Contacts of the helix formed by residues 355 - 371 (chain B) in PDB entry 5D3O
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 ASN 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B GLY 3.9 0.2 + - - -
354B VAL* 1.3 75.8 - - - +
356B ASN* 1.3 63.3 + - - +
357B ALA* 3.3 37.0 - - - +
358B GLU* 3.2 22.3 + - - +
359B LYS* 3.0 21.4 + - - +
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Residues in contact with ASN 356 (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 ASN* 1.3 71.9 - - - +
357B ALA* 1.3 60.5 + - - +
359B LYS* 3.2 25.1 + - - +
360B PHE* 2.8 33.2 + - - +
414B GLY* 3.1 34.9 + - - +
415B ILE* 5.0 1.7 - - - +
417B ASP* 4.5 5.3 + - - +
418B PHE* 3.9 23.6 - - + +
421B GLN* 4.4 14.9 - - - +
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Residues in contact with ALA 357 (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 ASN* 3.3 16.8 - - - +
356B ASN* 1.3 78.5 - - - +
358B GLU* 1.3 57.8 + - - +
360B PHE* 3.7 6.1 + - - +
361B ASP* 3.0 34.8 + - - +
421B GLN* 5.9 0.9 - - - +
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Residues in contact with GLU 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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351B LYS* 5.7 3.3 - - - -
354B VAL* 3.5 30.6 - - + +
355B ASN* 3.2 25.6 + - - +
356B ASN 3.0 0.6 - - - -
357B ALA* 1.3 78.2 - - - +
359B LYS* 1.3 65.4 + - - +
361B ASP* 3.2 11.6 + - + +
362B TYR* 2.9 22.8 + - + +
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Residues in contact with LYS 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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347B THR 5.7 0.2 - - - +
348B SER 5.7 1.7 + - - -
350B ILE* 3.8 10.0 - - + +
351B LYS* 3.0 38.3 - - + +
352B GLN* 4.0 8.9 - - - +
353B GLY 4.9 1.4 - - - +
354B VAL* 3.4 27.7 + - + +
355B ASN* 3.0 11.4 + - - +
356B ASN* 3.5 23.3 + - - +
358B GLU* 1.3 75.6 - - - +
360B PHE* 1.3 62.8 + - - +
362B TYR* 3.1 9.3 + - - +
363B VAL* 3.0 25.1 + - - +
415B ILE* 4.5 16.4 - - + +
418B PHE* 3.6 29.6 - - + -
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Residues in contact with PHE 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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356B ASN 2.8 21.8 + - - +
357B ALA* 3.7 6.7 - - - +
359B LYS* 1.3 70.7 - - - +
361B ASP* 1.3 74.9 + - - +
362B TYR 3.1 0.2 + - - -
363B VAL* 3.2 3.8 + - + +
364B MET* 2.9 44.9 + - + +
378B PHE* 3.7 31.2 - + + -
418B PHE* 3.8 21.9 - + + -
421B GLN* 3.6 46.0 - - + +
422B LEU* 4.3 4.7 - - + -
425B ILE* 4.1 17.3 - - + -
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Residues in contact with ASP 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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357B ALA* 3.0 23.4 + - - +
358B GLU* 3.2 14.0 + - + +
360B PHE* 1.3 82.7 - - - +
362B TYR* 1.3 57.2 + - - +
364B MET* 3.3 7.0 + - - +
365B GLN* 3.0 38.5 + - - +
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Residues in contact with TYR 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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300B ILE* 4.1 9.0 - - + -
304B ASP* 2.5 36.1 + - - -
350B ILE* 4.4 8.7 - - + -
351B LYS* 4.0 50.7 - - + -
358B GLU* 2.9 12.8 + - + +
359B LYS* 3.3 11.7 - - - +
360B PHE 3.0 0.2 - - - -
361B ASP* 1.3 73.6 - - - +
363B VAL* 1.3 68.4 + - - +
365B GLN* 3.1 18.8 + - + +
366B PHE* 3.0 50.3 + + - +
369B LYS* 6.6 0.4 - - - -
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Residues in contact with VAL 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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293B VAL* 5.8 2.5 - - + -
297B LYS* 5.7 3.6 - - + -
300B ILE* 4.2 19.7 - - + -
350B ILE* 4.0 31.2 - - + -
359B LYS 3.0 17.0 + - - +
360B PHE* 3.9 6.1 - - - +
362B TYR* 1.3 74.7 - - + +
364B MET* 1.3 59.6 + - + +
366B PHE* 3.0 9.0 + - - +
367B LEU* 2.8 39.4 + - + +
418B PHE* 4.4 11.7 - - + -
422B LEU* 3.7 27.4 - - + -
425B ILE* 4.5 5.6 - - + -
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Residues in contact with MET 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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360B PHE* 2.9 49.0 + - + +
361B ASP* 3.6 10.3 - - - +
363B VAL* 1.3 76.9 - - - +
365B GLN* 1.3 57.5 + - - +
367B LEU* 3.4 4.6 + - - -
368B ASN* 2.9 41.4 + - - +
376B VAL* 3.3 44.2 - - + +
377B GLY 4.2 15.5 - - - +
378B PHE* 5.3 2.0 - - - -
425B ILE* 4.4 10.5 - - + -
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Residues in contact with GLN 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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361B ASP* 3.0 25.8 + - - +
362B TYR* 3.2 18.6 - - + +
364B MET* 1.3 75.3 - - - +
366B PHE* 1.3 62.4 + - - +
368B ASN* 3.1 17.4 + - + +
369B LYS* 3.2 30.5 + - - +
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Residues in contact with PHE 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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300B ILE* 3.7 33.0 - - + -
303B ASN* 3.3 30.7 - - + -
304B ASP* 3.9 0.7 - - - -
362B TYR* 3.0 43.6 + + + +
363B VAL* 3.0 8.8 + - - +
365B GLN* 1.3 75.3 - - - +
367B LEU* 1.3 64.6 + - - +
369B LYS* 3.3 19.9 + - + +
370B MET* 3.1 37.0 + - + +
452B VAL* 3.4 32.8 - - + -
453B LEU* 3.8 15.9 - - + -
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Residues in contact with LEU 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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289B LEU* 4.1 15.7 - - + -
293B VAL* 4.7 5.2 - - + -
296B LEU* 4.2 21.8 - - + -
300B ILE* 4.4 7.6 - - + -
363B VAL* 2.8 24.4 + - + +
364B MET* 3.8 5.4 - - - +
366B PHE* 1.3 73.3 - - - +
368B ASN* 1.3 65.9 + - - +
370B MET* 3.5 29.9 + - + +
371B ALA* 3.1 24.6 + - - +
376B VAL* 4.0 16.9 - - + +
425B ILE* 4.0 36.6 - - + -
435B MET* 4.2 9.2 - - + +
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Residues in contact with ASN 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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364B MET* 2.9 28.2 + - - +
365B GLN* 3.1 14.2 + - + +
367B LEU* 1.3 76.0 - - - +
369B LYS* 1.3 64.0 + - + +
371B ALA 3.3 4.0 + - - -
373B ASN* 2.9 48.4 + - - +
374B GLU 4.0 9.7 + - - -
376B VAL* 3.4 27.9 + - - +
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Residues in contact with LYS 369 (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 TYR* 6.6 0.2 - - - -
365B GLN* 3.2 28.1 + - - +
366B PHE* 3.3 21.1 + - + +
368B ASN* 1.3 75.7 - - - +
370B MET* 1.3 63.6 + - - +
372B GLY* 3.1 13.1 + - - -
373B ASN* 5.0 5.2 - - - +
445B CYS* 3.7 15.2 - - - +
448B THR* 5.0 1.2 + - - -
450B GLU* 3.3 29.6 + - - +
451B ARG 5.6 0.9 - - - +
452B VAL* 3.8 28.7 - - + +
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Residues in contact with MET 370 (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 LEU* 4.0 28.0 - - + +
299B ALA* 5.0 0.2 - - + -
300B ILE* 3.6 24.9 - - + -
366B PHE* 3.1 32.0 + - + +
367B LEU* 3.6 28.0 - - + +
368B ASN 3.2 0.2 - - - -
369B LYS* 1.3 81.2 - - - +
371B ALA* 1.3 57.2 + - - +
372B GLY 3.3 0.9 + - - -
434B VAL* 3.5 3.8 - - - +
435B MET* 3.5 23.1 - - + +
438B THR* 2.9 28.7 + - + +
439B LEU* 6.2 0.7 - - - -
445B CYS* 4.0 1.0 - - - -
452B VAL* 3.6 17.5 - - + -
453B LEU* 3.8 26.2 - - + -
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Residues in contact with ALA 371 (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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367B LEU 3.1 16.4 + - - +
368B ASN 3.3 2.2 + - - +
369B LYS 3.2 0.4 - - - -
370B MET* 1.3 75.0 - - - +
372B GLY* 1.3 60.8 + - - +
373B ASN 3.0 3.8 - - - -
374B GLU* 2.9 29.1 + - - +
376B VAL* 4.3 7.6 - - + -
431B SER* 3.7 22.9 - - - +
434B VAL* 3.5 18.1 - - - +
435B MET* 3.8 17.3 - - + +
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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