Contacts of the helix formed by residues 407 - 421 (chain C) in PDB entry 1Z6T
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 GLU 407 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PRO 5.7 1.6 - - - +
48C THR* 5.7 3.6 - - - +
401C CYS* 4.2 0.4 - - - -
406C MET* 1.3 75.1 - - - +
408C THR* 1.3 75.3 + - - +
409C GLU* 3.3 31.7 - - + +
410C GLU* 3.1 16.8 + - + +
411C VAL* 3.1 18.9 + - - +
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Residues in contact with THR 408 (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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21C LYS* 4.5 7.6 - - - +
49C GLN* 5.4 3.1 - - - +
397C THR* 3.8 11.7 - - + -
398C LYS* 6.1 0.5 - - - +
401C CYS* 3.6 21.0 - - - -
407C GLU* 1.3 80.9 + - - +
409C GLU* 1.3 67.6 - - - +
411C VAL* 3.3 1.1 + - - +
412C GLU* 2.9 57.0 + - - +
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Residues in contact with GLU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO 3.9 17.9 - - - +
48C THR* 3.2 13.6 - - - +
49C GLN* 3.1 41.2 + - + +
52C ARG* 4.2 26.2 + - - +
407C GLU* 3.3 27.1 - - + +
408C THR* 1.3 84.7 - - - +
410C GLU* 1.3 57.7 + - - +
412C GLU* 3.9 8.3 - - - +
413C ASP* 3.0 35.9 + - - +
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Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C MET* 3.8 31.5 - - + +
407C GLU* 3.1 18.8 + - + +
409C GLU* 1.3 76.5 - - - +
411C VAL* 1.3 64.5 + - - +
413C ASP* 3.5 7.9 + - + +
414C ILE* 3.2 32.9 + - + +
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Residues in contact with VAL 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C THR* 4.0 15.5 - - + +
400C LEU* 4.0 16.2 - - + -
401C CYS* 3.7 25.8 - - - +
404C TRP* 4.1 7.8 - - + -
406C MET* 3.3 34.5 - - + -
407C GLU 3.1 12.5 + - - +
408C THR 3.6 6.5 - - - +
410C GLU* 1.3 74.8 - - - +
412C GLU* 1.3 58.4 + - - +
414C ILE* 3.3 4.1 + - - +
415C LEU* 2.9 47.9 + - + +
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Residues in contact with GLU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 2.7 38.3 + - - +
49C GLN* 4.7 1.9 - - - +
52C ARG* 5.9 2.9 + - - +
397C THR* 3.3 26.6 + - + +
408C THR* 2.9 37.7 + - - +
409C GLU* 4.0 7.6 - - - +
411C VAL* 1.3 77.7 - - - +
413C ASP* 1.3 63.5 + - - +
415C LEU* 3.9 2.2 - - - +
416C GLN* 3.0 25.2 + - - +
433C PHE* 3.6 18.0 - - + -
435C TYR* 3.4 21.1 + - + +
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Residues in contact with ASP 413 (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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23C SER* 6.1 1.6 - - - -
44C ARG* 3.2 49.9 + - - +
52C ARG* 3.0 33.9 + - - -
409C GLU 3.0 19.2 + - - +
410C GLU* 3.6 9.3 - - + +
412C GLU* 1.3 76.4 - - - +
414C ILE* 1.3 66.3 + - + +
416C GLN* 3.4 2.7 + - - +
417C GLU* 3.4 14.4 + - - +
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Residues in contact with ILE 414 (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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376C ARG* 5.1 3.4 - - - +
379C ILE* 4.3 16.2 - - + -
382C TYR* 3.9 36.1 - - + -
404C TRP* 4.4 6.3 - - + -
406C MET* 3.5 26.2 - - + -
410C GLU* 3.2 22.8 + - + +
411C VAL* 3.7 6.3 - - - +
413C ASP* 1.3 76.1 - - + +
415C LEU* 1.3 63.3 + - - +
417C GLU* 3.1 28.8 + - - +
418C PHE* 3.4 32.0 + - + -
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Residues in contact with LEU 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C LEU* 4.3 4.7 - - + -
397C THR* 5.1 0.2 - - + -
400C LEU* 3.8 14.6 - - + -
404C TRP* 3.6 27.1 - - + -
411C VAL* 2.9 39.4 + - + +
412C GLU 3.9 2.9 - - - +
414C ILE* 1.3 75.4 - - - +
416C GLN* 1.3 57.5 + - - +
418C PHE* 3.1 14.5 + - + +
419C VAL* 2.9 32.2 + - - +
424C LEU* 3.7 19.8 - - + +
435C TYR* 3.4 50.0 - - + +
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Residues in contact with GLN 416 (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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23C SER* 3.8 18.7 + - - +
24C TYR* 2.5 53.9 + - - -
27C ASP* 4.6 4.5 + - - -
44C ARG* 4.3 15.9 - - - +
412C GLU 3.0 18.4 + - - +
413C ASP* 3.5 8.3 - - - +
415C LEU* 1.3 73.3 - - - +
417C GLU* 1.3 60.6 + - - +
419C VAL* 4.1 8.9 - - - +
420C ASN* 2.6 73.1 + - - +
435C TYR* 5.2 0.6 - - - -
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Residues in contact with GLU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 4.3 10.1 - - - +
376C ARG* 2.8 49.6 + - - +
379C ILE* 3.8 24.0 - - + +
413C ASP 3.6 12.2 - - - +
414C ILE* 3.1 14.8 + - - +
416C GLN* 1.3 79.9 - - - +
418C PHE* 1.3 62.3 + - - +
420C ASN* 3.6 8.3 + - - +
421C LYS* 3.3 37.8 + - + +
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Residues in contact with PHE 418 (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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375C LEU* 4.1 14.8 - - + -
379C ILE* 3.6 39.0 - - + -
382C TYR* 4.2 3.6 - - + -
383C TYR* 3.7 42.8 - + + -
386C LEU* 4.1 13.5 - - + -
404C TRP* 4.5 0.9 - + - -
414C ILE* 3.4 35.0 + - + -
415C LEU* 3.1 24.8 + - + +
417C GLU* 1.3 81.1 - - - +
419C VAL* 1.3 62.3 + - - +
421C LYS* 3.1 7.4 + - - -
423C LEU* 3.0 34.1 + - + +
424C LEU* 3.7 15.9 - - + -
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Residues in contact with VAL 419 (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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24C TYR* 3.8 25.1 - - + +
124C VAL* 3.6 24.2 - - + +
415C LEU 2.9 22.1 + - - +
416C GLN* 3.2 10.9 + - - +
418C PHE* 1.3 75.2 - - - +
420C ASN* 1.3 62.6 + - - +
422C SER* 3.1 13.9 + - - -
424C LEU* 3.3 35.8 - - + +
425C PHE* 4.2 2.2 - - - -
426C CYS* 4.0 26.7 - - + +
428C ARG* 5.5 2.7 - - - +
435C TYR* 4.4 2.5 - - + -
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Residues in contact with ASN 420 (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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27C ASP* 4.8 4.9 - - - +
44C ARG* 5.2 6.1 - - - +
124C VAL* 4.5 16.7 - - - +
329C ALA* 4.1 2.3 - - - +
332C ARG* 3.1 33.6 + - - +
416C GLN* 2.6 56.6 + - - +
417C GLU* 3.9 9.6 - - - +
418C PHE 3.3 0.2 - - - -
419C VAL* 1.3 72.5 - - - +
421C LYS* 1.3 58.6 + - + +
422C SER 3.3 1.2 + - - -
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Residues in contact with LYS 421 (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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326C LEU* 3.7 13.2 - - - +
329C ALA* 3.7 19.4 - - + +
330C LEU* 5.3 3.4 - - - +
332C ARG* 4.4 1.6 - - - +
333C ASP* 3.0 34.4 + - - +
334C PHE* 4.2 19.0 - - - -
371C SER* 4.5 8.7 + - - +
374C MET* 4.4 10.5 + - - +
375C LEU* 3.7 30.1 - - + +
376C ARG 5.8 0.9 - - - +
379C ILE* 5.7 1.6 - - - -
417C GLU* 3.3 25.5 + - + +
418C PHE 3.1 10.3 + - - +
420C ASN* 1.3 80.1 - - + +
422C SER* 1.3 66.6 + - - +
423C LEU* 3.4 14.8 + - + +
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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