Contacts of the helix formed by residues 481 - 500 (chain A) in PDB entry 4RPP
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 ALA 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A GLN* 3.3 3.7 - - + +
480A GLU* 1.3 82.2 - - + +
482A TRP* 1.3 59.8 + - - +
483A ALA* 3.4 2.5 - - + +
484A GLU* 3.6 34.8 - - + +
485A ASP* 2.9 27.5 + - - +
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Residues in contact with TRP 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN 4.9 1.3 - - - -
480A GLU 3.5 5.9 + - - +
481A ALA* 1.3 68.9 - - - +
483A ALA* 1.3 76.0 + - + +
485A ASP* 3.1 9.2 + - + +
486A VAL* 2.9 53.5 + - + +
489A ARG* 4.5 11.8 - - - +
513A THR* 6.2 0.7 - - - -
514A GLY 3.4 30.7 - - - -
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Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ALA* 3.4 2.0 - - + -
482A TRP* 1.3 91.0 - - + +
484A GLU* 1.3 61.1 + - + +
486A VAL* 3.4 6.3 + - - +
487A ASP* 3.1 34.7 + - - +
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN* 4.7 18.3 + - + +
481A ALA* 3.3 28.2 + - + +
482A TRP 3.2 0.2 - - - -
483A ALA* 1.3 77.0 - - + +
485A ASP* 1.3 61.1 + - - +
487A ASP* 3.3 7.9 + - - +
488A LEU* 2.9 29.5 + - - +
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ARG* 2.6 43.0 + - - -
478A VAL* 4.2 6.7 - - - +
479A GLN* 3.1 39.3 + - + +
481A ALA 2.9 17.0 + - - +
482A TRP* 3.1 11.9 + - + +
484A GLU* 1.3 76.7 - - - +
486A VAL* 1.3 61.4 + - - +
488A LEU* 3.5 6.5 - - - +
489A ARG* 3.2 37.1 + - - +
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.7 22.8 - - + +
482A TRP* 2.9 57.1 + - + +
483A ALA* 3.6 6.3 - - - +
484A GLU 3.2 0.2 - - - -
485A ASP* 1.3 74.3 - - - +
487A ASP* 1.3 70.2 + - - +
489A ARG* 3.2 15.1 + - - +
490A VAL* 3.1 25.6 + - + +
513A THR* 3.8 21.5 - - + -
526A ARG* 4.7 6.3 - - - +
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Residues in contact with ASP 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ALA* 3.1 22.1 + - - +
484A GLU* 3.6 7.3 - - - +
486A VAL* 1.3 82.6 - - - +
488A LEU* 1.3 57.8 + - - +
490A VAL* 3.3 8.1 + - - +
491A ASN* 2.9 45.4 + - - +
526A ARG* 4.7 10.0 + - - -
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Residues in contact with LEU 488 (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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455A ARG* 4.5 3.6 - - - +
474A CYS* 5.1 2.0 - - - -
476A ASP* 3.8 39.7 - - + +
477A PRO* 4.3 6.1 - - + +
479A GLN* 4.0 31.2 - - + +
484A GLU 2.9 17.8 + - - +
485A ASP* 3.5 11.2 - - - +
486A VAL 3.2 0.4 - - - -
487A ASP* 1.3 77.5 - - - +
489A ARG* 1.3 58.7 + - - +
491A ASN* 3.5 4.8 + - + +
492A PHE* 3.0 29.6 + - + +
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Residues in contact with ARG 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 4.0 27.0 - - + +
432A THR 5.5 5.7 + - - +
433A LYS* 5.5 6.9 - - - +
453A VAL* 3.7 34.1 + - + +
454A THR* 5.7 1.3 - - - +
455A ARG* 3.6 46.6 - - - +
474A CYS* 4.1 14.4 - - - -
482A TRP* 4.5 9.5 - - - +
485A ASP* 3.2 28.0 + - - +
486A VAL* 3.2 26.9 + - - +
488A LEU* 1.3 77.9 - - + +
490A VAL* 1.3 65.0 + - - +
492A PHE* 3.5 7.8 - - - +
493A ALA* 3.2 18.4 + - - +
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 4.2 3.6 - - + +
431A LEU* 3.8 15.9 - - + -
486A VAL* 3.1 25.5 + - + +
487A ASP* 3.6 11.7 - - - +
488A LEU 3.2 0.2 - - - -
489A ARG* 1.3 74.9 - - - +
491A ASN* 1.3 63.8 + - - +
493A ALA* 3.1 9.8 + - - +
494A MET* 3.0 43.6 + - + +
511A VAL* 3.8 35.9 - - + -
513A THR* 4.7 0.9 - - + -
526A ARG* 5.0 5.4 - - - +
528A VAL* 5.8 1.1 - - + -
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Residues in contact with ASN 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ASP* 2.9 36.5 + - - +
488A LEU* 4.1 5.1 - - + +
490A VAL* 1.3 77.6 - - - +
492A PHE* 1.3 59.5 + - - +
494A MET* 3.1 11.6 + - + +
495A ASN* 2.9 38.6 + - - +
531A PRO* 4.0 23.0 - - - +
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Residues in contact with PHE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 3.7 27.1 - - + -
103A ILE* 4.1 29.6 - - + -
453A VAL* 4.6 3.6 - - + -
472A VAL* 3.4 29.2 - - + -
473A LEU 3.5 11.9 - - - -
474A CYS* 3.5 39.3 - - + -
475A LYS 5.2 0.7 - - - -
476A ASP* 4.7 12.8 - - - +
488A LEU* 3.0 21.0 + - + +
489A ARG* 3.5 8.3 - - - +
491A ASN* 1.3 76.7 - - - +
493A ALA* 1.3 55.8 + - - +
495A ASN* 3.3 11.2 + - - +
496A VAL* 2.8 32.3 + - + +
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.8 21.1 - - + -
451A ILE* 3.9 14.8 - - + +
453A VAL* 3.6 29.4 - - + -
472A VAL* 5.2 0.2 - - - -
489A ARG 3.2 3.9 + - - +
490A VAL 3.1 10.2 + - - +
492A PHE* 1.3 76.4 - - - +
494A MET* 1.3 56.9 + - - +
496A VAL* 3.1 13.9 - - - +
497A GLY* 2.7 32.2 + - - -
503A PHE* 4.1 0.5 - - - -
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Residues in contact with MET 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.9 16.8 - - + -
490A VAL* 3.0 30.5 + - + +
491A ASN* 3.1 17.4 + - - +
493A ALA* 1.3 77.2 - - - +
495A ASN* 1.3 59.2 + - - +
497A GLY 3.3 0.5 + - - -
498A LYS* 3.0 36.6 + - - +
503A PHE* 3.5 7.8 - - - -
509A VAL* 3.9 16.4 - - + -
511A VAL* 4.8 0.4 - - + -
528A VAL* 4.0 23.6 - - + -
530A VAL* 3.8 20.9 - - + -
531A PRO* 3.5 35.7 - - + -
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Residues in contact with ASN 495 (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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103A ILE* 4.2 24.9 - - + +
491A ASN* 2.9 24.0 + - - +
492A PHE* 3.6 11.3 - - - +
494A MET* 1.3 73.2 - - - +
496A VAL* 1.3 61.1 + - - +
498A LYS* 3.7 24.7 + - - +
499A ALA* 2.9 33.7 + - - +
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ILE* 4.0 11.9 - - - +
451A ILE* 4.0 15.0 - - + -
472A VAL* 3.6 44.4 - - + -
492A PHE* 2.8 33.2 + - + +
493A ALA* 3.1 13.2 - - - +
495A ASN* 1.3 77.9 - - - +
497A GLY* 1.3 62.9 + - - +
499A ALA* 3.7 1.2 + - - +
500A ARG* 2.9 57.3 + - - +
502A PHE* 5.2 0.9 - - + -
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Residues in contact with GLY 497 (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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451A ILE* 4.2 2.0 - - - -
493A ALA 2.7 14.5 + - - -
494A MET 3.3 0.4 + - - -
496A VAL* 1.3 72.2 - - - +
498A LYS* 1.3 64.6 + - - +
500A ARG 4.0 0.2 - - - -
501A GLY 3.2 3.1 + - - -
502A PHE* 2.8 42.3 + - - +
503A PHE* 3.4 31.1 + - - -
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Residues in contact with LYS 498 (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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494A MET* 3.0 22.2 + - - +
495A ASN* 3.7 26.8 + - - +
497A GLY* 1.3 76.0 - - - +
499A ALA* 1.3 61.8 + - - +
501A GLY* 3.3 12.3 + - - -
503A PHE* 3.5 21.0 - - + +
504A LYS* 4.6 3.4 - - - -
505A LYS* 4.5 8.7 - - + +
530A VAL* 4.1 16.6 - - + -
531A PRO* 3.2 33.1 + - - +
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Residues in contact with ALA 499 (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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103A ILE* 3.8 25.1 - - + -
104A LEU* 4.3 13.7 - - + +
495A ASN 2.9 18.6 + - - +
496A VAL 4.0 3.1 - - - +
497A GLY 3.4 0.2 - - - -
498A LYS* 1.3 77.9 - - - +
500A ARG* 1.3 60.6 + - + +
501A GLY* 3.2 1.3 + - - -
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Residues in contact with ARG 500 (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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102A PRO 4.5 1.2 + - - -
103A ILE* 2.4 36.1 + - - +
104A LEU* 3.7 24.2 + - + +
105A TYR 3.8 10.5 + - - -
106A ARG* 4.7 20.7 - - - +
470A PHE* 6.2 0.9 - - - -
471A PRO 5.6 0.8 + - - -
472A VAL* 4.5 10.6 - - - +
496A VAL* 2.9 50.5 + - - +
498A LYS 3.4 0.4 - - - -
499A ALA* 1.3 77.5 - - + +
501A GLY* 1.3 61.0 + - - +
502A PHE* 3.5 38.6 - - + -
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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
------------------------------------------------------------
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