Contacts of the helix formed by residues 469 - 486 (chain C) in PDB entry 5X8X
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 ALA 469 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C GLU* 3.6 33.6 + - + +
362C LEU* 4.2 4.6 - - + +
363C VAL* 5.7 1.8 - - + -
403C PHE* 3.7 29.2 - - + -
467C PRO 3.5 3.1 + - - +
468C PRO* 1.3 73.1 - - - +
470C GLY* 1.3 58.7 + - - +
471C LYS 3.6 1.3 - - - -
472C LEU* 3.6 9.4 + - - +
473C ALA* 3.1 30.8 + - - +
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Residues in contact with GLY 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C GLU* 4.5 10.8 + - - -
468C PRO* 3.7 3.0 - - - +
469C ALA* 1.3 75.9 - - - +
471C LYS* 1.3 64.1 + - - +
473C ALA* 3.5 2.8 + - - +
474C SER* 3.1 24.8 + - - -
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Residues in contact with LYS 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU* 5.8 2.0 + - - -
399C SER* 4.9 6.7 + - - -
469C ALA 3.6 0.2 - - - -
470C GLY* 1.3 73.8 - - - +
472C LEU* 1.3 87.0 + - + +
474C SER* 3.3 6.1 + - - -
475C LEU* 3.1 38.9 + - + +
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C LEU* 3.7 15.9 - - + -
396C LEU* 4.9 5.4 - - + +
399C SER* 3.8 26.9 - - - +
400C ILE* 3.9 20.0 - - + -
403C PHE* 3.7 36.8 - - + -
468C PRO 5.1 7.4 - - - +
469C ALA* 3.6 7.2 + - - +
470C GLY 3.3 0.6 - - - -
471C LYS* 1.3 100.3 - - + +
473C ALA* 1.3 65.8 + - - +
475C LEU* 3.3 9.6 + - + +
476C CYS* 3.1 26.5 + - - -
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Residues in contact with ALA 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 3.2 24.1 - - + +
359C GLU* 3.7 33.9 - - + +
362C LEU* 3.8 8.0 - - + +
469C ALA 3.1 18.5 + - - +
470C GLY* 4.0 4.0 - - - +
472C LEU* 1.3 76.1 - - - +
474C SER* 1.3 64.4 + - - +
476C CYS* 3.2 1.6 + - - -
477C SER* 3.0 20.8 + - - -
2346D THR* 5.1 1.3 - - - +
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Residues in contact with SER 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLY 3.1 18.5 + - - -
471C LYS* 3.6 7.0 - - - -
472C LEU 3.1 0.4 - - - -
473C ALA* 1.3 78.5 - - - +
475C LEU* 1.3 62.3 + - - +
477C SER* 3.1 5.2 + - - -
478C GLN* 3.0 36.5 + - - +
2346D THR* 3.4 33.0 - - - +
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Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU* 4.8 13.7 - - - +
396C LEU* 4.1 26.7 - - + -
471C LYS* 3.1 34.4 + - + +
472C LEU* 3.6 10.1 - - + +
474C SER* 1.3 75.6 + - - +
476C CYS* 1.3 61.0 + - - +
478C GLN* 3.2 26.2 + - - +
479C HIS* 3.0 42.5 + - + +
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Residues in contact with CYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LEU* 4.4 17.7 - - + +
358C MET* 3.9 20.2 - - + -
362C LEU* 4.5 13.9 - - - -
396C LEU* 4.8 6.1 - - - -
400C ILE* 3.8 28.5 - - - -
472C LEU 3.1 19.8 + - - +
473C ALA* 3.2 7.2 + - - +
475C LEU* 1.3 75.0 - - - +
477C SER* 1.3 64.0 + - - +
479C HIS* 3.3 7.9 + - - +
480C VAL* 3.0 27.9 + - - +
9000C 82O 5.8 0.7 - - - -
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Residues in contact with SER 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 3.5 22.2 - - - +
473C ALA 3.0 15.0 + - - -
474C SER 3.1 8.0 + - - -
476C CYS* 1.3 77.6 - - - +
478C GLN* 1.3 56.2 + - - +
480C VAL* 3.2 8.3 + - - +
481C GLU* 2.9 28.9 + - - +
2346D THR* 3.8 13.6 + - - -
2347D ASN* 3.7 18.8 + - - +
2350D LEU* 3.5 24.5 + - - +
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Residues in contact with GLN 478 (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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474C SER* 3.0 30.2 + - - +
475C LEU* 3.4 28.9 - - + +
477C SER* 1.3 73.2 - - - +
479C HIS* 1.3 63.0 + - + +
481C GLU* 3.3 6.3 + - - +
482C ARG* 2.9 29.5 + - - +
2346D THR* 5.9 1.1 - - + +
2347D ASN* 4.1 13.7 - - - +
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Residues in contact with HIS 479 (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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317C TRP* 3.5 37.5 - + + -
321C ALA* 5.7 0.2 - - - -
324C LEU* 5.7 0.4 - - + -
393C CYS* 3.7 19.2 - - - -
396C LEU* 3.4 30.8 - - + +
475C LEU* 3.0 37.9 + - + +
476C CYS* 3.8 6.0 - - - +
478C GLN* 1.3 78.3 - - + +
480C VAL* 1.3 62.2 + - + +
482C ARG* 3.3 29.7 + - - +
483C LEU* 3.2 29.5 + - - +
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Residues in contact with VAL 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ALA* 4.6 16.7 - - + +
324C LEU* 3.8 34.3 - - + -
325C THR* 4.0 9.6 - - - +
328C ILE* 6.3 0.4 - - + -
358C MET* 4.3 9.9 - - + -
476C CYS 3.0 19.2 + - - +
477C SER* 3.2 9.2 + - - +
479C HIS* 1.3 74.9 - - - +
481C GLU* 1.3 61.8 + - - +
483C LEU* 3.5 4.7 + - - +
484C GLN* 3.3 24.3 + - - +
2349D GLY 5.6 1.3 - - - -
2350D LEU* 5.1 5.6 - - + +
2353D ILE* 3.7 29.8 - - + -
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Residues in contact with GLU 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C SER 2.9 16.4 + - - +
478C GLN* 3.6 6.8 - - - +
480C VAL* 1.3 75.6 - - - +
482C ARG* 1.3 65.3 + - - +
484C GLN* 3.1 15.0 + - + +
485C ILE* 3.0 43.9 + - + +
2347D ASN* 3.6 23.9 + - - +
2348D MET* 3.4 16.3 + - - +
2349D GLY* 2.9 32.4 + - - -
2350D LEU 5.8 0.2 - - - +
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Residues in contact with ARG 482 (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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317C TRP* 3.7 22.6 - - - +
478C GLN 2.9 19.7 + - - +
479C HIS* 3.3 32.7 + - - +
481C GLU* 1.3 71.3 - - - +
483C LEU* 1.3 91.3 + - - +
485C ILE* 3.4 5.0 + - - +
486C PHE* 3.0 56.8 + - + +
490C HIS* 5.9 4.9 - - - -
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Residues in contact with LEU 483 (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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314C TRP* 4.9 13.0 - - + +
317C TRP* 3.3 48.2 - - + +
318C GLU* 3.7 16.8 - - + +
321C ALA* 4.0 12.8 - - + -
479C HIS 3.2 16.1 + - - +
480C VAL 3.8 7.6 - - - +
481C GLU 3.2 0.2 - - - -
482C ARG* 1.3 113.4 - - - +
484C GLN* 1.3 61.4 + - - +
486C PHE* 3.8 2.3 - - - +
487C GLN* 3.3 24.6 + - - +
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Residues in contact with GLN 484 (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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480C VAL* 3.3 19.0 + - - +
481C GLU* 3.1 30.1 + - + +
483C LEU* 1.3 76.9 - - - +
485C ILE* 1.3 65.9 + - + +
486C PHE 3.5 0.3 + - - -
487C GLN* 3.6 27.6 - - - +
2349D GLY* 3.2 42.7 + - - +
2352D ALA* 4.3 12.1 - - - +
2353D ILE* 4.3 6.3 - - - +
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Residues in contact with ILE 485 (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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481C GLU* 3.0 45.5 + - + +
482C ARG* 3.7 6.7 - - - +
484C GLN* 1.3 81.1 - - + +
486C PHE* 1.3 85.8 + - + +
487C GLN* 3.4 3.0 + - - +
488C HIS* 5.0 4.3 + - - -
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Residues in contact with PHE 486 (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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482C ARG* 3.0 50.8 + - + +
483C LEU* 3.5 4.0 + - - +
484C GLN 3.4 0.2 - - - -
485C ILE* 1.3 97.4 - - + +
487C GLN* 1.3 64.1 + - - +
488C HIS 3.3 2.7 - - - -
489C LEU* 3.2 33.8 + - + +
490C HIS* 3.0 32.1 + - + -
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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