Contacts of the helix formed by residues 447 - 456 (chain C) in PDB entry 1D7W
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 THR 447 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C GLU* 1.3 86.4 + - + +
448C VAL* 1.4 61.9 + - - +
449C GLY* 3.6 3.8 + - - -
450C GLN* 3.1 39.4 + - - +
451C LEU* 2.9 28.8 + - - +
465C MET* 4.0 8.5 - - - -
471C PRO* 4.4 1.0 - - - +
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Residues in contact with VAL 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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447C THR* 1.4 74.6 - - - +
449C GLY* 1.4 63.8 + - - +
451C LEU* 3.2 3.6 + - - +
452C GLY* 2.6 34.0 + - - -
458C LEU* 3.8 21.1 - - + +
461C ALA* 3.7 5.7 - - - +
462C ARG* 3.8 39.5 - - + +
465C MET* 3.9 22.1 - - + +
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Residues in contact with GLY 449 (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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447C THR* 3.3 5.0 + - - -
448C VAL* 1.4 85.6 - - - +
450C GLN* 1.3 61.0 + - - +
452C GLY* 3.2 2.4 + - - -
453C THR* 3.0 25.2 + - - -
458C LEU* 4.7 9.2 - - - -
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Residues in contact with GLN 450 (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 GLN 4.4 1.4 - - - +
445C PRO* 3.5 14.9 - - + +
446C GLU* 2.9 28.0 + - - +
447C THR* 3.1 33.0 + - - +
449C GLY* 1.3 76.9 - - - +
451C LEU* 1.4 61.9 + - - +
453C THR* 3.2 10.4 + - - -
454C VAL* 3.0 26.2 + - - +
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Residues in contact with LEU 451 (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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433C TYR* 3.9 17.7 - - + +
445C PRO* 3.5 26.3 - - + +
447C THR 2.9 16.9 + - - +
448C VAL* 3.6 5.2 - - - +
450C GLN* 1.4 73.0 - - - +
452C GLY* 1.4 61.6 + - - +
454C VAL* 3.2 1.6 + - + -
455C LEU* 2.9 51.1 + - + +
461C ALA* 3.8 23.3 - - + +
464C LEU* 3.6 29.6 - - + -
465C MET* 4.3 10.5 - - + -
471C PRO* 4.5 9.6 - - + -
474C ILE* 4.0 11.4 - - + -
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Residues in contact with GLY 452 (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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448C VAL 2.6 21.1 + - - -
449C GLY 3.6 3.4 - - - -
451C LEU* 1.4 73.4 - - - +
453C THR* 1.3 55.4 + - - +
456C ARG* 2.9 23.9 + - - -
457C ASN 3.0 17.1 + - - -
458C LEU* 4.0 13.9 + - - -
461C ALA* 3.4 14.3 - - - +
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Residues in contact with THR 453 (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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449C GLY 3.0 14.3 + - - -
450C GLN* 3.4 11.6 - - - -
451C LEU 3.1 0.2 - - - -
452C GLY* 1.3 75.2 - - - +
454C VAL* 1.3 67.4 + - + +
456C ARG* 3.2 19.2 + - - +
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Residues in contact with VAL 454 (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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433C TYR* 3.6 24.0 - - + +
437C ARG* 3.6 28.7 - - - +
443C PRO* 4.8 6.3 - - + +
445C PRO* 4.0 24.5 - - + -
450C GLN 3.0 13.5 + - - +
451C LEU* 3.2 5.8 + - + +
453C THR* 1.3 79.8 - - + +
455C LEU* 1.4 65.0 + - + +
456C ARG* 3.5 3.8 + - - +
483C GLU* 4.5 3.1 - - + +
484C PRO* 3.8 13.7 - - - +
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Residues in contact with LEU 455 (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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394C GLN* 2.9 29.2 + - - +
433C TYR* 4.4 8.7 - - + +
451C LEU* 2.9 33.9 + - + +
454C VAL* 1.4 76.4 - - - +
456C ARG* 1.3 69.2 + - - +
457C ASN* 4.1 10.8 - - + +
460C LEU* 3.9 16.4 - - + -
461C ALA* 4.2 6.5 - - - +
464C LEU* 3.5 32.1 - - + -
479C GLY 4.9 0.9 - - - +
482C SER* 3.9 5.6 - - - +
483C GLU* 3.8 40.8 - - + +
484C PRO* 3.5 7.0 - - - +
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Residues in contact with ARG 456 (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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394C GLN* 4.4 3.0 - - - +
452C GLY 2.9 9.7 + - - -
453C THR* 3.2 13.2 + - - +
454C VAL 4.5 3.1 - - - +
455C LEU* 1.3 77.2 - - - +
457C ASN* 1.3 58.9 + - - +
484C PRO* 3.2 41.9 + - + +
485C LEU 4.5 7.1 + - - -
486C LYS* 5.9 0.4 - - - +
493C PRO* 6.0 2.2 - - - +
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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