Contacts of the helix formed by residues 405 - 418 (chain A) in PDB entry 5I94
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 ASP 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A GLY 4.0 2.8 + - - -
404A THR* 1.3 69.6 - - - +
406A MET* 1.3 55.4 + - - +
407A VAL* 3.9 8.5 + - - +
408A GLY* 2.8 42.4 + - - -
409A ILE* 2.9 13.5 + - - +
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Residues in contact with MET 406 (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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391A GLY* 3.6 28.7 - - - +
392A TYR* 3.5 49.4 - - + -
395A LYS* 4.2 21.5 - - + +
400A PHE* 3.7 24.0 - - + -
404A THR* 3.2 15.2 + - - +
405A ASP* 1.3 73.5 + - - +
407A VAL* 1.3 74.1 + - + +
409A ILE* 3.1 6.3 + - - +
410A LEU* 2.9 45.7 + - + +
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Residues in contact with VAL 407 (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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388A PHE* 4.3 23.1 - - + -
392A TYR* 4.2 13.2 - - + +
405A ASP* 3.4 8.7 + - - +
406A MET* 1.3 94.3 - - + +
408A GLY* 1.3 66.0 + - - +
410A LEU* 3.3 14.4 + - - +
411A ASP* 3.3 16.7 + - - +
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Residues in contact with GLY 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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350A ASN* 3.1 29.2 + - - -
405A ASP* 2.8 25.5 + - - -
407A VAL* 1.3 78.2 - - - +
409A ILE* 1.3 61.3 + - - -
411A ASP* 3.1 14.7 + - - +
412A PHE 3.1 0.9 + - - -
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Residues in contact with ILE 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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338A ILE* 3.7 28.7 - - + +
341A THR* 3.9 13.6 - - + +
342A SER* 3.7 26.7 - - - +
350A ASN* 5.4 0.9 - - - +
353A LYS* 4.0 22.9 - - - +
400A PHE* 4.5 6.7 - - + -
404A THR* 3.6 28.3 - - + -
405A ASP 2.9 12.3 + - - +
406A MET* 3.1 9.4 + - - +
408A GLY* 1.3 72.2 - - - +
410A LEU* 1.3 68.3 + - + +
412A PHE* 3.1 9.5 + - + +
413A TYR* 2.9 20.0 + - + +
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Residues in contact with LEU 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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338A ILE* 4.0 29.8 - - + -
387A ASN* 3.7 22.9 - - + +
388A PHE* 3.5 44.2 - - + -
391A GLY* 4.4 6.1 - - - -
400A PHE* 6.0 0.2 - - + -
406A MET* 2.9 38.6 + - + +
407A VAL* 3.5 8.5 - - - +
408A GLY 3.3 0.4 - - - -
409A ILE* 1.3 74.6 - - + +
411A ASP* 1.3 59.2 + - - +
413A TYR* 3.0 10.8 + - + +
414A PHE* 2.8 42.6 + - + -
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Residues in contact with ASP 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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350A ASN* 4.6 3.6 - - - +
377A PHE* 3.7 9.5 - - + -
381A ARG* 3.0 42.2 + - - +
388A PHE* 4.7 7.8 - - - -
407A VAL* 3.3 12.8 + - - +
408A GLY* 3.1 10.9 + - - +
410A LEU* 1.3 76.0 - - - +
412A PHE* 1.3 67.2 + - - +
414A PHE* 3.6 18.7 - - - +
415A GLN* 2.9 36.8 + - - +
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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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341A THR* 3.4 31.2 - - + -
344A ILE* 4.5 11.0 - - + -
350A ASN* 3.9 22.9 - - - +
353A LYS* 3.7 49.4 - - + -
354A PHE* 3.8 31.4 - + + -
357A VAL* 4.2 10.5 - - + -
408A GLY 3.1 6.5 + - - +
409A ILE* 3.1 12.9 + - + +
411A ASP* 1.3 75.6 - - - +
413A TYR* 1.3 57.6 + - - +
415A GLN* 3.0 11.3 + - + +
416A LEU* 2.9 48.2 + - + +
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Residues in contact with TYR 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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288A LYS* 3.0 23.3 + - - -
291A LYS* 3.4 20.2 - - - -
334A ASN* 3.1 21.6 + - - -
337A ALA* 3.6 24.7 - - + -
338A ILE* 3.9 26.2 - - + -
341A THR* 3.8 17.4 - - + +
380A GLU* 5.9 0.9 - - - -
387A ASN* 4.0 24.0 - - + -
409A ILE* 2.9 11.7 + - + +
410A LEU* 3.1 16.2 - - - +
412A PHE* 1.3 76.2 - - - +
414A PHE* 1.3 68.3 + + - +
416A LEU* 3.3 5.9 + - - +
417A CYS* 3.0 46.7 + - - -
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Residues in contact with PHE 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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377A PHE* 3.7 17.8 - - + -
380A GLU* 3.4 38.6 - - + +
381A ARG* 3.9 20.4 - - + -
384A GLY 4.2 4.0 - - - -
387A ASN* 3.2 44.6 - - + -
388A PHE* 3.8 29.4 - + - -
410A LEU* 2.8 35.6 + - + -
411A ASP* 3.2 12.3 + - - +
413A TYR* 1.3 79.0 - + - +
415A GLN* 1.3 63.8 + - - +
417A CYS* 3.5 5.9 + - - +
418A SER* 2.9 26.7 + - - -
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Residues in contact with GLN 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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350A ASN* 4.5 16.7 - - - +
351A ALA* 5.8 0.5 - - - -
354A PHE* 3.6 44.5 - - + +
372A PHE* 3.6 16.0 - - + -
377A PHE* 3.6 34.6 - - + -
411A ASP* 2.9 27.7 + - - +
412A PHE* 3.2 13.1 - - - +
414A PHE* 1.3 75.4 - - - +
416A LEU* 1.3 58.6 + - - +
418A SER* 3.0 20.1 + - - -
419A ILE 3.4 7.6 + - - -
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Residues in contact with LEU 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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283A LEU* 5.0 0.5 - - - +
287A VAL* 3.8 19.1 - - + +
291A LYS* 3.7 40.4 - - + +
341A THR* 4.0 11.9 - - + +
344A ILE* 5.7 1.3 - - + -
354A PHE* 3.7 20.4 - - + -
357A VAL* 3.7 31.9 - - + -
412A PHE* 2.9 38.6 + - + +
413A TYR 3.3 7.8 + - - +
415A GLN* 1.3 77.9 - - - +
417A CYS* 1.3 61.5 + - - +
418A SER 3.2 0.5 + - - -
419A ILE* 3.4 25.3 + - + +
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Residues in contact with CYS 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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282A CYS* 3.7 7.8 - - - +
284A GLN* 3.0 63.8 + - - +
287A VAL* 4.8 4.3 - - - -
288A LYS* 4.7 4.0 - - - -
380A GLU* 5.0 10.8 - - - +
413A TYR* 3.0 55.5 + - - +
414A PHE* 3.9 8.1 - - - +
415A GLN 3.3 0.4 - - - -
416A LEU* 1.3 76.3 - - - +
418A SER* 1.3 59.2 + - - +
419A ILE 3.4 1.6 + - - -
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Residues in contact with SER 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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282A CYS* 3.8 8.5 - - - -
372A PHE* 3.6 15.8 - - - -
373A SER* 3.0 39.9 + - - -
376A THR* 3.6 11.9 + - - +
377A PHE* 3.3 19.4 + - - -
380A GLU* 4.8 1.4 - - - +
414A PHE 2.9 14.4 + - - -
415A GLN 3.0 12.3 + - - -
417A CYS* 1.3 77.8 - - - +
419A ILE* 1.3 64.2 + - - +
420A GLU 3.6 0.2 + - - -
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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