Contacts of the helix formed by residues 408 - 417 (chain X) in PDB entry 3I39
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 SER 408 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236X THR* 3.7 8.3 - - - +
237X PRO* 2.7 31.8 + - - -
302X MET* 4.2 2.2 - - - +
406X GLY 3.0 5.3 + - - -
407X PHE* 1.3 78.7 - - - +
409X THR* 1.3 59.1 + - - +
410X GLU* 3.7 11.0 + - - +
411X ALA* 3.0 17.3 + - - +
412X ILE* 2.9 26.6 + - - +
531X ARG* 3.8 29.2 - - - +
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Residues in contact with THR 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408X SER* 1.3 73.6 - - - +
410X GLU* 1.3 65.7 + - - +
412X ILE* 3.2 5.5 + - - +
413X ILE* 2.8 47.5 + - + +
523X MET* 3.5 10.2 - - - +
531X ARG* 2.7 38.1 + - - +
534X ALA* 4.2 11.7 - - + +
535X LEU* 3.9 28.9 + - + +
538X ALA* 5.8 0.7 - - + -
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Residues in contact with GLU 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X LYS* 2.8 37.7 + - + +
236X THR* 3.5 23.0 - - + +
237X PRO 5.5 0.2 - - - +
408X SER* 3.8 5.9 - - - +
409X THR* 1.3 88.1 + - + +
411X ALA* 1.3 56.2 + - - +
413X ILE* 3.4 9.9 + - + +
414X ASN* 2.8 29.5 + - - +
531X ARG* 4.3 1.7 + - - -
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Residues in contact with ALA 411 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237X PRO 4.0 4.5 - - - +
238X ALA* 4.2 1.8 - - + -
239X PRO* 3.9 21.5 - - + +
406X GLY 3.5 19.5 - - - +
407X PHE* 4.1 6.0 - - + -
408X SER* 3.0 25.4 + - - +
410X GLU* 1.3 77.2 - - - +
412X ILE* 1.3 56.7 + - - +
414X ASN* 3.3 8.4 + - - +
415X ALA* 2.9 30.4 + - - +
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Residues in contact with ILE 412 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X PHE* 3.8 35.9 - - + +
408X SER 2.9 14.3 + - - +
409X THR* 3.7 4.9 - - - +
411X ALA* 1.3 75.3 - - - +
413X ILE* 1.3 64.8 + - - +
415X ALA* 3.2 6.8 + - + +
416X LEU* 2.9 43.2 + - + +
428X LEU* 5.6 2.9 - - + -
470X LEU* 6.4 1.3 - - + -
472X VAL* 5.2 0.7 - - + -
521X LEU* 4.0 25.1 - - + -
523X MET* 3.8 27.1 - - + -
535X LEU* 4.3 24.7 - - + -
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Residues in contact with ILE 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409X THR* 2.8 38.9 + - + +
410X GLU* 3.7 7.6 - - + +
412X ILE* 1.3 76.4 - - - +
414X ASN* 1.3 57.4 + - - +
416X LEU* 3.3 6.9 + - - +
417X SER* 2.8 28.0 + - - -
424X PRO* 3.6 27.3 - - + +
425X LEU* 4.2 25.4 - - + -
535X LEU* 4.9 4.3 - - + -
538X ALA* 5.3 9.0 - - + -
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Residues in contact with ASN 414 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410X GLU 2.8 20.7 + - - +
411X ALA* 3.6 8.8 + - - +
412X ILE 3.3 0.2 - - - -
413X ILE* 1.3 74.8 - - - +
415X ALA* 1.3 63.0 + - - +
417X SER* 2.6 29.5 + - - -
418X LYS* 3.5 27.3 + - - +
511X ASN* 4.4 6.9 - - - +
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Residues in contact with ALA 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X PHE* 5.4 5.8 - - + -
411X ALA 2.9 17.4 + - - +
412X ILE* 3.6 7.6 - - - +
414X ASN* 1.3 75.0 - - - +
416X LEU* 1.3 65.4 + - + +
418X LYS* 3.3 10.7 + - - +
419X LEU* 4.3 1.7 + - - +
507X ILE* 3.8 19.0 - - + +
511X ASN* 3.0 38.9 - - - +
517X LEU* 5.0 11.0 - - + -
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Residues in contact with LEU 416 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412X ILE* 2.9 37.3 + - + +
413X ILE* 3.7 4.9 - - - +
415X ALA* 1.3 80.5 - - + +
417X SER* 1.3 57.8 + - - +
419X LEU* 2.9 25.8 + - + +
420X ASN 3.3 6.6 + - - -
424X PRO 3.2 24.0 - - - +
425X LEU* 4.5 13.7 - - + -
427X PRO* 3.9 11.6 - - + +
428X LEU* 4.1 41.1 - - + +
507X ILE* 3.8 31.0 - - + -
535X LEU* 5.6 0.2 - - + -
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Residues in contact with SER 417 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413X ILE* 2.8 15.5 + - - -
414X ASN* 2.6 30.8 + - - -
416X LEU* 1.3 75.9 - - - +
418X LYS* 1.3 65.0 + - - +
419X LEU 3.0 1.6 - - - -
420X ASN 3.4 13.2 - - - -
421X ALA* 3.2 36.2 + - - +
424X PRO* 3.8 12.8 - - - +
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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