Contacts of the helix formed by residues 445 - 460 (chain X) in PDB entry 2DE0
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 445 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434X TRP* 3.4 10.1 - - - +
440X ASN* 3.0 24.9 - - - +
443X THR* 2.1 48.6 + - - -
444X GLU* 1.3 72.0 + - - +
446X SER* 1.3 60.5 + - - +
447X LEU 3.5 3.1 - - - +
448X ARG* 2.8 53.9 + - + +
449X GLY 4.4 1.7 + - - -
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Residues in contact with SER 446 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249X ARG* 5.8 0.9 - - - +
250X TYR* 3.6 19.8 - - - -
444X GLU* 2.9 15.0 + - - +
445X ASN* 1.3 74.1 - - - +
447X LEU* 1.3 60.7 + - - +
448X ARG 3.5 0.4 + - - -
449X GLY* 3.7 3.3 + - - -
450X VAL* 3.4 26.7 + - - +
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Residues in contact with LEU 447 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220X TYR* 4.2 28.0 - - + -
248X TRP* 5.0 4.0 - - + -
250X TYR* 3.7 44.2 - - + +
251X ALA 4.8 0.2 - - - +
258X VAL* 4.4 9.4 - - + -
259X PHE* 6.0 0.2 - - + -
434X TRP* 5.9 0.2 - - + -
443X THR* 3.7 30.7 - - + -
444X GLU 3.9 9.0 - - - +
445X ASN* 2.9 0.6 - - - -
446X SER* 1.3 79.5 + - - +
448X ARG* 1.3 68.3 + - - +
450X VAL* 4.4 4.7 - - + -
451X ILE* 3.0 48.2 + - + +
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Residues in contact with ARG 448 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429X ASP* 5.0 1.0 + - - -
431X SER* 3.3 29.9 + - - +
432X ILE* 3.3 20.4 + - - +
433X SER* 3.0 41.8 - - - +
434X TRP* 3.6 47.0 - - + +
445X ASN* 2.8 59.0 + - + +
446X SER 3.5 0.6 - - - -
447X LEU* 1.3 81.3 - - - +
449X GLY* 1.3 63.8 + - - +
451X ILE* 3.2 2.4 + - - +
452X LEU* 3.1 30.6 + - + +
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Residues in contact with GLY 449 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429X ASP* 3.2 24.2 - - - -
445X ASN 4.4 2.0 + - - -
446X SER 3.7 6.4 + - - -
447X LEU 3.3 0.2 - - - -
448X ARG* 1.3 79.1 - - - +
450X VAL* 1.3 60.0 + - - +
452X LEU* 4.0 0.6 - - - +
453X ASP* 2.8 39.9 + - - +
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Residues in contact with VAL 450 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220X TYR* 3.2 44.0 - - + -
250X TYR* 5.6 4.0 - - + -
446X SER* 3.4 20.1 + - - +
447X LEU* 3.4 8.9 + - + +
448X ARG 3.3 0.6 - - - -
449X GLY* 1.3 74.1 - - - +
451X ILE* 1.3 65.5 + - - +
453X ASP* 4.0 4.9 - - - +
454X ILE* 3.1 33.6 + - + +
471X VAL* 5.0 10.8 - - + -
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Residues in contact with ILE 451 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220X TYR* 4.7 10.1 - - + -
258X VAL* 3.8 21.3 - - + -
259X PHE* 4.1 14.6 - - + -
342X LEU* 4.1 28.5 - - + -
346X ILE* 4.4 13.2 - - + -
434X TRP* 4.9 6.1 - - + -
447X LEU* 3.0 53.1 + - + +
448X ARG 3.7 4.0 - - - +
450X VAL* 1.3 76.2 - - - +
452X LEU* 1.3 59.8 + - + +
454X ILE* 3.8 6.1 - - - +
455X HIS* 2.8 27.9 + - + +
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Residues in contact with LEU 452 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345X GLU 5.1 0.2 - - - +
346X ILE* 3.9 26.9 - - + +
349X ALA* 4.3 28.5 - - + -
353X LEU* 5.6 1.1 - - + -
405X TYR* 4.3 1.3 - - - +
429X ASP* 3.6 30.5 - - + +
431X SER* 4.2 8.3 - - - +
434X TRP* 4.2 20.0 - - + -
448X ARG* 3.1 26.4 + - + +
449X GLY 4.0 3.4 - - - +
451X ILE* 1.3 76.7 - - - +
453X ASP* 1.3 65.7 + - - +
455X HIS* 3.1 3.7 + - - +
456X PHE* 2.9 44.0 + - + -
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Residues in contact with ASP 453 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363X HIS* 5.4 1.5 - - + -
405X TYR* 3.0 27.4 + - - -
407X ALA* 3.5 29.6 - - + +
408X THR 4.5 7.1 + - - +
429X ASP* 3.9 10.6 + - - +
449X GLY 2.8 26.7 + - - +
450X VAL* 4.0 4.8 - - - +
452X LEU* 1.3 72.5 - - - +
454X ILE* 1.3 66.3 + - + +
456X PHE* 3.8 0.7 - - - +
457X LEU* 2.8 33.7 + - + +
471X VAL* 5.4 5.4 - - + -
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Residues in contact with ILE 454 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220X TYR* 3.9 19.3 - - + -
221X GLY* 5.6 0.4 - - - -
336X ILE* 5.4 4.9 - - + -
450X VAL* 3.1 36.0 + - + +
451X ILE* 3.9 3.8 - - - +
453X ASP* 1.3 76.4 - - - +
455X HIS* 1.3 69.6 + - - +
457X LEU* 3.8 5.1 - - - +
458X SER* 2.9 20.3 + - - -
471X VAL* 3.5 37.9 - - + +
474X VAL* 3.9 20.2 - - + -
475X ALA* 4.1 6.1 - - - +
478X ILE* 3.6 28.5 - - + -
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Residues in contact with HIS 455 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346X ILE* 3.2 44.7 - - + +
350X THR* 4.5 2.0 + - - -
355X PHE* 6.1 0.2 - - - -
451X ILE* 2.8 20.3 + - + +
452X LEU* 3.1 8.9 + - - +
454X ILE* 1.3 77.5 - - - +
456X PHE* 1.3 85.2 + + - +
458X SER* 2.5 26.7 + - - -
459X GLN* 3.0 45.6 + - + +
478X ILE* 5.8 1.1 - - - -
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Residues in contact with PHE 456 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346X ILE* 4.3 2.5 - - + -
349X ALA* 3.8 12.6 - - + -
350X THR* 3.2 45.1 - - - -
353X LEU* 3.6 17.9 - - + -
355X PHE* 3.4 46.2 - + + -
405X TYR* 3.6 45.7 - + + +
452X LEU* 2.9 38.4 + - + +
455X HIS* 1.3 89.7 - + - +
457X LEU* 1.3 66.8 + - - +
459X GLN* 3.3 9.1 + - - +
460X ALA* 3.4 11.3 + - - +
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Residues in contact with LEU 457 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361X GLY* 3.7 26.0 - - - -
362X VAL 3.9 10.5 - - - +
363X HIS* 3.6 33.9 - - + -
405X TYR* 3.9 20.6 - - + +
407X ALA* 4.2 5.8 - - + -
453X ASP 2.8 28.1 + - - +
454X ILE 3.8 0.2 - - - +
456X PHE* 1.3 68.0 - - - +
458X SER* 1.3 58.5 + - - +
459X GLN 2.8 10.6 + - - -
460X ALA* 3.0 21.6 + - - +
463X LEU* 3.8 20.5 - - + +
471X VAL* 4.6 9.2 - - + -
472X CYS* 5.1 2.5 - - - -
475X ALA* 3.6 20.6 - - + -
479X MET* 5.3 1.9 - - - +
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Residues in contact with SER 458 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454X ILE 2.9 16.4 + - - -
455X HIS* 2.5 23.9 + - - -
457X LEU* 1.3 73.1 - - - +
459X GLN* 1.3 64.6 + - - +
463X LEU* 5.9 0.2 - - - -
475X ALA* 3.2 29.9 - - - +
478X ILE* 3.5 32.6 - - - +
479X MET* 3.5 20.7 - - - +
482X LEU* 3.4 14.0 - - - +
483X HIS* 5.4 0.5 + - - -
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Residues in contact with GLN 459 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355X PHE* 3.7 18.8 - - + -
357X HIS* 3.1 30.8 + - - -
455X HIS* 3.0 51.8 + - + +
456X PHE* 3.6 7.4 - - - +
457X LEU 2.8 1.6 + - - -
458X SER* 1.3 79.6 + - - +
460X ALA* 1.3 63.4 + - - +
478X ILE* 5.8 0.6 - - - +
482X LEU* 3.3 33.3 - - - +
483X HIS* 5.2 4.4 + - - -
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Residues in contact with ALA 460 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355X PHE* 5.2 0.4 - - + -
359X VAL* 3.4 25.1 - - + +
360X ILE 4.1 1.1 - - - -
361X GLY* 3.4 24.7 - - - +
405X TYR* 5.9 0.7 - - + -
456X PHE 3.4 9.5 + - - +
457X LEU 3.0 14.7 + - - +
458X SER 3.4 1.2 - - - +
459X GLN* 1.3 81.8 - - - +
461X ASP* 1.3 66.8 + - - +
462X PHE 3.2 5.6 - - - +
479X MET* 4.3 14.6 - - - +
483X HIS* 4.5 8.3 + - - -
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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