Contacts of the helix formed by residues 407 - 421 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C LYS* 3.4 45.7 + - - +
315C LYS* 4.8 14.4 - - + +
401D CYS* 4.1 1.5 - - - -
406D MET* 1.3 75.3 - - - +
408D THR* 1.3 77.6 + - - +
409D GLU* 3.0 30.8 - - + +
410D GLU* 3.1 11.8 + - + +
411D VAL* 3.1 18.5 + - - +
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Residues in contact with THR 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 4.4 5.6 - - - +
49D GLN* 4.3 15.9 - - - +
397D THR* 4.3 5.6 - - + +
398D LYS* 5.9 1.4 - - - +
401D CYS* 3.8 21.3 - - - -
407D GLU* 1.3 81.8 + - - +
409D GLU* 1.3 69.7 + - + +
411D VAL* 3.4 1.5 + - - +
412D GLU* 3.0 55.9 + - + +
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Residues in contact with GLU 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LYS* 5.1 6.0 - - - +
47D PRO 4.3 6.7 - - - +
48D THR* 3.5 17.9 - - - +
49D GLN* 3.0 45.6 + - + +
52D ARG* 4.4 22.7 - - - +
407D GLU* 3.0 29.7 + - + +
408D THR* 1.3 79.6 - - + +
410D GLU* 1.3 59.0 + - - +
412D GLU* 3.4 7.6 + - - +
413D ASP* 3.0 36.1 + - - +
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Residues in contact with GLU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 5.2 1.0 + - - -
376D ARG* 5.8 1.4 + - - -
406D MET* 4.0 23.1 - - + -
407D GLU* 3.1 13.9 + - + +
409D GLU* 1.3 76.6 - - - +
411D VAL* 1.3 65.3 + - - +
413D ASP* 3.4 21.4 + - - +
414D ILE* 3.1 33.2 + - + +
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Residues in contact with VAL 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D THR* 3.8 18.2 - - + +
400D LEU* 3.9 17.5 - - + +
401D CYS* 3.6 37.9 - - - +
404D TRP* 4.3 3.3 - - + -
406D MET* 3.2 28.7 - - + +
407D GLU 3.1 11.0 + - - +
408D THR 3.7 6.5 - - - +
410D GLU* 1.3 76.4 - - - +
412D GLU* 1.3 58.8 + - - +
414D ILE* 3.3 2.6 + - - +
415D LEU* 3.0 53.5 + - + +
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Residues in contact with GLU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 2.4 48.6 + - - +
23D SER* 6.2 0.2 - - - +
24D TYR* 5.4 0.5 + - - -
49D GLN* 4.9 0.7 - - - +
397D THR* 3.2 23.1 + - + -
408D THR* 3.0 32.8 + - - +
409D GLU* 3.9 6.1 - - - +
411D VAL* 1.3 75.0 - - - +
413D ASP* 1.3 59.3 + - - +
415D LEU* 3.4 2.0 + - - +
416D GLN* 3.0 30.6 + - - +
433D PHE* 3.6 16.7 - - + -
435D TYR* 3.5 22.6 + - - +
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Residues in contact with ASP 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D SER* 5.6 5.5 - - - -
44D ARG* 3.8 30.9 + - - +
52D ARG* 3.0 40.6 + - - -
409D GLU 3.0 18.9 + - - +
410D GLU* 3.6 22.7 - - - +
412D GLU* 1.3 75.8 - - - +
414D ILE* 1.3 66.3 + - - +
416D GLN* 3.4 7.2 + - - +
417D GLU* 3.3 26.4 + - - +
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Residues in contact with ILE 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D ARG* 5.1 2.9 - - - +
379D ILE* 4.2 16.3 - - + +
382D TYR* 3.9 31.0 - - + -
404D TRP* 4.4 9.2 - - + -
406D MET* 3.5 31.6 - - + -
410D GLU* 3.1 32.5 + - + +
411D VAL* 3.6 5.2 - - - +
413D ASP* 1.3 74.2 - - - +
415D LEU* 1.3 65.2 + - - +
417D GLU* 3.2 27.9 + - - +
418D PHE* 3.5 32.2 + - + -
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D LEU* 4.4 4.5 - - + -
400D LEU* 3.6 17.0 - - + -
404D TRP* 3.5 28.5 - - + -
411D VAL* 3.0 39.1 + - + +
412D GLU 3.9 3.1 - - - +
413D ASP 3.3 0.2 - - - -
414D ILE* 1.3 75.1 - - - +
416D GLN* 1.3 56.7 + - - +
418D PHE* 3.1 16.0 + - + +
419D VAL* 2.9 32.7 + - - +
424D LEU* 3.8 17.2 - - + +
435D TYR* 3.3 47.8 - - + +
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Residues in contact with GLN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D SER* 3.8 21.0 - - - +
24D TYR* 3.5 38.6 + - + +
27D ASP* 3.6 17.4 + - - +
44D ARG* 5.7 8.3 - - - +
412D GLU 3.0 17.7 + - - +
413D ASP* 3.6 9.4 - - - +
414D ILE 3.3 0.2 - - - -
415D LEU* 1.3 72.9 - - - +
417D GLU* 1.3 57.1 + - + +
419D VAL* 4.0 10.8 - - - +
420D ASN* 2.7 73.2 + - - +
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Residues in contact with GLU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ARG* 4.7 12.9 + - - +
376D ARG* 2.6 46.0 + - - +
379D ILE* 3.7 20.9 - - + +
413D ASP* 3.4 17.4 - - - +
414D ILE* 3.2 17.7 + - - +
416D GLN* 1.3 78.8 - - + +
418D PHE* 1.3 61.8 + - - +
420D ASN* 3.6 8.5 + - - +
421D LYS* 3.3 36.3 + - + +
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Residues in contact with PHE 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D LEU* 3.8 22.2 - - + -
379D ILE* 3.5 42.2 - - + -
382D TYR* 4.3 3.1 - - + -
383D TYR* 3.7 40.8 - + + -
386D LEU* 4.2 7.4 - - + -
404D TRP* 4.8 0.4 - + - -
414D ILE* 3.5 35.4 + - + -
415D LEU* 3.1 25.1 + - + +
417D GLU* 1.3 74.0 - - - +
419D VAL* 1.3 66.1 + - - +
421D LYS* 3.0 8.4 + - - -
423D LEU* 3.0 35.2 + - + +
424D LEU* 3.7 16.4 - - + -
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Residues in contact with VAL 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D TYR* 3.9 22.2 - - + +
124D VAL* 3.7 22.2 - - + +
415D LEU 2.9 28.5 + - - +
416D GLN* 3.2 19.9 + - - +
418D PHE* 1.3 76.9 - - - +
420D ASN* 1.3 57.4 + - - +
422D SER* 3.0 20.3 + - - -
424D LEU* 3.3 35.1 - - + +
425D PHE* 4.7 1.3 - - + -
426D CYS* 4.0 21.8 - - + +
428D ARG* 5.6 2.0 - - - +
435D TYR* 4.4 2.2 - - + -
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Residues in contact with ASN 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASP* 5.1 3.5 - - - +
44D ARG* 6.2 0.4 - - - +
124D VAL* 4.5 15.1 - - - +
298D PHE* 4.5 4.3 - - - -
329D ALA* 4.1 2.3 - - - +
332D ARG* 3.0 35.5 + - - +
416D GLN* 2.7 55.5 + - - +
417D GLU* 4.0 8.8 - - - +
418D PHE 3.3 0.2 - - - -
419D VAL* 1.3 71.3 - - - +
421D LYS* 1.3 58.8 + - + +
422D SER 3.4 1.3 + - - -
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Residues in contact with LYS 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D LEU* 3.7 12.8 - - - +
329D ALA* 3.7 19.5 - - + +
330D LEU* 5.5 4.0 - - - +
332D ARG* 4.3 1.6 - - - +
333D ASP* 2.6 40.6 + - - +
334D PHE* 4.4 13.3 - - - -
371D SER* 4.4 10.5 + - - +
374D MET* 4.8 7.5 + - - +
375D LEU* 3.9 29.5 - - + +
376D ARG 6.1 0.7 - - - +
379D ILE* 5.9 1.6 - - - -
417D GLU* 3.3 24.0 + - - +
418D PHE 3.0 9.5 + - - +
420D ASN* 1.3 78.8 - - + +
422D SER* 1.3 68.6 + - - +
423D LEU* 3.4 13.9 + - + +
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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