Contacts of the helix formed by residues 493 - 506 (chain A) in PDB entry 3CMM
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 ASN 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A ASP 5.5 0.4 - - - +
471A ASN 4.7 6.1 - - - +
472A ASP 4.0 7.0 - - - +
473A SER* 4.2 11.3 + - - -
474A ILE* 3.9 0.9 - - - -
491A GLY 5.0 1.1 - - - +
492A LYS* 1.3 75.2 - - - +
494A LYS* 1.3 67.3 + - - +
495A SER 3.4 0.4 - - - +
496A GLU* 3.2 35.9 + - + +
497A VAL* 3.2 24.3 + - - +
517A ILE* 3.9 33.1 - - + +
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Residues in contact with LYS 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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442A SER* 3.4 26.5 + - - +
443A GLY* 3.7 7.7 - - - -
470A ASP* 3.8 15.7 + - - +
472A ASP* 3.1 37.0 + - + +
473A SER 3.7 20.0 - - - -
474A ILE* 3.8 16.2 - - + +
478A ASN* 3.4 20.2 - - - +
482A GLN* 3.1 34.6 + - - +
485A PHE* 3.4 7.4 - - + -
492A LYS 3.6 1.6 + - - -
493A ASN* 1.3 71.2 - - - +
495A SER* 1.3 62.4 + - - +
498A ALA* 3.1 25.3 + - - +
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER* 3.6 19.5 - - - -
468A VAL* 4.1 21.0 - - - +
470A ASP* 3.9 11.7 + - - +
494A LYS* 1.3 79.5 - - - +
496A GLU* 1.3 59.4 + - - +
498A ALA* 3.4 1.6 + - - +
499A ALA* 3.0 30.5 + - - +
515A ALA* 3.7 5.5 - - - +
516A LYS 2.8 31.2 + - - -
517A ILE* 3.8 11.3 - - - +
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Residues in contact with GLU 496 (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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492A LYS* 5.8 0.3 - - - +
493A ASN* 3.2 41.6 + - + +
494A LYS 3.3 0.4 - - - -
495A SER* 1.3 85.4 + - - +
497A VAL* 1.3 66.4 + - + +
499A ALA* 3.9 1.6 - - - +
500A GLU* 3.1 29.0 + - + +
515A ALA* 4.0 21.1 - - + +
517A ILE* 4.0 14.4 - - + +
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Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 3.5 21.1 - - + -
484A LEU 4.0 5.2 - - - +
485A PHE* 3.7 17.7 - - + -
489A ASP* 3.5 25.4 - - + +
492A LYS* 3.7 27.1 - - + -
493A ASN 3.2 14.4 + - - +
494A LYS 4.1 0.7 - - - +
496A GLU* 1.3 77.9 - - + +
498A ALA* 1.3 57.5 + - - +
500A GLU* 3.5 7.5 - - + +
501A ALA* 2.9 27.9 + - + +
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER* 3.5 15.7 - - - +
447A CYS* 4.7 2.5 - - - -
450A LEU* 4.0 13.6 - - + +
484A LEU* 3.7 24.6 - - + +
485A PHE* 3.9 11.0 - - + -
494A LYS 3.1 18.7 + - - +
495A SER 3.8 3.4 - - - +
496A GLU 3.3 0.4 - - - -
497A VAL* 1.3 75.3 - - - +
499A ALA* 1.3 64.2 + - - +
501A ALA* 3.4 1.5 + - - -
502A VAL* 3.1 26.0 + - - +
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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
----------------------------------------------------------
450A LEU* 4.9 3.7 - - - +
468A VAL* 5.3 1.3 - - + -
495A SER 3.0 16.5 + - - +
496A GLU 3.9 2.0 - - - +
498A ALA* 1.3 72.7 - - - +
500A GLU* 1.3 69.7 + - - +
502A VAL* 3.1 3.8 + - - +
503A CYS* 3.1 28.0 + - - -
513A ILE* 3.9 37.5 - - + +
515A ALA* 3.9 15.0 - - + -
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Residues in contact with GLU 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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496A GLU 3.1 18.9 + - - +
497A VAL* 3.5 7.6 - - + +
499A ALA* 1.3 80.5 - - - +
501A ALA* 1.3 62.7 + - - +
502A VAL 3.2 0.3 + - - -
503A CYS* 3.3 9.3 + - - +
504A ALA* 3.2 18.2 + - - +
510A LYS* 5.9 1.6 + - - -
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Residues in contact with ALA 501 (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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484A LEU* 3.9 35.0 - - + +
497A VAL* 2.9 22.8 + - + +
498A ALA 3.8 4.3 - - - +
499A ALA 3.2 0.4 - - - -
500A GLU* 1.3 74.3 - - - +
502A VAL* 1.3 61.0 + - - +
504A ALA* 3.4 19.3 - - - +
505A MET* 3.5 17.0 + - + +
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Residues in contact with VAL 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 3.6 38.4 - - + +
451A LYS* 3.9 8.1 - - - +
454A ALA* 4.0 10.5 - - + +
484A LEU* 3.8 20.6 - - + -
498A ALA 3.1 12.1 + - - +
499A ALA* 3.1 0.6 + - - +
501A ALA* 1.3 76.5 - - - +
503A CYS* 1.3 62.0 + - - +
504A ALA 3.2 1.3 - - - -
505A MET* 3.1 15.9 + - - +
506A ASN* 2.9 24.3 + - - +
509A LEU* 3.7 26.2 - - + -
513A ILE* 3.7 14.1 - - + -
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Residues in contact with CYS 503 (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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499A ALA* 3.1 18.1 + - - -
500A GLU* 3.3 9.8 + - - +
502A VAL* 1.3 73.6 - - - +
504A ALA* 1.3 64.4 + - - +
506A ASN 3.8 8.1 - - - -
507A PRO* 3.1 25.1 - - - +
509A LEU* 3.9 17.0 - - - -
510A LYS* 4.0 31.8 + - - +
511A GLY 5.6 0.2 - - - -
513A ILE* 3.6 22.7 - - - -
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Residues in contact with ALA 504 (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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83A THR* 4.3 15.4 - - - +
500A GLU 3.2 9.8 + - - +
501A ALA* 3.4 15.0 - - - +
502A VAL 3.2 0.4 - - - -
503A CYS* 1.3 80.5 - - - +
505A MET* 1.3 61.2 + - + +
507A PRO* 4.2 5.4 - - - +
510A LYS* 5.3 2.7 - - - +
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Residues in contact with MET 505 (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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80A PHE* 3.0 46.6 - - + +
81A PHE* 4.3 11.4 - - + -
82A LEU 4.2 11.4 - - - +
83A THR* 5.0 2.7 - - - +
84A GLU* 5.0 2.3 - - - +
416A ARG* 3.1 16.1 + - - -
451A LYS* 4.2 13.5 - - - -
454A ALA* 4.7 7.9 - - + -
455A LEU* 6.1 2.2 - - + -
483A PHE* 4.1 15.7 - - + -
484A LEU* 3.7 23.3 - - + -
501A ALA* 3.5 14.3 + - + +
502A VAL* 3.1 21.8 + - - +
504A ALA* 1.3 80.8 - - + +
506A ASN* 1.3 59.8 + - + +
507A PRO* 3.7 4.0 - - - +
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Residues in contact with ASN 506 (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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84A GLU* 4.9 0.2 + - - -
416A ARG* 3.4 27.6 + - - +
417A TYR* 2.9 20.0 + - - -
454A ALA* 2.8 38.3 - - + +
455A LEU* 6.4 0.2 - - + -
457A GLY* 4.4 1.7 - - - -
502A VAL 2.9 7.3 + - - +
503A CYS* 3.3 8.3 - - - +
505A MET* 1.3 77.6 - - + +
507A PRO* 1.3 60.4 - - - +
508A ASP* 2.8 38.3 + - - +
509A LEU* 3.0 22.9 + - + +
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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