Contacts of the helix formed by residues 408 - 421 (chain A) in PDB entry 5IVH
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 THR 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A VAL* 3.4 16.4 - - - +
369A LEU* 4.5 1.0 - - - +
406A THR* 4.0 9.6 - - + +
407A PRO* 1.3 79.6 - - - +
409A ALA* 1.3 64.7 + - - +
410A ASP* 3.5 9.0 + - - +
411A ASN* 3.4 29.1 + - - +
412A PHE* 3.3 20.6 + - - +
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Residues in contact with ALA 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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359A LEU* 4.6 11.7 - - + -
366A VAL* 4.9 5.7 - - + +
408A THR* 1.3 75.6 - - - +
410A ASP* 1.3 55.6 + - - +
412A PHE* 2.9 6.7 + - - -
413A MET* 2.5 56.1 + - + +
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Residues in contact with ASP 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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350A TYR* 3.0 32.0 + - - +
353A LEU* 5.4 0.3 - - - +
408A THR* 3.5 7.4 + - - +
409A ALA* 1.3 78.5 - - - +
411A ASN* 1.3 57.2 + - - +
413A MET* 4.1 6.8 - - - +
414A ASP* 2.6 38.9 + - - +
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Residues in contact with ASN 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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369A LEU* 3.7 15.7 - - + +
401A HIS* 3.0 30.3 - - - +
402A VAL* 3.8 12.0 - - - +
403A THR* 3.5 25.8 + - - +
404A GLY 5.3 0.2 - - - +
406A THR 3.9 6.5 + - - -
407A PRO* 3.8 9.9 - - - +
408A THR* 3.4 29.6 + - - +
409A ALA 3.2 0.4 - - - -
410A ASP* 1.3 78.5 - - - +
412A PHE* 1.3 55.3 + - - +
414A ASP* 3.6 4.1 - - - +
415A LEU* 2.6 37.6 + - - +
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Residues in contact with PHE 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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306A LYS* 5.8 0.4 - - - -
355A PHE* 4.6 8.7 - + + -
359A LEU* 3.6 36.3 - - + -
365A LEU* 3.3 16.6 - - + -
366A VAL* 4.1 8.3 - - + -
368A GLU* 3.2 31.0 - - - -
369A LEU* 3.3 29.1 - - + +
375A PHE* 3.8 18.6 - + - -
408A THR 3.3 15.3 + - - +
409A ALA* 2.9 10.2 + - - +
411A ASN* 1.3 77.7 - - - +
413A MET* 1.3 60.7 + - + +
415A LEU* 3.2 3.7 + - - +
416A CYS* 2.8 46.7 + - - -
420A TYR* 6.2 0.2 - - - -
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Residues in contact with MET 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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350A TYR* 3.3 30.5 - - - +
352A GLY* 3.3 28.4 - - - +
353A LEU* 3.8 27.4 - - + +
355A PHE* 4.7 0.9 - - + -
356A THR* 3.6 28.7 - - - +
359A LEU* 3.8 19.3 - - + -
409A ALA* 2.5 39.5 + - + +
410A ASP* 4.1 6.3 - - - +
412A PHE* 1.3 75.3 - - + +
414A ASP* 1.3 62.5 + - - +
416A CYS* 3.0 3.9 + - - -
417A SER* 3.0 18.5 + - - -
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Residues in contact with ASP 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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350A TYR* 3.8 10.6 - - + -
401A HIS* 3.1 20.7 + - - +
410A ASP 2.6 24.0 + - - +
411A ASN* 3.7 4.7 - - - +
413A MET* 1.3 72.3 - - - +
415A LEU* 1.3 63.2 + - - +
417A SER* 3.1 17.1 + - - -
418A HIS* 3.3 22.9 + - - -
552A GLU* 5.9 0.5 - - - +
555A LYS* 3.0 31.4 + - - -
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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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369A LEU* 3.9 17.9 - - + -
372A CYS* 3.9 17.5 - - - -
375A PHE* 3.4 43.7 - - + -
397A ILE* 3.7 23.1 - - + -
401A HIS* 3.6 29.8 + - + -
411A ASN 2.6 22.0 + - - +
412A PHE* 3.4 6.5 - - - +
414A ASP* 1.3 72.8 - - - +
416A CYS* 1.3 64.5 + - - +
418A HIS* 2.9 14.7 + - - +
419A PHE* 3.0 12.0 + - + -
559A TRP* 4.1 9.8 - - + -
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Residues in contact with CYS 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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352A GLY* 4.1 2.2 - - - -
355A PHE* 3.8 28.0 - - + -
375A PHE* 4.5 7.6 - - - -
412A PHE* 2.8 49.6 + - - +
413A MET* 3.0 8.7 + - - +
415A LEU* 1.3 78.7 - - - +
417A SER* 1.3 64.3 + - - +
419A PHE* 4.4 1.1 - - - +
420A TYR* 3.1 52.4 + - + +
421A PHE* 4.3 0.9 - - - -
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Residues in contact with SER 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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350A TYR* 4.0 9.8 - - - -
351A GLU* 3.5 19.8 + - - -
352A GLY* 2.8 28.4 + - - +
413A MET 3.0 10.6 + - - -
414A ASP* 3.1 12.7 + - - -
416A CYS* 1.3 75.6 - - - +
418A HIS* 1.3 60.7 + - - +
421A PHE* 3.1 26.1 + - - +
422A TRP* 3.1 24.9 + - - -
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Residues in contact with HIS 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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401A HIS* 3.3 22.9 - + - +
414A ASP* 3.3 23.2 + - - -
415A LEU 2.9 7.2 + - - +
417A SER* 1.3 82.9 - - - +
419A PHE* 1.3 65.3 + - - +
422A TRP* 3.6 16.5 + + + +
423A PHE* 3.0 30.9 + - + +
424A PRO* 3.5 1.4 - - - +
552A GLU* 3.6 40.6 - - + +
555A LYS* 3.3 38.3 - - + +
556A ILE* 4.0 10.5 + - + +
559A TRP* 3.9 11.4 + - + +
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Residues in contact with PHE 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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250A PRO* 3.4 44.7 - - + +
305A ASN 5.3 0.9 - - - -
306A LYS* 3.8 30.3 - - + -
374A ASN 4.8 0.4 - - - -
375A PHE* 3.2 50.9 - + + -
376A VAL 4.7 6.5 - - - -
377A PRO* 4.9 7.0 - - + -
378A SER 6.0 1.1 - - - -
415A LEU* 3.0 13.7 + - + +
416A CYS* 3.4 2.9 + - - +
418A HIS* 1.3 78.5 - - - +
420A TYR* 1.3 96.0 + + + +
423A PHE* 5.1 0.9 - - - -
424A PRO* 3.7 6.6 - - - +
559A TRP* 3.7 23.3 - + + -
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Residues in contact with TYR 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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249A CYS* 3.4 10.7 - - - -
250A PRO* 4.4 1.6 - - + -
251A TRP* 3.1 43.5 + + - +
306A LYS* 4.1 10.9 - - - +
308A MET* 2.9 48.0 - - + +
355A PHE* 3.1 41.0 - + - -
375A PHE* 4.4 5.3 - + - -
416A CYS* 3.1 38.3 + - + +
419A PHE* 1.3 105.5 - + - +
421A PHE* 1.3 77.5 + - + +
424A PRO* 4.0 2.6 - - - +
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Residues in contact with PHE 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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218A SER* 4.7 0.4 - - - -
244A SER* 3.3 35.4 - - - -
245A GLY* 4.5 1.6 - - - +
249A CYS* 4.9 3.2 - - - -
251A TRP* 4.0 16.6 - + - -
347A ASN* 3.6 18.5 - - - +
351A GLU* 3.6 37.7 - - + -
352A GLY 5.4 0.2 - - - -
354A PHE* 6.0 1.1 - + + -
355A PHE* 5.2 7.6 - + - -
416A CYS 4.3 3.1 - - - -
417A SER 3.1 12.6 + - - +
419A PHE 3.6 1.2 - - - -
420A TYR* 1.3 104.8 - + + +
422A TRP* 1.3 66.2 + - + +
423A PHE 3.5 0.9 - - - -
424A PRO* 3.5 3.9 - - - +
425A MET* 3.2 22.0 + - - +
471A HIS* 3.4 31.6 - + + -
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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