Contacts of the helix formed by residues 457 - 469 (chain C) in PDB entry 1D2V
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 457 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C GLN* 2.9 39.9 + - - +
395C ASN* 6.3 0.6 - - - +
452C GLY* 3.0 9.0 + - - +
455C LEU* 3.7 7.8 - - + +
456C ARG* 1.3 81.0 + - - +
458C LEU* 1.3 63.4 + - - +
459C LYS* 3.2 12.6 + - - +
460C LEU* 2.9 34.4 + - + +
461C ALA* 3.2 20.8 + - - +
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Residues in contact with LEU 458 (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* 3.9 36.6 - - + +
449C GLY* 4.6 6.5 - - - +
452C GLY* 4.0 13.5 + - - -
457C ASN* 1.3 71.6 + - - +
459C LYS* 1.3 60.8 + - - +
461C ALA 3.4 0.3 + - - -
462C ARG* 2.8 56.6 + - + +
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Residues in contact with LYS 459 (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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457C ASN* 3.2 8.5 + - - +
458C LEU* 1.3 77.9 - - - +
460C LEU* 1.3 63.4 + - - +
462C ARG* 3.1 12.1 + - - +
463C LYS* 2.9 55.4 + - + +
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Residues in contact with LEU 460 (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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68A ILE* 4.0 26.7 - - + +
394C GLN* 3.6 46.0 - - + +
397C ILE* 5.2 1.1 - - + -
455C LEU* 4.0 11.4 - - + -
457C ASN* 2.9 24.2 + - + +
459C LYS* 1.3 77.8 - - - +
461C ALA* 1.4 58.7 + - - +
463C LYS* 3.1 15.2 + - + +
464C LEU* 2.9 34.3 + - + +
482C SER* 3.7 29.6 - - - +
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Residues in contact with ALA 461 (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* 3.8 10.1 - - + +
451C LEU* 3.5 26.7 - - + -
452C GLY* 3.4 37.2 - - - +
455C LEU* 4.1 3.9 - - + +
457C ASN 3.2 6.2 + - - +
458C LEU 3.7 4.7 - - - +
460C LEU* 1.4 77.7 - - - +
462C ARG* 1.4 58.1 + - - +
464C LEU* 3.3 3.0 + - - +
465C MET* 3.0 32.7 + - - +
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Residues in contact with ARG 462 (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* 3.7 27.3 - - + +
458C LEU* 2.8 47.2 + - + +
459C LYS* 3.1 13.0 + - - +
461C ALA* 1.4 76.3 - - - +
463C LYS* 1.3 57.1 + - + +
465C MET* 3.2 2.3 + - - -
466C GLU* 2.9 47.6 + - + +
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Residues in contact with LYS 463 (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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67A GLU* 4.1 20.6 + - + +
68A ILE* 3.9 18.4 - - + +
459C LYS* 2.9 55.0 + - + +
460C LEU* 3.1 17.9 + - + +
462C ARG* 1.3 74.6 - - + +
464C LEU* 1.3 63.0 + - - +
466C GLU* 3.3 8.9 + - - +
467C GLN* 3.1 28.1 + - - +
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Residues in contact with LEU 464 (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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68A ILE* 3.4 24.7 - - + -
451C LEU* 4.0 14.6 - - + -
455C LEU* 3.6 32.3 - - + -
460C LEU* 2.9 18.8 + - + +
461C ALA 3.5 7.4 - - - +
463C LYS* 1.3 76.7 - - - +
465C MET* 1.3 52.6 + - - +
467C GLN 3.4 0.3 + - - -
468C TYR* 2.7 60.0 + - + +
474C ILE* 4.1 16.8 - - + -
478C MET* 4.0 15.5 - - + -
479C GLY* 5.7 0.7 - - - -
482C SER* 4.1 17.7 - - - +
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Residues in contact with MET 465 (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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446C GLU 4.2 4.5 - - - +
447C THR* 4.1 2.7 - - - -
448C VAL* 4.0 38.6 - - + +
451C LEU* 4.4 7.9 - - + -
461C ALA 3.0 20.3 + - - +
462C ARG* 3.2 4.9 + - - +
464C LEU* 1.3 75.2 - - - +
466C GLU* 1.3 69.2 + - - +
469C GLY* 2.8 44.0 + - - +
470C THR* 3.9 6.5 - - - -
471C PRO* 3.3 46.9 - - + -
474C ILE* 5.5 1.3 - - - -
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Residues in contact with GLU 466 (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* 5.8 0.5 - - - +
462C ARG* 2.9 43.7 + - + +
463C LYS* 3.3 8.2 + - - +
465C MET* 1.3 82.5 - - - +
467C GLN* 1.3 67.4 + - + +
469C GLY 4.8 0.3 + - - -
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Residues in contact with GLN 467 (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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57A PRO* 5.1 4.0 - - - +
59A ALA* 3.2 21.5 - - - +
63A ALA* 3.2 34.9 - - - +
64A VAL* 3.2 13.6 + - + +
67A GLU* 3.7 27.1 - - + +
68A ILE* 4.0 19.1 - - + -
463C LYS 3.1 16.5 + - - +
464C LEU 3.8 2.5 - - - +
466C GLU* 1.3 84.6 + - + +
468C TYR* 1.3 71.5 + - + +
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Residues in contact with TYR 468 (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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56A PHE* 3.8 15.2 - - - +
57A PRO 4.7 4.8 - - - +
59A ALA* 4.4 9.6 - - + -
64A VAL* 3.4 25.6 - - + +
422C MET* 3.3 20.4 - - - -
426C ARG* 4.1 9.4 - - - -
464C LEU* 2.7 46.1 + - + +
465C MET* 5.1 0.4 - - - -
467C GLN* 1.3 80.3 - - + +
469C GLY* 1.3 55.9 + - - +
470C THR 3.0 24.2 + - - +
473C ASN* 3.2 36.3 + - + +
474C ILE* 3.6 18.2 - - + -
475C ASP* 2.7 35.6 + - - -
478C MET* 3.5 9.9 - - + +
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Residues in contact with GLY 469 (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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56A PHE* 3.5 33.8 - - - -
465C MET* 2.8 42.8 + - - +
466C GLU 4.8 0.4 + - - -
467C GLN 3.7 0.6 - - - -
468C TYR* 1.3 69.3 - - - +
470C THR* 1.3 56.6 + - - +
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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