Contacts of the helix formed by residues 357 - 368 (chain B) in PDB entry 4O9U
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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B ALA* 6.1 0.7 - - - -
330B ILE 4.4 7.6 - - - +
332B PRO* 5.9 0.4 - - + -
356B LYS* 1.3 75.5 - - - +
358B LEU* 1.3 72.2 + - + +
359B GLU* 3.1 24.9 + - - +
360B GLU* 3.6 21.0 + - - +
361B ILE* 3.3 19.2 + - - +
159F THR* 4.5 13.5 - - + +
164F THR* 2.7 38.0 + - + +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ILE 4.7 4.2 + - - -
331B HIS* 6.1 0.4 - - + -
332B PRO* 4.1 27.8 - - + +
357B ASP* 1.3 84.2 + - + +
359B GLU* 1.3 74.7 + - + +
361B ILE* 3.2 7.9 + - - -
362B ASN* 2.8 50.5 + - - +
395B PRO* 3.6 28.5 - - + -
396B ILE 3.6 22.0 - - - +
397B LEU* 4.9 11.7 - - + -
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ASP* 3.1 11.3 + - - +
358B LEU* 1.3 95.9 - - + +
360B GLU* 1.3 58.2 + - + +
361B ILE 3.5 0.4 + - - -
362B ASN* 4.6 2.9 - - - +
363B PRO* 4.1 12.0 - - - +
26E ARG* 4.9 16.6 + - - -
328E LYS* 5.7 0.9 + - - -
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Residues in contact with GLU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B LEU 5.2 0.2 - - - +
356B LYS* 3.3 52.2 + - + +
357B ASP* 3.8 25.0 + - - +
359B GLU* 1.3 76.8 - - + +
361B ILE* 1.3 57.3 + - - +
362B ASN 3.9 0.2 - - - -
363B PRO* 4.4 7.5 - - - +
364B GLU* 3.4 16.8 - - - +
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Residues in contact with ILE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B VAL* 4.7 10.1 - - + -
327B LYS* 4.3 21.3 - - + -
328B PHE 4.3 9.4 - - - +
329B ALA* 4.6 12.1 - - + -
356B LYS* 3.9 30.7 - - + +
357B ASP 3.3 20.4 - - - +
358B LEU* 3.6 10.8 - - - +
360B GLU* 1.3 80.9 - - - +
362B ASN* 1.3 72.7 + - - +
363B PRO* 3.5 2.2 - - - -
364B GLU* 3.2 31.7 + - + +
365B PHE* 3.2 27.9 - - + -
397B LEU* 4.3 6.3 - - + -
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Residues in contact with ASN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B LEU* 2.8 40.3 + - - +
359B GLU* 4.6 2.5 - - - +
361B ILE* 1.3 73.1 - - - +
363B PRO* 1.4 64.0 - - + +
364B GLU 3.0 9.1 + - - -
365B PHE* 3.4 20.3 + - - +
366B PRO* 3.9 4.0 - - - +
396B ILE 3.5 16.7 + - - -
397B LEU* 3.5 16.3 - - - +
398B ASP* 3.2 46.1 + - - +
401B LYS* 5.4 1.9 - - - +
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Residues in contact with PRO 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B GLU 4.1 12.8 - - - +
360B GLU* 4.9 6.1 - - - +
361B ILE 3.6 7.0 - - - +
362B ASN* 1.4 91.6 - - + +
364B GLU* 1.3 57.0 + - + +
365B PHE 3.5 0.7 - - - -
366B PRO* 4.0 11.6 - - + +
367B THR* 5.2 0.7 + - - -
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LYS* 3.1 36.6 + - - +
325B GLU* 4.8 1.0 - - - +
327B LYS* 3.1 37.8 + - - +
356B LYS* 4.6 2.1 + - - -
360B GLU 3.4 18.2 - - - +
361B ILE* 3.2 23.0 - - + +
362B ASN 3.0 0.6 - - - -
363B PRO* 1.3 78.8 - - + +
365B PHE* 1.3 61.3 + - - +
366B PRO* 3.6 2.0 - - - -
367B THR* 3.0 22.7 + - - +
368B VAL* 3.3 14.9 - - + +
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B VAL* 4.3 28.9 - - + -
298B VAL* 5.0 2.5 - - + -
329B ALA* 4.7 1.3 - - + -
361B ILE* 3.2 33.0 - - + -
362B ASN* 3.4 15.0 + - - +
364B GLU* 1.3 75.2 - - - +
366B PRO* 1.4 62.9 - - + +
367B THR 3.0 5.6 - - - -
368B VAL* 2.9 30.5 + - + +
371B ALA* 4.7 3.6 - - + -
397B LEU* 3.5 33.2 - - + -
398B ASP* 2.9 24.7 - - + +
399B VAL* 3.6 29.2 - - + -
401B LYS* 4.3 7.0 - - + -
402B ALA* 3.4 32.1 - - + -
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ASN 3.9 8.5 - - - +
363B PRO* 4.0 10.8 - - + +
364B GLU 3.6 3.8 - - - -
365B PHE* 1.4 91.9 - - + +
367B THR* 1.3 62.4 + - + +
368B VAL 3.4 0.8 + - - -
401B LYS* 3.7 37.6 - - + +
403B LYS* 3.6 25.6 - - - +
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LYS* 3.3 34.5 + - - +
363B PRO 5.2 1.0 + - - -
364B GLU* 3.0 18.9 + - - -
366B PRO* 1.3 81.1 - - + +
368B VAL* 1.3 59.3 + - - +
369B ASP* 3.7 5.9 + - - +
403B LYS* 5.0 10.1 + - - +
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Residues in contact with VAL 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LYS* 3.2 35.7 - - + +
296B VAL* 3.8 27.8 - - + +
361B ILE* 6.4 0.7 - - + -
364B GLU* 3.3 19.5 - - + +
365B PHE* 2.9 24.7 + - + +
367B THR* 1.3 78.7 - - - +
369B ASP* 1.3 58.8 + - - +
370B VAL 3.5 16.8 - - - +
371B ALA* 4.7 0.4 - - + +
402B ALA* 3.4 14.6 - - + -
403B LYS* 3.0 27.2 + - - +
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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