 3.7 22.6 - - - +
619A PHE* 3.3 34.5 + - + +
621A GLY* 3.4 23.8 - - - +
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Residues in contact with ASP 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ASP 5.0 2.6 - - - +
471A ARG 5.0 7.6 - - - +
472A GLU 3.2 0.4 - - - -
473A ARG* 1.3 102.8 + - - +
475A ARG* 1.3 61.5 + - + +
477A ILE* 3.2 10.4 + - - +
478A GLN* 2.8 28.4 + - - +
599A ARG* 2.9 28.9 + - - +
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Residues in contact with ARG 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A TRP* 3.7 21.2 - - + -
416A HIS* 2.6 38.4 + - - +
417A GLY* 4.3 2.8 + - - -
418A VAL* 4.1 7.3 - - + +
471A ARG 5.6 0.7 - - - +
472A GLU* 2.8 54.1 + - - +
473A ARG 3.3 0.4 - - - -
474A ASP* 1.3 79.4 - - + +
476A VAL* 1.3 56.1 - - - +
478A GLN* 3.4 9.9 + - + +
479A TYR* 2.9 27.2 + - - +
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR* 4.0 36.8 - - + +
412A TRP* 4.2 9.6 - - + -
413A ALA* 4.1 11.4 - - + -
418A VAL* 3.5 34.5 - - + -
468A PHE* 4.0 24.7 - - + -
472A GLU 3.9 5.6 - - - +
473A ARG 3.4 7.2 + - - +
474A ASP 3.3 0.6 - - - -
475A ARG* 1.3 73.4 - - - +
477A ILE* 1.3 66.5 + - - +
479A TYR* 3.3 3.6 + - - +
480A VAL* 3.1 27.4 + - - +
619A PHE* 4.6 7.2 - - + -
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Residues in contact with ILE 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ARG* 3.3 41.9 + - - +
474A ASP* 3.2 10.0 + - - +
476A VAL* 1.3 74.2 - - - +
478A GLN* 1.3 66.9 + - - +
480A VAL* 3.1 6.0 + - - +
481A ARG* 3.0 38.7 + - + +
489A VAL* 5.2 1.6 - - + -
491A GLN* 4.0 30.1 - - + +
579A VAL* 4.0 22.0 - - + -
599A ARG* 4.6 3.6 - - - +
619A PHE* 3.5 26.7 - - + -
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Residues in contact with GLN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ASP 2.8 17.4 + - - +
475A ARG* 3.5 11.0 - - + +
477A ILE* 1.3 76.4 - - - +
479A TYR* 1.3 62.8 + - - +
481A ARG* 2.8 42.8 + - - +
482A GLU* 3.0 57.5 + - - +
486A GLU* 4.7 9.3 + - - -
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Residues in contact with TYR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP* 2.6 37.9 + - - -
409A TYR* 3.7 32.3 - - + -
412A TRP* 3.3 57.0 - + + -
475A ARG 2.9 15.1 + - - +
476A VAL 3.5 6.7 - - - +
477A ILE 3.2 0.4 - - - -
478A GLN* 1.3 75.5 - - - +
480A VAL* 1.3 54.5 - - + +
482A GLU* 3.1 14.1 + - + +
483A ARG* 2.7 67.5 + - + +
484A TYR* 5.4 1.1 - + - -
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR* 4.0 32.5 - - + -
476A VAL 3.1 17.0 - - - +
477A ILE* 3.1 9.1 + - - +
479A TYR* 1.3 74.2 - - + +
481A ARG* 1.3 59.7 + - - +
483A ARG* 4.0 6.7 - - - -
484A TYR* 2.9 41.1 + - + +
489A VAL* 3.7 17.6 - - + +
579A VAL* 5.2 3.4 - - + -
581A ILE* 3.4 31.2 - - + -
619A PHE* 4.5 10.1 - - + -
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Residues in contact with ARG 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ILE* 3.0 26.3 + - + +
478A GLN* 2.8 37.8 + - - +
480A VAL* 1.3 75.3 - - - +
482A GLU* 1.3 60.5 + - - +
485A GLY* 3.1 18.8 + - - -
486A GLU* 3.2 50.4 + - - +
489A VAL* 3.6 30.7 - - + +
490A ALA* 5.8 0.2 - - - +
594A ARG* 4.8 5.3 - - - +
598A GLY 4.6 10.1 + - - -
599A ARG* 5.8 1.0 - - - +
600A PRO* 3.2 41.3 - - - +
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Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLN* 3.0 43.5 + - - +
479A TYR* 3.5 13.1 - - + +
481A ARG* 1.3 76.2 - - - +
483A ARG* 1.3 63.2 + - - +
484A TYR 5.0 0.2 - - - -
485A GLY* 4.7 1.4 + - - -
486A GLU* 5.0 5.8 - - - +
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Residues in contact with ARG 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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298A PHE* 3.7 31.5 - - - -
299A PRO* 4.6 17.5 + - + +
300A LEU* 4.7 10.1 - - - +
408A ASP* 3.4 12.0 + - - +
479A TYR* 2.7 52.9 + - + +
480A VAL* 3.1 6.0 + - - +
482A GLU* 1.3 77.1 - - - +
484A TYR* 1.3 89.9 + - + +
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Residues in contact with TYR 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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296A PRO* 5.3 2.0 - - + -
297A ARG 3.6 25.4 - - - -
298A PHE* 3.3 27.2 - + - -
299A PRO* 5.2 4.3 - - + -
405A ILE* 3.2 46.1 + - + +
408A ASP* 3.8 5.4 + - - -
409A TYR* 5.2 2.0 - + - -
479A TYR* 5.4 0.9 - + - -
480A VAL* 2.9 44.0 + - + +
482A GLU 5.0 0.2 - - - -
483A ARG* 1.3 98.6 - - + +
485A GLY* 1.3 55.6 + - - +
488A LYS* 3.9 23.7 + - + +
489A VAL* 4.0 11.0 - - + -
581A ILE* 4.2 17.7 - - + -
582A ALA 5.8 0.4 - - - +
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Residues in contact with GLY 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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480A VAL 3.9 0.6 + - - -
481A ARG 3.1 11.7 + - - -
482A GLU 5.3 1.3 - - - -
483A ARG 3.8 0.4 - - - -
484A TYR* 1.3 80.5 - - - +
486A GLU* 1.3 56.3 + - - -
487A ASP* 3.1 15.0 - - - -
488A LYS* 2.8 6.7 + - - -
489A VAL* 2.8 34.7 + - - +
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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