Contacts of the helix formed by residues 448 - 463 (chain C) in PDB entry 5A31
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 GLN 448 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 5.9 0.8 + - - -
167A LYS* 3.2 41.0 + - - +
443C TYR* 3.0 18.7 + - + +
446C LEU* 3.5 24.6 - - + +
447C ASN* 1.3 75.2 - - - +
449C LEU* 1.3 63.2 + - - +
450C VAL* 3.5 3.1 - - - -
451C GLU* 3.3 24.1 + - + +
452C ALA* 3.2 16.5 + - - +
319O GLN* 4.5 4.0 + - - +
322O LEU* 3.2 33.5 - - + +
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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
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444C GLU* 4.4 17.7 - - + +
447C ASN* 3.4 28.5 + - - +
448C GLN* 1.3 73.2 - - - +
450C VAL* 1.3 62.6 + - - +
452C ALA* 3.1 4.4 + - - +
453C LYS* 2.9 34.9 + - - +
476C LEU* 3.9 17.6 - - + +
479C GLN* 3.5 31.6 - - + +
480C LEU* 4.1 29.6 - - + -
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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
----------------------------------------------------------
133A ILE* 4.2 30.1 - - + -
134A SER* 4.5 14.6 - - - +
448C GLN* 5.0 0.9 - - - -
449C LEU* 1.3 80.4 - - - +
451C GLU* 1.3 78.1 + - - +
453C LYS* 3.6 14.3 + - + +
454C LYS* 3.1 49.2 + - + +
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Residues in contact with GLU 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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133A ILE* 5.0 2.4 - - - +
167A LYS* 3.9 10.9 - - - +
169A TYR* 3.9 18.1 + - - -
215A HIS* 4.2 14.4 + - - -
217A LEU* 3.6 20.7 - - + +
443C TYR* 3.6 22.0 - - + -
448C GLN* 3.5 42.1 - - + +
450C VAL* 1.3 89.6 - - - +
452C ALA* 1.3 65.8 + - - +
454C LYS* 3.1 3.8 + - - +
455C CYS* 2.9 26.5 + - - +
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Residues in contact with ALA 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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440C GLY* 3.6 24.0 - - - +
443C TYR* 3.8 7.1 - - - +
444C GLU* 3.8 14.6 - - - +
448C GLN 3.2 9.7 + - - +
449C LEU* 3.1 9.1 + - - +
451C GLU* 1.3 76.2 - - - +
453C LYS* 1.3 64.0 + - - +
455C CYS* 3.2 2.9 + - - +
456C TYR* 2.9 33.1 + - + -
476C LEU* 3.6 20.0 - - + -
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Residues in contact with LYS 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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134A SER 5.0 9.6 + - - +
449C LEU 2.9 21.2 + - - +
450C VAL* 3.6 14.8 - - + +
452C ALA* 1.3 78.6 - - - +
454C LYS* 1.3 59.7 + - + +
456C TYR* 3.3 2.5 + - - +
457C TRP* 2.8 32.9 + - - +
473C LEU* 4.2 16.2 - - + +
476C LEU* 4.4 11.6 - - + +
477C HIS* 3.7 30.0 + - + +
480C LEU* 3.5 40.1 - - - +
482C GLU* 3.9 15.8 + - - -
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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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132A ILE 4.2 1.4 + - - -
133A ILE* 3.6 32.3 - - - +
134A SER 4.4 9.6 - - - +
215A HIS* 3.4 40.2 + - + +
217A LEU* 3.9 19.5 - - + +
218A ASP* 3.3 32.7 - - - +
450C VAL* 3.1 29.5 + - + +
451C GLU* 3.1 3.1 + - - +
453C LYS* 1.3 81.2 - - + +
455C CYS* 1.3 57.2 + - - +
457C TRP* 3.9 5.4 - - - +
458C ARG* 3.0 30.7 + - - +
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Residues in contact with CYS 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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217A LEU* 3.5 30.5 - - - -
436C LEU* 3.5 25.8 - - - +
439C LEU* 3.6 28.0 - - - -
440C GLY* 3.7 9.2 - - - -
443C TYR* 3.7 10.1 - - - -
451C GLU 2.9 14.3 + - - +
452C ALA 3.5 7.2 - - - +
454C LYS* 1.3 73.2 - - - +
456C TYR* 1.3 61.0 + - - +
458C ARG* 3.3 5.6 + - - +
459C ALA* 2.9 27.4 + - - +
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Residues in contact with TYR 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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437C VAL* 3.8 28.3 - - - -
440C GLY* 3.3 26.3 + - - -
441C GLU* 3.4 5.0 + - - -
444C GLU* 3.0 20.6 + - - -
452C ALA* 2.9 29.6 + - + +
453C LYS* 3.9 4.3 - - - +
455C CYS* 1.3 75.8 - - - +
457C TRP* 1.3 58.7 + - - +
459C ALA* 2.9 7.3 + - - +
460C TYR* 2.8 29.2 + - - +
469C ALA* 4.1 15.9 - - + +
472C LYS* 3.7 35.5 + - + -
473C LEU* 4.0 25.1 - - + -
476C LEU* 3.4 26.7 - - + -
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Residues in contact with TRP 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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218A ASP* 6.0 2.2 - - - -
402A PRO* 6.4 1.8 - - + -
453C LYS 2.8 18.8 + - - +
454C LYS* 4.0 5.4 - - - +
456C TYR* 1.3 77.4 - - - +
458C ARG* 1.3 58.7 + - - +
460C TYR* 3.6 33.9 + + + +
461C ALA* 3.1 27.8 + - + +
470C LEU* 4.2 7.9 - - + -
473C LEU* 3.5 29.2 - - + -
489C CYS* 5.6 3.8 - - - -
492C LYS* 4.2 23.1 - - + -
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Residues in contact with ARG 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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172A SER 5.2 7.5 + - - -
174A PRO* 6.0 2.2 - - - +
217A LEU 3.1 24.3 + - - +
218A ASP* 4.1 2.3 + - - -
219A GLU* 3.7 34.3 - - + +
220A ILE* 5.1 3.8 - - - +
291A PHE* 5.2 12.9 - - - -
426C HIS* 3.6 20.6 + - - -
430C PRO* 3.4 29.5 + - - +
431C ASN* 5.5 2.8 + - - -
436C LEU* 3.8 19.2 - - + +
454C LYS 3.0 19.3 + - - +
455C CYS* 3.7 4.7 - - - +
457C TRP* 1.3 75.6 - - - +
459C ALA* 1.3 61.4 + - - +
461C ALA* 3.2 6.0 + - + +
462C VAL* 2.9 34.3 + - + +
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Residues in contact with ALA 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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433C SER* 3.7 10.4 + - - +
436C LEU* 4.0 6.9 - - + +
437C VAL* 3.7 29.6 - - + +
455C CYS 2.9 14.4 + - - +
456C TYR* 2.9 11.0 + - - +
458C ARG* 1.3 73.6 - - - +
460C TYR* 1.3 65.3 + - - +
462C VAL* 3.3 11.3 - - - +
463C GLY 3.1 18.5 + - - -
464C ASP 3.6 8.2 + - - -
469C ALA* 3.9 8.5 - - + -
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Residues in contact with TYR 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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402A PRO* 5.1 17.7 - - + +
456C TYR 2.8 12.3 + - - +
457C TRP* 3.6 40.2 - + + +
459C ALA* 1.3 78.7 - - - +
461C ALA* 1.3 66.4 + - - +
463C GLY* 3.4 12.7 + - - +
464C ASP* 4.8 12.8 - - + -
469C ALA* 4.3 6.6 - - + +
470C LEU* 3.2 47.8 - - + +
473C LEU* 5.6 0.2 - - + -
492C LYS* 5.0 20.1 + - + +
496C ASP* 5.5 7.2 - - + +
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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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219A GLU* 5.5 9.0 - - + -
402A PRO* 4.6 21.7 - - + +
403A ILE* 5.3 17.7 - - + +
457C TRP* 3.1 21.6 + - + +
458C ARG* 3.2 14.6 + - + +
460C TYR* 1.3 80.1 - - - +
462C VAL* 1.3 64.5 + - - +
463C GLY* 3.4 0.9 + - - -
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Residues in contact with VAL 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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430C PRO 4.4 2.9 - - - +
431C ASN* 3.2 45.6 - - + +
433C SER* 3.5 28.9 - - - +
436C LEU* 3.9 8.7 - - + -
458C ARG* 2.9 20.6 + - + +
459C ALA* 3.3 17.5 - - - +
461C ALA* 1.3 79.2 - - - +
463C GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 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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433C SER* 5.0 0.2 - - - -
459C ALA 3.1 6.8 + - - -
460C TYR* 3.4 10.1 + - - +
461C ALA 3.4 2.9 - - - -
462C VAL* 1.3 79.8 - - - +
464C ASP* 1.3 73.0 + - - +
465C VAL* 5.6 1.6 - - - -
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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