Contacts of the helix formed by residues 437 - 457 (chain C) in PDB entry 1Q57
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 437 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436C SER* 1.3 82.2 - - - +
438C GLU* 1.3 63.2 + - - +
439C ARG* 2.9 63.6 + - + +
440C LYS* 3.0 18.4 + - + +
441C MET* 3.2 9.5 + - - +
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Residues in contact with GLU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C SER* 3.1 20.8 - - - +
428C ILE* 5.1 0.2 - - - -
429C VAL* 2.9 50.4 - - + +
436C SER 3.5 2.0 + - - -
437C ASP* 1.3 71.6 + - - +
439C ARG* 1.3 50.6 + - - +
441C MET* 4.4 7.4 - - + -
442C ILE* 2.8 47.8 + - - +
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Residues in contact with ARG 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C ASP* 3.0 43.5 + - + +
438C GLU* 1.3 74.9 - - - +
440C LYS* 1.3 57.8 + - + +
442C ILE* 2.7 25.1 - - - +
443C ASP* 3.5 9.4 - - - +
488C GLY* 4.7 7.0 - - - +
489C SER* 3.1 34.8 - - - +
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Residues in contact with LYS 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C SER 5.5 2.5 - - - +
437C ASP* 3.0 15.1 + - + +
439C ARG* 1.3 78.2 - - - +
441C MET* 1.3 102.2 + - + +
443C ASP* 3.0 24.2 + - - +
444C ASN* 2.9 35.3 + - - +
489C SER* 5.7 0.4 - - - -
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Residues in contact with MET 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C THR* 4.5 19.3 - - + +
429C VAL* 4.0 26.7 - - + -
435C GLU* 4.0 21.1 - - + +
436C SER 4.9 2.0 - - - +
437C ASP 3.2 11.7 + - - +
438C GLU* 4.3 7.0 - - + +
440C LYS* 1.3 92.4 - - + +
442C ILE* 1.3 69.4 + - - +
443C ASP 2.9 3.5 + - - -
444C ASN* 2.9 23.9 + - + +
445C LEU* 2.9 32.9 - - + +
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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
----------------------------------------------------------
426C ILE* 3.7 27.3 - - + +
427C SER* 6.5 0.4 - - - -
429C VAL* 4.8 6.0 - - + +
438C GLU* 2.8 29.7 + - - +
439C ARG* 2.7 31.2 - - - +
441C MET* 1.3 74.5 - - - +
443C ASP* 1.3 64.5 + - - +
445C LEU* 3.6 3.9 + - - +
446C MET* 3.0 26.0 + - + +
487C ARG* 6.5 0.7 - - - -
488C GLY* 3.1 18.8 - - - +
492C LEU* 3.0 47.8 - - + -
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Residues in contact with ASP 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ARG 3.8 8.3 - - - -
440C LYS* 3.0 13.2 + - - +
441C MET 2.9 0.8 + - - -
442C ILE* 1.3 90.6 - - - +
444C ASN* 1.3 64.1 + - - +
446C MET* 2.9 17.7 + - - +
447C THR* 3.0 15.1 + - + +
489C SER* 3.4 25.1 + - - +
490C GLY 4.1 0.3 - - - -
491C ALA* 3.1 40.3 + - + +
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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
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440C LYS* 2.9 36.4 + - - +
441C MET* 2.9 10.9 + - + +
443C ASP* 1.3 77.6 - - - +
445C LEU* 1.3 61.7 + - - +
447C THR* 2.8 23.0 + - - -
448C LYS* 3.1 36.7 + - - +
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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
----------------------------------------------------------
402C THR* 4.0 15.3 - - - +
405C LEU* 5.7 7.2 - - + -
406C LEU* 3.3 31.6 - - + -
423C LEU* 5.4 5.4 - - + -
426C ILE* 4.0 31.6 - - + +
428C ILE 5.2 2.5 - - - +
429C VAL* 5.1 15.5 - - + +
441C MET* 2.9 26.9 + - + +
442C ILE* 3.9 6.3 - - - +
444C ASN* 1.3 75.9 - - - +
446C MET* 1.3 66.5 + - - +
448C LYS* 2.9 8.0 + - - +
449C LEU* 2.9 37.7 + - + +
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Residues in contact with MET 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 4.5 8.7 - - + -
309C MET* 3.5 17.5 - - + -
426C ILE* 5.3 7.6 - - - -
442C ILE* 3.0 13.4 + - + +
443C ASP 2.9 14.6 - - - +
445C LEU* 1.3 76.4 - - - +
447C THR* 1.3 54.2 + - - +
449C LEU* 3.0 20.9 - - - +
450C LYS* 2.9 24.5 + - + +
462C VAL* 5.5 1.1 - - - -
491C ALA* 3.3 15.5 - - + +
492C LEU* 3.2 46.2 - - + +
495C LEU* 3.5 7.8 - - + +
496C SER* 3.1 34.5 - - - +
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Residues in contact with THR 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ASP* 3.2 15.5 - - + +
444C ASN* 2.8 19.5 + - - -
446C MET* 1.3 71.3 - - - +
448C LYS* 1.3 70.8 + - - +
449C LEU 2.8 2.7 + - - -
450C LYS* 2.9 3.2 + - - +
451C GLY* 2.9 21.0 + - - -
491C ALA* 4.8 2.7 - - + -
495C LEU* 3.1 27.1 - - + -
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Residues in contact with LYS 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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402C THR* 3.9 23.4 + - - +
403C ASP* 3.1 29.1 + - - +
406C LEU* 3.9 23.6 - - + +
444C ASN* 3.1 37.8 + - - +
445C LEU* 2.9 7.6 + - - +
447C THR* 1.3 76.9 + - - +
449C LEU* 1.3 58.5 + - - +
451C GLY* 3.4 1.8 + - - -
452C PHE* 2.9 29.3 + - - +
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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
----------------------------------------------------------
307C VAL* 5.4 2.0 - - + -
405C LEU* 5.9 0.4 - - + -
406C LEU* 3.3 38.8 - - + -
409C LEU* 5.4 4.5 - - + -
423C LEU* 4.2 16.6 - - + -
426C ILE* 5.0 2.5 - - + -
445C LEU* 2.9 29.0 + - + +
446C MET* 3.0 21.8 - - - +
447C THR 2.8 0.6 + - - -
448C LYS* 1.3 73.5 - - - +
450C LYS* 1.3 60.4 + - - +
451C GLY 3.0 1.7 + - - -
452C PHE* 3.1 9.1 - - + +
453C ALA* 2.8 28.8 + - - +
460C LEU* 3.8 29.8 - - + +
462C VAL* 3.8 19.1 - - + -
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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
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305C GLY 3.6 3.4 - - - -
307C VAL* 3.6 23.7 - - + +
446C MET* 2.9 11.5 + - - +
447C THR 2.9 9.8 + - - +
449C LEU* 1.3 74.3 - - - +
451C GLY* 1.3 56.8 - - - +
453C ALA* 3.1 3.1 - - - +
454C LYS* 2.7 62.4 + - + +
495C LEU* 3.6 36.9 + - + +
497C ASP* 2.9 16.4 + - - -
522C ARG* 2.9 32.5 - - - +
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Residues in contact with GLY 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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447C THR 2.9 12.2 + - - -
448C LYS* 3.6 4.3 - - - -
450C LYS* 1.3 72.5 - - - +
452C PHE* 1.3 67.0 + - - +
453C ALA 2.9 0.9 + - - -
454C LYS* 5.2 1.6 - - - -
455C SER* 2.7 33.9 + - - -
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Residues in contact with PHE 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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406C LEU* 4.2 20.4 - - + -
409C LEU* 3.3 35.0 - - + -
410C ALA* 3.4 26.7 - - + -
413C ARG* 3.5 21.8 - - + -
414C SER* 6.0 0.4 - - - -
421C ILE* 4.3 4.7 - - + -
448C LYS 2.9 15.5 + - - +
449C LEU* 3.1 10.3 - - + +
451C GLY* 1.3 68.7 - - - -
453C ALA* 1.3 57.4 + - - +
455C SER* 4.2 5.4 + - - -
456C THR* 2.7 50.5 + - + +
458C VAL* 4.0 9.4 - - + -
460C LEU* 3.8 32.1 - - + -
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Residues in contact with ALA 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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305C GLY* 3.3 14.7 - - - +
306C GLU 3.9 4.7 - - - +
307C VAL* 3.4 31.6 - - + -
449C LEU 2.8 10.9 + - - +
450C LYS* 3.1 11.2 - - + +
451C GLY 2.9 2.4 + - - -
452C PHE* 1.3 72.9 - - - +
454C LYS* 1.3 54.5 + - - +
457C GLY* 2.6 37.9 + - - -
458C VAL* 3.6 14.9 + - - +
460C LEU* 4.6 4.3 - - + -
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Residues in contact with LYS 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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343A GLU 5.0 9.1 + - - -
305C GLY* 2.9 23.7 + - - +
306C GLU* 4.9 1.3 - - - +
450C LYS* 2.7 38.1 + - + +
451C GLY* 4.2 1.3 - - - +
453C ALA* 1.3 73.4 - - - +
455C SER* 1.3 66.2 + - - +
456C THR 3.1 2.0 + - - -
457C GLY* 3.9 4.9 + - - -
497C ASP* 3.8 4.5 - - - -
522C ARG* 3.0 38.9 - - - +
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Residues in contact with SER 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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451C GLY* 2.7 26.0 + - - -
452C PHE* 3.8 2.9 + - - -
454C LYS* 1.3 74.7 - - - +
456C THR* 1.3 74.7 + - - +
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Residues in contact with THR 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ARG* 2.9 36.8 + - + +
414C SER* 5.6 4.3 - - - +
452C PHE* 2.7 34.4 + - + +
455C SER* 1.3 96.0 - - - +
457C GLY* 1.3 58.9 + - - +
458C VAL* 3.1 16.4 - - - +
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Residues in contact with GLY 457 (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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304C GLY* 3.3 10.7 - - - -
305C GLY* 3.0 18.3 + - - -
413C ARG* 2.9 13.0 + - - -
419C ASP* 4.8 1.0 - - - +
453C ALA 2.6 18.0 + - - -
454C LYS 3.9 5.0 + - - -
455C SER 3.8 0.4 - - - -
456C THR* 1.3 70.0 - - - +
458C VAL* 1.3 63.0 + - - -
459C VAL* 3.6 0.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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