Contacts of the helix formed by residues 333 - 339 (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 ARG 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A THR* 5.6 2.4 + - - -
605A HEM 2.8 90.0 + - + +
329C THR* 2.8 24.2 + - - +
330C ASN* 3.1 30.0 - - - +
331C ALA 3.1 1.2 - - - -
332C PHE* 1.3 73.1 - - - +
334C TYR* 1.4 59.9 + - - +
335C GLY 2.9 5.8 - - - -
336C HIS* 3.0 24.8 + - + +
421C ASN* 2.9 39.2 - - - +
424C ARG* 3.5 17.2 - - - +
428C HIS* 5.8 0.6 - - - -
477C TRP* 2.9 21.9 + - + -
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Residues in contact with TYR 334 (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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86A PHE* 3.8 7.8 - - - -
605A HEM 4.2 1.8 - - + -
296C TYR* 2.9 21.8 + - - -
300C VAL* 3.4 26.7 - - + +
331C ALA 3.1 11.9 + - - +
332C PHE* 2.9 35.2 - + - -
333C ARG* 1.4 77.0 - - - +
335C GLY* 1.3 66.6 + - - +
337C THR* 2.6 37.4 + - - +
338C LEU* 3.7 27.6 - - + +
392C ASN* 6.3 0.2 - - - -
477C TRP* 3.9 1.0 - - - +
481C VAL* 4.0 15.0 - - + -
490C ARG* 3.9 15.3 - - + -
491C VAL* 3.5 19.3 - - + -
495C LEU* 3.8 22.0 - - + -
499C ILE* 3.8 15.7 - - + -
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Residues in contact with GLY 335 (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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605A HEM 3.4 35.1 - - - +
332C PHE 3.4 1.8 + - - -
333C ARG 2.9 2.2 - - - -
334C TYR* 1.3 80.9 - - - +
336C HIS* 1.3 51.9 + - - +
337C THR 3.0 5.4 - - - -
338C LEU* 2.7 44.5 + - - +
339C ILE* 3.8 5.9 + - - +
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Residues in contact with HIS 336 (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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605A HEM 2.2 76.4 + + + -
333C ARG* 3.0 19.9 + - + +
335C GLY* 1.3 75.5 - - - +
337C THR* 1.3 59.5 + - - +
338C LEU 3.2 1.0 + - - -
339C ILE* 3.5 16.8 + - + +
390C LYS* 5.7 0.2 - - - +
398C ALA* 4.4 4.2 - - - +
402C ILE* 3.5 28.6 - - + +
417C LEU* 3.5 18.5 - - + +
418C PRO* 6.1 2.0 - - + -
421C ASN* 2.8 42.2 + - - +
477C TRP* 4.7 7.2 - - + -
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Residues in contact with THR 337 (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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334C TYR* 2.6 23.9 + - - +
335C GLY 3.0 1.0 - - - -
336C HIS* 1.3 76.9 - - - +
338C LEU* 1.3 62.8 + - - +
339C ILE 3.4 0.4 - - - -
390C LYS* 2.9 35.4 + - - +
392C ASN* 3.5 25.7 + - - +
397C ILE* 3.3 27.4 - - + +
398C ALA* 4.8 1.1 - - + -
477C TRP* 3.8 15.9 - - + -
481C VAL* 3.8 29.2 - - + -
490C ARG 5.5 0.3 + - - -
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Residues in contact with LEU 338 (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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79A ASP* 5.5 1.8 - - - +
84A LEU* 4.1 0.9 - - - +
86A PHE* 3.7 41.5 - - + +
87A MET* 3.9 26.0 - - + +
605A HEM 5.0 2.2 - - + -
334C TYR* 3.7 25.6 - - + +
335C GLY* 2.7 23.4 + - - +
337C THR* 1.3 86.3 - - - +
339C ILE* 1.3 55.8 - - - -
340C GLN 3.5 0.9 + - - -
389C ALA* 3.9 9.8 - - + +
390C LYS* 2.9 40.3 + - - +
391C LEU* 5.5 0.4 - - - -
392C ASN* 5.2 6.3 - - + +
490C ARG* 4.8 12.1 - - + +
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Residues in contact with ILE 339 (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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87A MET* 3.9 26.7 - - + -
605A HEM 3.8 34.3 - - + -
243C MET* 5.1 4.3 - - + -
335C GLY 3.9 3.1 - - - +
336C HIS* 3.6 33.9 - - + +
337C THR 3.4 1.6 - - - -
338C LEU* 1.3 76.0 - - - +
340C GLN* 1.3 75.7 + - - +
361C LEU* 3.4 22.4 - - + -
390C LYS* 3.5 20.1 - - - +
399C VAL* 3.9 10.6 + - + +
402C ILE* 4.1 21.8 - - + -
417C LEU* 5.0 0.4 - - + -
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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