Contacts of the helix formed by residues 455 - 469 (chain C) in PDB entry 1ZMD
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 LEU 455 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C PHE* 3.9 4.8 - - + -
391C ASN* 3.5 19.1 - - - +
393C ARG* 4.0 11.6 - - + +
394C ALA* 3.8 25.6 - - + +
397C ASN* 4.9 7.0 - - - +
423C PRO* 3.7 39.9 - - + +
424C GLY* 4.0 8.7 - - - +
428C MET* 3.5 20.0 - - + +
454C THR* 1.3 72.5 - - - +
456C SER* 1.3 63.3 + - - +
458C ALA* 3.0 23.9 + - - +
427D GLU* 2.8 27.3 + - + +
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Residues in contact with SER 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C MET* 4.1 13.2 - - - +
431C GLU* 4.0 10.5 - - - -
450C HIS* 3.2 19.2 - - - +
454C THR* 3.0 16.1 + - - -
455C LEU* 1.3 77.1 - - - +
457C GLU* 1.3 56.8 + - - +
458C ALA 3.1 0.2 - - - -
459C PHE* 3.0 24.0 + - - +
460C ARG 3.0 9.7 + - - -
427D GLU* 2.9 17.7 + - - -
430D ASN* 3.0 26.1 + - - -
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Residues in contact with GLU 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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386C PHE* 5.3 0.4 - - - -
391C ASN* 3.8 7.8 + - - +
392C SER* 4.9 2.1 - - - -
450C HIS* 4.2 13.9 - - + +
451C ALA 3.4 20.8 - - - +
452C HIS* 2.7 39.2 + - - +
453C PRO* 3.2 1.7 - - - +
454C THR* 2.9 30.6 + - - +
455C LEU 3.1 0.6 - - - -
456C SER* 1.3 79.2 + - - +
458C ALA* 1.3 56.6 + - - +
460C ARG* 3.5 13.6 + - + +
461C GLU* 2.8 37.8 + - + +
329D HIS* 5.3 0.9 - - - +
332D GLU* 4.4 8.3 - - - +
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Residues in contact with ALA 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C PHE* 3.6 33.3 - - + +
388C PHE* 3.6 27.8 - - + -
391C ASN* 3.5 7.8 - - + +
404C VAL* 3.9 10.7 - - + +
455C LEU 3.0 14.6 + - - +
457C GLU* 1.3 78.5 - - - +
459C PHE* 1.3 57.4 + - - +
461C GLU 3.5 0.2 + - - -
462C ALA* 2.9 30.3 + - - +
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Residues in contact with PHE 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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404C VAL* 3.9 22.3 - - + +
406C ILE* 3.6 20.2 - - + -
415C VAL* 6.1 0.9 - - + -
418C ALA* 4.0 4.7 - - + -
420C ILE* 4.8 4.3 - - + -
428C MET* 3.8 28.3 - - + -
431C GLU* 3.4 43.3 - - + -
432C ALA* 3.7 35.7 - - + -
445C ILE* 3.6 27.4 - - + -
455C LEU 4.0 0.4 + - - -
456C SER* 3.0 11.3 + - - +
458C ALA* 1.3 77.9 - - - +
460C ARG* 1.3 65.9 + - - +
462C ALA* 3.3 2.6 + - - +
463C ASN* 3.0 36.7 + - - -
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Residues in contact with ARG 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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445C ILE* 3.9 13.2 - - - +
446C ALA* 2.9 29.9 + - - +
447C ARG* 4.2 4.4 + - - +
448C VAL 3.1 14.1 + - - -
449C CYS* 3.7 1.4 - - - +
450C HIS* 3.2 58.2 + - + +
456C SER 3.0 9.8 + - - +
457C GLU* 3.5 14.1 + - - +
459C PHE* 1.3 78.8 - - - +
461C GLU* 1.3 60.0 + - - +
463C ASN* 3.3 5.4 + - - +
464C LEU* 3.0 25.8 + - + +
329D HIS* 5.2 1.4 - - - +
332D GLU* 5.8 2.0 + - - +
333D ASP* 2.9 39.7 + - - -
336D ILE* 5.3 8.0 - - - +
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Residues in contact with GLU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C PHE* 3.4 20.9 - - + -
457C GLU* 2.8 26.4 + - + +
458C ALA 3.9 0.2 - - - +
460C ARG* 1.3 75.8 - - + +
462C ALA* 1.3 59.7 + - - +
464C LEU* 3.2 14.4 + - + +
465C ALA* 2.9 25.3 + - - +
471C SER* 2.6 35.8 + - - +
472C ILE* 2.7 21.0 + - - +
473C ASN* 2.8 47.7 + - - +
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Residues in contact with ALA 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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384C GLY* 3.6 12.9 - - - +
386C PHE* 3.9 9.6 - - + +
404C VAL* 3.5 39.0 - - + +
406C ILE* 3.6 10.5 - - + -
458C ALA 2.9 19.2 + - - +
459C PHE 3.9 0.9 - - - +
460C ARG 3.3 0.2 - - - -
461C GLU* 1.3 76.2 - - - +
463C ASN* 1.3 57.9 + - - +
465C ALA* 3.4 4.7 + - - -
466C ALA* 2.9 29.5 + - - +
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Residues in contact with ASN 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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406C ILE* 3.5 26.3 - - - +
415C VAL* 3.7 2.1 - - - +
442C CYS* 3.4 36.4 - - - +
445C ILE* 3.4 41.3 - - + +
446C ALA 4.2 0.7 - - - +
459C PHE* 3.0 36.1 + - - +
460C ARG 3.4 9.2 - - - +
462C ALA* 1.3 75.1 - - - +
464C LEU* 1.3 59.3 + - - +
466C ALA* 3.3 2.6 + - - -
467C SER* 2.8 31.4 + - - -
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Residues in contact with LEU 464 (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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446C ALA* 3.8 24.1 - - + +
460C ARG* 3.0 14.6 + - + +
461C GLU* 3.2 28.9 + - - +
463C ASN* 1.3 73.2 - - - +
465C ALA* 1.3 66.4 + - - +
467C SER* 3.1 2.4 + - - -
468C PHE* 2.9 42.1 + - + +
470C LYS 3.4 16.1 - - - +
471C SER 4.2 0.2 - - - -
472C ILE* 3.9 22.2 - - + +
24D LYS* 4.3 15.3 - - + +
27D GLN* 5.8 0.2 - - - +
336D ILE* 5.5 5.8 - - + -
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Residues in contact with ALA 465 (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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383C VAL 4.7 2.7 - - - +
384C GLY* 4.0 12.8 - - - -
385C LYS 4.3 12.1 - - - +
461C GLU 2.9 15.8 + - - +
462C ALA 3.6 5.6 - - - +
464C LEU* 1.3 76.0 - - - +
466C ALA* 1.3 59.7 + - - +
469C GLY* 2.7 32.6 + - - +
470C LYS* 3.6 16.0 + - - +
471C SER* 3.9 16.6 - - - +
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Residues in contact with ALA 466 (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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382C LYS* 3.3 31.8 - - + +
383C VAL* 4.2 6.1 - - - -
384C GLY* 3.6 21.7 - - - +
406C ILE* 4.1 11.4 - - + +
408C GLY 5.1 0.7 - - - +
413C ASP* 4.6 0.2 - - - -
442C CYS* 3.9 19.1 - - - -
462C ALA 2.9 18.2 + - - +
463C ASN 3.6 4.5 - - - +
464C LEU 3.2 0.2 - - - -
465C ALA* 1.3 77.3 - - - +
467C SER* 1.3 63.0 + - - +
469C GLY* 4.4 1.0 + - - -
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Residues in contact with SER 467 (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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382C LYS* 3.5 11.1 + - - +
413C ASP* 3.2 31.0 + - - -
442C CYS* 3.8 1.1 - - - +
443C GLU* 3.4 26.9 + - - +
446C ALA* 5.2 1.3 - - - -
463C ASN 2.8 21.3 + - - -
464C LEU* 3.1 5.8 + - - -
466C ALA* 1.3 77.0 - - - +
468C PHE* 1.3 62.3 + - - +
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Residues in contact with PHE 468 (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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464C LEU* 2.9 24.5 + - + +
467C SER* 1.3 74.5 - - - +
469C GLY* 1.3 58.2 + - - +
470C LYS* 3.4 28.1 + - + +
24D LYS* 3.6 33.7 - - - -
27D GLN* 3.8 32.5 - - + -
28D LEU* 4.1 22.2 - - + -
340D GLU* 5.9 1.1 - - - -
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Residues in contact with GLY 469 (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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465C ALA* 2.7 28.9 + - - +
466C ALA 4.4 1.3 + - - -
467C SER 3.5 1.4 - - - -
468C PHE* 1.3 73.7 - - - +
470C LYS* 1.3 65.4 + - - +
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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