Contacts of the helix formed by residues 441 - 455 (chain C) in PDB entry 3IAD
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 LYS 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C SER* 4.1 18.9 + - - -
435C LEU* 3.8 37.9 + - - +
436C ALA* 4.6 10.5 - - - +
438C ASP* 3.0 16.4 + - + +
440C SER* 1.3 83.8 - - - +
442C HIS* 1.3 65.3 + - - +
443C MET 3.4 2.5 - - - -
444C ASN* 3.4 20.8 + - + +
445C LEU* 3.0 29.3 + - + +
606C ASP* 5.1 5.4 - - - +
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Residues in contact with HIS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ASP 4.3 0.8 + - - -
439C MET 3.1 16.9 + - - +
440C SER 3.5 1.2 - - - -
441C LYS* 1.3 76.4 - - - +
443C MET* 1.3 78.3 + - + +
445C LEU* 3.3 4.8 + - - +
446C LEU* 2.8 43.8 + - + +
481C HIS* 3.1 34.6 + + + +
485C LEU* 4.0 4.4 - - - +
541C TYR 5.1 0.8 + - - -
542C ILE* 3.6 51.2 + - + +
546C LEU* 4.0 19.1 - - + -
604C PHE* 3.8 18.6 - + + +
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Residues in contact with MET 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C SER 5.4 0.2 + - - -
441C LYS 3.4 0.4 - - - -
442C HIS* 1.3 91.0 - - + +
444C ASN* 1.3 61.0 + - - +
446C LEU* 3.8 13.6 - - + +
447C ALA* 2.8 36.8 + - - +
541C TYR 5.8 3.6 - - - +
542C ILE* 5.9 1.6 - - - -
604C PHE* 3.6 11.3 + - + +
605C LEU* 3.6 33.9 - - + -
606C ASP 6.0 0.7 - - - +
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Residues in contact with ASN 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C SER 4.2 0.2 + - - -
441C LYS* 3.4 29.1 + - + +
443C MET* 1.3 79.6 - - - +
445C LEU* 1.3 61.9 + - + +
447C ALA* 3.6 5.1 + - - +
448C ASP* 3.2 29.4 + - - +
606C ASP* 4.1 27.6 + - - +
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ALA* 3.3 35.9 - - + +
441C LYS* 3.0 22.3 + - + +
442C HIS* 3.5 7.2 - - - +
444C ASN* 1.3 78.6 - - + +
446C LEU* 1.3 56.7 + - - +
448C ASP* 3.1 12.4 + - - +
449C LEU 2.9 23.4 + - - -
474C GLN* 5.6 1.3 - - + -
477C GLN* 4.0 33.4 - - + +
478C ASN* 3.4 25.3 + - - +
481C HIS* 3.9 31.0 - - + +
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C HIS* 2.8 44.9 + - + +
443C MET* 3.8 17.3 - - + +
445C LEU* 1.3 73.2 - - - +
447C ALA* 1.3 57.5 + - - +
449C LEU* 3.3 5.5 + - + -
450C LYS* 2.9 43.8 + - + +
478C ASN* 4.5 1.8 - - - -
481C HIS* 6.1 0.2 - - - -
541C TYR 6.1 0.7 - - - +
545C PRO* 4.1 22.7 - - + +
546C LEU* 3.8 27.3 - - + +
549C THR* 3.8 27.6 - - + +
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Residues in contact with ALA 447 (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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443C MET 2.8 23.0 + - - +
444C ASN* 3.7 6.3 - - - +
446C LEU* 1.3 71.6 - - - +
448C ASP* 1.3 58.9 + - - +
450C LYS* 3.8 8.8 - - - +
451C THR* 2.8 33.3 + - - -
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Residues in contact with ASP 448 (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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444C ASN 3.2 15.0 + - - +
445C LEU* 3.1 14.3 + - - +
447C ALA* 1.3 76.0 - - - +
449C LEU* 1.3 60.3 + - - +
451C THR* 3.2 8.9 + - - -
452C MET* 2.9 32.0 + - - +
474C GLN* 3.1 43.0 + - + +
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C LEU 2.9 15.6 + - - +
446C LEU* 3.7 7.2 - - + +
448C ASP* 1.3 76.8 - - - +
450C LYS* 1.3 57.3 + - - +
452C MET* 3.2 14.9 + - + +
453C VAL* 2.9 32.2 + - - +
474C GLN 5.3 0.9 - - - +
475C VAL* 5.4 1.8 - - - -
478C ASN* 3.7 39.2 - - + +
546C LEU* 4.2 17.9 - - + +
549C THR* 4.0 13.2 - - + +
550C TRP* 4.1 29.8 - - + +
553C LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 2.9 35.6 + - + +
447C ALA* 3.8 8.3 - - - +
449C LEU* 1.3 75.9 - - - +
451C THR* 1.3 57.3 + - - +
453C VAL* 3.2 4.4 + - - +
454C GLU* 3.0 40.5 + - - +
545C PRO* 5.3 7.0 - - - +
549C THR* 3.7 30.5 - - + +
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Residues in contact with THR 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ALA 2.8 19.1 + - - -
448C ASP* 3.4 11.5 - - - -
450C LYS* 1.3 77.6 - - - +
452C MET* 1.3 59.1 + - - +
454C GLU* 3.7 13.1 + - - +
455C THR* 3.0 33.1 + - - +
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Residues in contact with MET 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ASP 2.9 10.8 + - - +
449C LEU* 3.5 16.2 - - + +
450C LYS 3.2 0.2 - - - -
451C THR* 1.3 75.6 - - - +
453C VAL* 1.3 60.8 + - - +
455C THR* 3.4 4.5 + - - -
456C LYS* 3.0 26.7 + - - +
466C LEU* 4.5 9.6 - - + -
471C ASP* 3.1 32.8 - - - +
474C GLN* 3.5 43.1 - - + +
475C VAL* 3.7 28.0 - - - -
553C LEU* 4.6 15.2 - - + +
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Residues in contact with VAL 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C LEU* 2.9 19.4 + - + +
450C LYS* 3.2 8.0 + - - +
452C MET* 1.3 78.3 - - - +
454C GLU* 1.3 61.4 - - + +
456C LYS* 3.2 28.2 + - + +
549C THR* 3.4 35.2 - - + +
552C ASP* 3.8 27.8 - - + +
553C LEU* 4.0 20.0 - - + +
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Residues in contact with GLU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C LYS* 3.0 25.9 + - - +
451C THR* 4.0 12.9 + - + +
452C MET 3.4 0.2 - - - -
453C VAL* 1.3 77.9 - - + +
455C THR* 1.3 60.9 + - - +
456C LYS 3.5 0.2 - - - -
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Residues in contact with THR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C THR* 3.0 23.0 + - - +
452C MET* 3.5 6.1 - - - -
453C VAL 3.2 0.8 - - - -
454C GLU* 1.3 77.7 + - - +
456C LYS* 1.3 67.0 + - - +
457C LYS* 3.1 25.4 + - + +
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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