Contacts of the helix formed by residues 478 - 494 (chain A) in PDB entry 1CWS
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 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A LYS* 2.8 28.9 + - - -
395A HIS* 4.5 7.4 + - - -
477A SER* 1.3 84.7 + - - +
479A ARG* 1.3 72.1 + - + +
480A GLY 3.3 1.3 + - - -
481A PRO* 3.4 4.4 - - - +
482A ARG* 3.1 31.4 + - - +
567A WO4 3.2 15.0 + - - +
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Residues in contact with ARG 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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426A CYS* 4.0 19.9 - - + +
427A ARG* 3.6 9.6 - - - +
428A TYR* 3.5 44.9 - - - +
431A GLU* 2.6 43.8 + - - -
473A CYS* 3.7 8.2 - - + +
474A GLU* 3.7 7.7 + - - +
478A GLU* 1.3 74.4 - - + +
480A GLY* 1.3 62.2 + - - +
482A ARG* 3.3 26.7 + - - +
483A MET* 3.1 24.3 + - - +
531A MET* 3.7 17.9 - - - +
567A WO4 2.5 45.4 + - - +
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Residues in contact with GLY 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A CYS* 4.1 15.0 - - - -
471A PHE* 4.0 8.1 - - - +
472A HIS* 4.3 14.4 - - - -
473A CYS* 3.2 13.0 - - - +
479A ARG* 1.3 78.9 - - - +
481A PRO* 1.3 71.2 - - - +
483A MET* 3.2 3.1 + - - +
484A CYS* 3.0 21.7 + - - +
507A ILE* 4.5 1.6 - - - -
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Residues in contact with PRO 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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395A HIS* 3.6 29.8 - - + +
398A LEU* 4.2 8.0 - - + +
400A TYR* 4.7 1.3 - - - +
476A SER* 3.6 25.8 - - - +
477A SER 3.5 15.5 - - - +
478A GLU* 3.4 13.0 - - - +
480A GLY* 1.3 90.0 - - - +
482A ARG* 1.3 56.4 + - - +
484A CYS* 3.3 2.5 + - + +
485A ARG* 2.8 37.4 + - - +
507A ILE* 4.0 23.1 - - + -
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Residues in contact with ARG 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A PRO 4.9 5.5 + - - -
446A GLU* 4.6 20.4 + - - +
478A GLU* 3.1 23.8 + - - +
479A ARG* 3.5 33.1 + - - +
481A PRO* 1.3 75.6 - - - +
483A MET* 1.3 77.2 + - - +
485A ARG* 3.2 8.8 + - + +
486A PHE* 2.8 31.4 + - + +
547A THR* 6.3 1.4 - - - +
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Residues in contact with MET 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A VAL* 4.9 0.9 - - + -
426A CYS* 3.7 22.7 - - + -
443A LEU 3.8 12.6 - - - +
444A PRO* 3.5 24.9 - - + +
445A LEU 3.9 0.2 - - - -
446A GLU* 3.8 28.5 - - + +
449A ALA* 3.7 27.6 - - + -
471A PHE* 3.9 17.0 - - + -
479A ARG 3.1 7.0 + - - +
480A GLY 3.7 7.9 - - - +
482A ARG* 1.3 92.7 - - - +
484A CYS* 1.3 56.7 + - - +
486A PHE* 3.3 12.1 + - - +
487A ILE* 3.0 29.6 + - + +
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Residues in contact with CYS 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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4A BME 2.0 53.2 - - - +
471A PHE* 3.6 35.6 - - + -
480A GLY 3.0 13.4 + - - +
481A PRO 3.4 7.6 - - - +
482A ARG 3.1 0.2 - - - -
483A MET* 1.3 74.7 - - - +
485A ARG* 1.3 65.8 + - - +
487A ILE* 3.3 4.0 + - - +
488A ARG 3.2 16.3 + - - -
505A MET* 4.0 14.7 - - - +
507A ILE* 3.8 15.3 - - + -
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Residues in contact with ARG 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A BME 4.0 7.4 - - + -
395A HIS* 3.6 22.8 + - - +
397A ASP* 2.8 42.8 + - - -
398A LEU* 3.4 34.9 - - + +
481A PRO* 2.8 21.2 + - - +
482A ARG* 3.7 6.7 - - + +
484A CYS* 1.3 75.3 - - - +
486A PHE* 1.3 64.9 + - - +
488A ARG* 3.3 3.7 + - - +
489A GLU* 3.1 24.1 + - - +
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Residues in contact with PHE 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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446A GLU* 3.6 62.8 - - + +
450A GLU* 4.1 15.9 - - + -
482A ARG* 2.8 17.1 + - + +
483A MET* 3.6 19.1 - - - +
485A ARG* 1.3 78.6 - - - +
487A ILE* 1.3 81.6 + - + +
489A GLU* 3.2 21.1 + - - +
490A ARG* 3.1 50.5 + - + +
548A ARG* 5.0 4.7 - - - -
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Residues in contact with ILE 487 (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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449A ALA* 4.0 31.2 - - + +
450A GLU 4.4 0.7 - - - +
453A LEU* 4.1 15.3 - - + -
454A LEU* 4.4 17.2 - - + +
469A LEU* 4.6 3.4 - - + -
471A PHE* 4.0 20.9 - - + -
483A MET* 3.0 21.1 + - + +
484A CYS 3.3 4.2 + - - +
486A PHE* 1.3 91.6 - - + +
488A ARG* 1.3 57.6 + - - +
490A ARG* 3.4 3.9 + - - +
491A ASP* 2.9 28.4 + - + +
502A TYR* 4.5 18.6 - - + -
505A MET* 4.3 16.6 - - - -
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A BME 3.9 19.6 + - + -
380A GLY* 4.1 7.9 - - - +
484A CYS 3.2 9.7 + - - +
485A ARG* 3.8 7.0 - - - +
487A ILE* 1.3 78.0 - - - +
489A GLU* 1.3 58.6 + - - +
491A ASP* 4.2 3.7 + - - -
492A ARG* 2.9 38.2 + - + +
500A LEU* 3.5 27.5 - - - +
502A TYR 3.1 11.1 + - - -
503A PRO 3.1 25.5 + - - -
505A MET* 3.1 41.3 - - + +
568A SO4 2.9 44.9 + - - +
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Residues in contact with GLU 489 (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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485A ARG 3.1 12.4 + - - +
486A PHE* 3.2 24.9 + - - +
488A ARG* 1.3 78.4 - - - +
490A ARG* 1.3 71.2 + - - +
492A ARG* 3.3 7.1 + - - +
493A ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 490 (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 GLU* 3.1 25.4 + - - +
454A LEU* 3.3 23.8 - - + -
486A PHE* 3.1 48.3 + - + +
487A ILE 3.8 0.9 - - - +
489A GLU* 1.3 84.1 + - - +
491A ASP* 1.3 65.9 + - - +
493A ALA* 3.2 22.1 + - - +
494A VAL* 3.2 49.4 + - + +
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Residues in contact with ASP 491 (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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454A LEU* 4.2 9.6 - - + +
487A ILE* 2.9 21.3 + - + +
488A ARG* 3.7 7.4 + - - +
490A ARG* 1.3 77.8 - - - +
492A ARG* 1.3 63.0 + - - +
494A VAL* 3.6 5.3 + - - +
495A ASN* 2.8 48.7 + - - +
500A LEU* 3.5 14.5 - - + +
501A TYR* 2.7 31.3 + - - -
502A TYR* 2.8 39.1 + - - +
505A MET* 5.8 0.3 - - - +
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Residues in contact with ARG 492 (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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380A GLY 3.1 22.4 + - - -
382A TYR* 3.5 14.5 + - - -
488A ARG* 2.9 26.9 + - + +
489A GLU* 3.5 7.4 - - - +
491A ASP* 1.3 77.4 - - - +
493A ALA* 1.3 63.6 + - - +
494A VAL 3.4 0.2 + - - -
495A ASN* 3.3 19.3 + - - +
497A TYR* 3.8 22.2 - - - +
498A PRO* 3.3 35.6 + - - +
499A SER 4.4 1.1 + - - -
500A LEU* 3.7 18.9 - - + +
568A SO4 2.7 45.8 + - - +
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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
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489A GLU 3.0 17.4 + - - +
490A ARG* 3.2 29.6 + - - +
492A ARG* 1.3 78.9 - - - +
494A VAL* 1.3 60.8 + - + +
495A ASN 3.5 2.8 + - - +
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Residues in contact with VAL 494 (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 GLU* 5.7 0.7 - - - +
454A LEU* 4.9 7.6 - - + +
490A ARG* 3.2 38.5 + - + +
491A ASP* 3.7 9.2 - - - +
493A ALA* 1.3 77.4 - - + +
495A ASN* 1.3 70.4 + - - +
501A TYR* 3.9 21.0 + - + +
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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