Contacts of the helix formed by residues 407 - 421 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A CYS* 4.1 1.6 - - - -
406A MET* 1.3 76.0 - - - +
408A THR* 1.3 66.4 + - - +
409A GLU* 3.3 15.2 - - - +
410A GLU* 3.0 24.0 + - + +
411A VAL* 3.1 10.4 + - - +
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Residues in contact with THR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.3 7.0 - - - +
49A GLN* 4.6 11.2 - - - +
397A THR* 4.3 6.5 - - + +
401A CYS* 3.7 21.6 - - - -
407A GLU* 1.3 72.2 - - - +
409A GLU* 1.3 71.2 + - + +
411A VAL* 3.4 1.3 + - - +
412A GLU* 2.9 56.6 + - + +
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Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PRO 4.8 4.9 - - - +
48A THR* 3.7 17.1 - - - +
49A GLN* 3.2 43.5 + - + +
52A ARG* 4.2 22.4 - - - +
407A GLU* 3.2 15.5 + - - +
408A THR* 1.3 89.8 + - + +
410A GLU* 1.3 57.2 + - - +
412A GLU* 3.4 6.6 + - - +
413A ASP* 2.9 36.9 + - - +
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A TYR* 4.8 2.8 + - - -
406A MET* 3.2 37.4 - - + +
407A GLU* 3.0 16.1 + - + +
409A GLU* 1.3 76.2 - - - +
411A VAL* 1.3 64.7 + - - +
413A ASP* 3.5 8.4 + - + +
414A ILE* 3.1 36.2 + - + +
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A THR* 3.9 13.0 - - + +
400A LEU* 3.9 20.2 - - + +
401A CYS* 3.6 28.3 - - - +
404A TRP* 4.2 4.9 - - + -
406A MET* 3.1 33.0 - - + -
407A GLU 3.1 16.7 + - - +
408A THR 3.7 6.3 - - - +
410A GLU* 1.3 76.3 - - - +
412A GLU* 1.3 57.5 + - - +
414A ILE* 3.2 4.8 + - - +
415A LEU* 3.0 52.7 + - + +
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 2.3 48.8 + - - +
23A SER* 6.0 0.9 - - - +
24A TYR* 5.2 1.6 + - + -
49A GLN* 5.0 0.9 - - - +
397A THR* 3.3 21.4 + - + -
408A THR* 2.9 33.3 + - - +
409A GLU* 3.9 6.1 - - - +
411A VAL* 1.3 74.6 - - - +
413A ASP* 1.3 59.7 + - - +
415A LEU* 3.4 2.6 + - - +
416A GLN* 3.0 30.6 + - - +
433A PHE* 3.6 15.3 - - + -
435A TYR* 3.6 21.6 + - - +
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER* 5.5 5.9 - - - -
44A ARG* 3.9 30.5 + - - +
52A ARG* 2.9 41.6 + - - -
409A GLU 2.9 21.2 + - - +
410A GLU* 3.7 7.6 - - + +
412A GLU* 1.3 75.0 - - - +
414A ILE* 1.3 66.4 + - + +
416A GLN* 3.4 8.1 + - - +
417A GLU* 3.4 26.3 + - - +
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Residues in contact with ILE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ARG* 5.2 3.4 - - - +
379A ILE* 4.3 15.2 - - + +
382A TYR* 3.8 32.1 - - + -
404A TRP* 4.5 7.9 - - + -
406A MET* 3.5 31.9 - - + -
410A GLU* 3.1 24.7 + - + +
411A VAL* 3.2 5.6 + - - +
413A ASP* 1.3 75.1 - - + +
415A LEU* 1.3 64.0 + - - +
417A GLU* 3.2 29.1 + - - +
418A PHE* 3.5 32.6 + - + -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU* 4.4 3.8 - - + -
400A LEU* 3.5 22.4 - - + -
404A TRP* 3.5 30.1 - - + -
411A VAL* 3.0 33.2 + - + +
412A GLU 3.9 2.7 - - - +
413A ASP 3.3 0.2 - - - -
414A ILE* 1.3 75.2 - - - +
416A GLN* 1.3 57.4 + - - +
418A PHE* 3.1 16.2 + - + +
419A VAL* 2.9 32.9 + - - +
424A LEU* 3.9 17.4 - - + +
435A TYR* 3.3 46.4 - - + +
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Residues in contact with GLN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER* 3.6 28.3 + - - -
24A TYR* 3.2 35.7 + - + +
27A ASP* 3.4 24.0 + - - +
44A ARG* 5.6 9.4 - - - +
412A GLU 3.0 17.9 + - - +
413A ASP* 3.6 9.6 - - - +
414A ILE 3.3 0.2 - - - -
415A LEU* 1.3 72.5 - - - +
417A GLU* 1.3 57.8 + - + +
419A VAL* 3.6 7.0 - - - +
420A ASN* 2.7 69.3 + - - +
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.8 13.0 + - - +
376A ARG* 2.6 46.3 + - - -
379A ILE* 3.8 20.7 - - + +
413A ASP* 3.4 16.2 - - - +
414A ILE* 3.2 17.5 + - - +
416A GLN* 1.3 79.2 - - + +
418A PHE* 1.3 61.4 + - - +
420A ASN* 3.7 6.5 + - - +
421A LYS* 3.3 36.0 + - + +
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Residues in contact with PHE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LEU* 3.8 22.2 - - + -
379A ILE* 3.5 41.1 - - + -
382A TYR* 4.2 2.9 - - + -
383A TYR* 3.7 43.3 - + + -
386A LEU* 4.1 10.1 - - + -
404A TRP* 4.7 0.2 - + - -
414A ILE* 3.5 35.0 + - + -
415A LEU* 3.1 23.8 + - + +
417A GLU* 1.3 74.1 - - - +
419A VAL* 1.3 65.2 + - - +
421A LYS* 3.1 8.4 + - - -
423A LEU* 3.0 34.4 + - + +
424A LEU* 3.8 16.4 - - + -
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.9 28.7 - - + +
124A VAL* 3.8 23.0 - - + +
415A LEU 2.9 26.5 + - - +
416A GLN* 3.2 12.5 + - - +
418A PHE* 1.3 77.1 - - - +
420A ASN* 1.3 57.2 + - - +
422A SER* 3.0 20.4 + - - -
424A LEU* 3.3 36.9 - - + +
425A PHE* 4.6 1.3 - - + -
426A CYS* 4.1 21.3 - - + +
428A ARG* 5.7 2.2 - - - +
435A TYR* 4.4 1.8 - - + -
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 5.4 6.8 + - - +
124A VAL* 4.4 19.3 - - - +
298A PHE* 4.5 4.0 - - - -
329A ALA* 4.2 2.3 - - - +
332A ARG* 3.0 35.7 + - - +
416A GLN* 2.7 51.9 + - - +
417A GLU* 4.0 6.9 + - - +
418A PHE 3.3 0.2 - - - -
419A VAL* 1.3 71.9 - - - +
421A LYS* 1.3 58.0 + - + +
422A SER 3.4 0.6 + - - -
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LEU* 3.7 13.3 - - - +
329A ALA* 3.7 19.7 - - + +
330A LEU* 5.4 3.8 - - - +
332A ARG* 4.2 1.8 - - - +
333A ASP* 2.8 39.5 + - - +
334A PHE* 4.3 13.3 - - - -
371A SER* 4.4 10.7 + - - +
374A MET* 4.7 10.7 + - - +
375A LEU* 3.9 29.0 - - + +
376A ARG 6.1 0.4 - - - +
379A ILE* 5.9 1.8 - - - -
417A GLU* 3.3 23.7 + - - +
418A PHE 3.1 9.8 + - - +
420A ASN* 1.3 79.4 - - + +
422A SER* 1.3 66.7 + - - +
423A LEU* 3.2 14.0 + - + +
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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