Contacts of the helix formed by residues 493 - 506 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C ASP 5.4 0.2 - - - +
471C ASN 4.8 4.2 - - - +
472C ASP 3.9 10.2 - - - +
473C SER* 4.2 6.8 - - - +
474C ILE* 4.3 0.7 - - - -
491C GLY 5.4 0.4 - - - +
492C LYS* 1.3 74.0 - - - +
494C LYS* 1.3 66.7 + - - +
495C SER 3.4 1.3 + - - +
496C GLU* 3.3 33.8 + - + +
497C VAL* 3.3 25.7 + - - +
517C ILE* 3.8 37.4 - - + +
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Residues in contact with LYS 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C SER* 3.3 24.3 + - - +
443C GLY* 3.8 8.1 - - - +
470C ASP* 4.2 13.4 + - - +
472C ASP* 3.1 39.7 + - + +
473C SER 3.7 13.0 - - - -
474C ILE* 3.8 22.0 - - + +
475C GLU* 5.7 0.8 + - - -
478C ASN* 3.4 26.2 + - - +
482C GLN* 2.9 28.9 + - - +
485C PHE* 3.4 10.4 - - + -
492C LYS 3.6 0.4 + - - -
493C ASN* 1.3 72.1 - - - +
495C SER* 1.3 63.0 + - - +
498C ALA* 3.1 24.9 + - - +
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Residues in contact with SER 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C SER* 3.5 18.6 + - - -
450C LEU* 5.4 0.9 - - - +
468C VAL* 4.0 19.0 - - - +
470C ASP* 3.9 10.3 + - - +
494C LYS* 1.3 79.5 - - - +
496C GLU* 1.3 62.0 + - - +
498C ALA* 3.1 2.1 + - - +
499C ALA* 2.8 32.4 + - - +
515C ALA* 3.9 9.2 - - - +
516C LYS 2.7 28.6 + - - -
517C ILE* 3.7 12.0 - - - +
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Residues in contact with GLU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C ASN* 3.3 36.3 + - + +
494C LYS 3.4 0.4 - - - -
495C SER* 1.3 88.5 + - - +
497C VAL* 1.3 64.4 + - + +
499C ALA* 3.5 1.3 + - - +
500C GLU* 3.1 31.7 + - + +
515C ALA* 4.0 23.8 - - + +
517C ILE* 4.3 10.0 - - + +
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Residues in contact with VAL 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C ILE* 3.7 9.6 - - + -
484C LEU 4.3 4.3 - - - +
485C PHE* 3.8 15.3 - - + -
489C ASP* 3.7 28.3 - - - +
492C LYS* 3.7 33.2 - - + -
493C ASN 3.3 18.4 + - - +
495C SER 3.2 0.4 - - - -
496C GLU* 1.3 80.8 - - + +
498C ALA* 1.3 58.4 + - - +
500C GLU* 3.9 5.0 - - + +
501C ALA* 3.1 28.2 + - + +
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Residues in contact with ALA 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C SER* 3.5 14.6 - - - +
447C CYS* 4.9 2.0 - - - -
450C LEU* 3.7 18.6 - - + -
484C LEU* 4.0 13.7 - - + +
485C PHE* 3.8 13.4 - - + -
494C LYS 3.1 19.2 + - - +
495C SER 3.5 3.1 - - - +
497C VAL* 1.3 77.4 - - - +
499C ALA* 1.3 65.7 + - - +
501C ALA* 3.2 4.0 + - - +
502C VAL* 3.1 27.4 + - - +
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Residues in contact with ALA 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C LEU* 4.6 4.6 - - - +
468C VAL* 5.2 1.1 - - + -
495C SER 2.8 19.5 + - - +
496C GLU* 3.8 4.3 - - - +
498C ALA* 1.3 72.5 - - - +
500C GLU* 1.3 64.6 + - + +
502C VAL* 3.3 5.4 + - - +
503C CYS* 3.2 27.4 + - - +
513C ILE* 3.9 36.5 - - + +
515C ALA* 3.9 14.4 - - + -
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Residues in contact with GLU 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C GLU* 3.1 18.7 + - + +
497C VAL* 3.9 5.4 - - + +
499C ALA* 1.3 77.5 - - + +
501C ALA* 1.3 63.4 + - - +
502C VAL 3.4 0.2 + - - -
503C CYS* 3.4 15.5 + - - +
504C ALA* 3.5 12.0 + - - +
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Residues in contact with ALA 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C LEU* 3.9 35.9 - - + +
497C VAL* 3.1 18.3 + - + +
498C ALA 3.2 5.1 + - - +
500C GLU* 1.3 77.1 - - - +
502C VAL* 1.3 61.6 + - - +
504C ALA* 3.3 13.4 + - - +
505C MET* 3.3 20.7 + - + +
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Residues in contact with VAL 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C LEU* 3.4 44.4 - - + +
451C LYS* 3.8 7.9 - - - +
454C ALA* 3.9 18.4 - - + +
466C ILE* 6.0 0.4 - - + -
484C LEU* 4.0 9.9 - - + -
498C ALA 3.1 14.9 + - - +
499C ALA 3.9 0.2 - - - +
501C ALA* 1.3 76.6 - - - +
503C CYS* 1.3 60.9 - - - +
505C MET* 3.5 12.6 + - - +
506C ASN* 2.9 25.3 + - - +
509C LEU* 4.2 5.2 - - + -
513C ILE* 3.6 29.6 - - + -
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Residues in contact with CYS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C ALA 3.2 15.8 + - - +
500C GLU* 3.6 12.6 - - - +
502C VAL* 1.3 77.2 - - - +
504C ALA* 1.3 59.2 + - - +
506C ASN 3.3 6.2 - - - +
507C PRO* 3.1 28.6 - - - +
509C LEU* 3.6 36.8 - - - -
510C LYS* 3.6 27.0 - - + -
511C GLY 4.8 0.9 - - - -
513C ILE* 4.8 6.1 - - - -
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Residues in contact with ALA 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C THR* 4.3 15.8 - - - +
500C GLU 3.5 7.6 + - - +
501C ALA* 3.3 13.3 + - - +
502C VAL 3.3 0.6 - - - -
503C CYS* 1.3 76.0 - - - +
505C MET* 1.3 66.2 + - + +
507C PRO* 3.9 8.6 - - - +
510C LYS* 6.0 0.9 - - - +
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Residues in contact with MET 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PHE* 3.6 47.5 - - + +
81C PHE* 4.4 10.3 - - + -
82C LEU 4.4 10.3 - - - +
83C THR* 5.3 2.9 - - - +
416C ARG* 3.1 23.3 + - - +
451C LYS* 4.4 11.0 - - - +
454C ALA* 5.0 5.2 - - + -
455C LEU* 6.4 1.1 - - + -
483C PHE* 3.8 18.6 - - + -
484C LEU* 3.6 31.6 - - + -
501C ALA* 3.3 13.5 - - + +
502C VAL* 3.6 14.8 - - - +
504C ALA* 1.3 79.4 - - + +
506C ASN* 1.3 59.0 + - + +
507C PRO* 3.6 2.8 - - - +
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Residues in contact with ASN 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ARG* 3.6 26.0 + - - +
417C TYR* 2.9 24.3 + - - -
454C ALA* 2.7 36.7 + - + +
457C GLY* 4.3 2.4 - - - -
502C VAL 2.9 12.0 + - - +
503C CYS* 3.2 16.4 - - - +
505C MET* 1.3 77.5 - - - +
507C PRO* 1.3 60.5 - - - +
508C ASP* 3.0 32.1 + - - +
509C LEU* 3.0 16.3 + - + +
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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