Contacts of the helix formed by residues 438 - 452 (chain C) in PDB entry 4PS1
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 ASP 438 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436C GLY 3.7 1.4 + - - -
437C ASP* 1.3 77.2 - - - +
439C ILE* 1.3 59.2 + - - +
440C LEU* 3.0 30.8 + - - +
441C THR* 2.7 32.2 + - - -
442C ILE* 3.0 26.2 + - - +
473C LYS* 3.5 40.1 + - + +
474C LEU 3.2 18.5 + - - +
475C VAL* 3.8 10.1 - - + -
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Residues in contact with ILE 439 (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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354C VAL* 5.7 0.2 - - + -
356C PHE* 4.6 12.8 - - + -
400C LEU* 3.5 33.9 - - + -
425C LEU* 5.1 0.4 - - + -
429C LEU* 3.7 30.5 - - + -
438C ASP* 1.3 74.5 - - - +
440C LEU* 1.3 65.4 + - + +
442C ILE* 3.3 11.3 + - + +
443C LEU* 2.8 36.8 + - + +
470C LEU* 4.1 9.0 - - + -
474C LEU* 2.8 42.0 + - + +
476C PHE* 4.1 16.2 - - + -
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C LEU* 4.1 20.9 - - + -
438C ASP* 3.0 12.5 + - - +
439C ILE* 1.3 84.1 - - + +
441C THR* 1.3 60.3 + - - +
443C LEU* 3.4 7.9 + - + +
444C THR* 2.9 33.4 + - - -
466C PRO* 5.3 3.8 - - + -
468C PHE* 3.7 53.6 - - + -
470C LEU* 4.6 7.9 - - + -
472C LYS 6.1 0.7 - - - +
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Residues in contact with THR 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ARG* 3.8 26.0 - - - +
437C ASP* 4.4 8.7 - - + -
438C ASP* 2.7 33.2 + - - -
440C LEU* 1.3 77.4 - - - +
442C ILE* 1.3 62.1 + - - +
444C THR* 3.3 8.5 + - - -
445C GLU* 3.2 19.9 + - - +
473C LYS* 5.0 1.9 + - - -
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Residues in contact with ILE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C LEU* 4.9 2.5 - - + +
428C SER* 3.1 27.3 + - - +
429C LEU* 3.9 22.7 - - + +
432C ARG* 3.8 35.4 - - + +
433C CYS* 3.9 26.2 - - - +
437C ASP* 4.0 13.2 - - + +
438C ASP 3.0 15.5 + - - +
439C ILE* 3.6 14.4 - - + +
440C LEU 3.3 0.2 - - - -
441C THR* 1.3 76.8 - - - +
443C LEU* 1.3 57.3 + - - +
445C GLU* 3.1 6.6 + - - +
446C VAL* 2.9 30.2 + - + +
476C PHE* 6.2 0.2 - - + -
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Residues in contact with LEU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C PHE* 4.3 7.2 - - + -
400C LEU* 3.8 39.7 - - + -
402C GLY* 5.0 2.5 - - - -
421C TYR* 4.1 17.3 - - + +
425C LEU* 3.8 28.5 - - + -
439C ILE* 2.8 31.0 + - + +
440C LEU* 3.4 7.8 + - + +
442C ILE* 1.3 70.8 - - - +
444C THR* 1.3 62.0 + - - +
446C VAL* 3.6 10.8 - - + +
447C ASN* 2.9 34.0 + - - +
466C PRO* 3.9 26.5 - - + -
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Residues in contact with THR 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C LEU 2.9 19.3 + - - -
441C THR* 3.5 12.0 - - - -
443C LEU* 1.3 76.8 - - - +
445C GLU* 1.3 57.3 + - - +
447C ASN* 3.2 14.2 + - + +
448C TYR* 2.9 26.3 + - + +
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Residues in contact with GLU 445 (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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428C SER* 3.0 29.7 + - - +
431C GLU* 4.3 8.6 - - - +
432C ARG* 2.8 43.5 + - - +
441C THR 3.2 8.2 + - - +
442C ILE 3.1 8.7 + - - +
444C THR* 1.3 79.1 - - - +
446C VAL* 1.3 53.9 + - - +
448C TYR* 3.0 9.9 + - + +
449C GLU* 2.8 52.3 + - + +
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Residues in contact with VAL 446 (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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421C TYR* 3.8 35.0 - - + -
424C SER* 3.6 26.0 - - - +
425C LEU* 3.7 33.4 - - + +
428C SER* 4.0 8.7 - - - -
442C ILE* 2.9 20.2 + - + +
443C LEU* 3.6 15.3 - - + +
444C THR 3.2 0.2 - - - -
445C GLU* 1.3 74.7 - - - +
447C ASN* 1.3 64.6 + - - +
449C GLU 3.2 0.3 + - - -
450C VAL* 2.9 29.9 + - + +
464C PRO* 4.8 1.8 - - + -
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Residues in contact with ASN 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 LEU 2.9 16.0 + - - +
444C THR* 3.2 15.5 + - + +
446C VAL* 1.3 76.2 - - - +
448C TYR* 1.3 61.0 + - - +
450C VAL* 4.2 0.7 - - - +
451C SER* 2.8 31.6 + - - -
463C MET* 3.7 19.7 - - + +
464C PRO* 3.3 33.7 + - - +
466C PRO* 3.7 24.0 - - - +
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Residues in contact with TYR 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 THR* 2.9 12.9 + - + +
445C GLU* 3.0 11.9 + - + +
447C ASN* 1.3 77.8 - - - +
449C GLU* 1.3 83.2 + - + +
451C SER* 3.4 6.9 + - - -
452C ASN* 3.3 37.8 + - + +
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Residues in contact with GLU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C SER* 3.5 22.0 - - - +
427C GLN* 5.7 7.6 + - - +
428C SER* 6.4 0.4 - - - -
445C GLU* 2.8 36.1 + - + +
448C TYR* 1.3 88.8 - - + +
450C VAL* 1.3 66.4 + - - +
452C ASN* 3.3 16.6 + - - +
453C LYS* 3.5 16.2 + - - +
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Residues in contact with VAL 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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420C TRP* 3.8 23.2 - - + +
421C TYR* 4.1 5.2 - - - -
424C SER* 3.8 22.4 - - - -
446C VAL* 2.9 24.4 + - + +
449C GLU* 1.3 75.2 - - - +
451C SER* 1.3 61.9 - - - +
452C ASN 3.0 1.2 + - - -
453C LYS* 3.1 24.6 + - + +
462C GLN* 3.5 41.4 + - + +
464C PRO* 3.6 26.5 - - + -
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Residues in contact with SER 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ASN 2.8 22.6 + - - -
448C TYR* 3.5 9.2 - - - -
450C VAL* 1.3 76.5 - - - +
452C ASN* 1.3 57.4 + - - +
453C LYS 3.3 0.4 - - - -
461C LYS* 2.9 28.3 + - - +
462C GLN 3.8 9.2 + - - -
463C MET* 3.3 29.2 - - - +
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Residues in contact with ASN 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 TYR* 3.3 29.5 + - + +
449C GLU* 3.3 12.0 + - - +
450C VAL 3.0 1.2 - - - -
451C SER* 1.3 76.6 - - - +
453C LYS* 1.3 64.4 + - - +
454C ASP* 3.7 9.9 - - - +
461C LYS* 4.0 3.4 + - - +
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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