Contacts of the helix formed by residues 366 - 380 (chain B) in PDB entry 5ULM
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 GLY 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B LEU 3.0 1.2 + - - -
365B PRO* 1.3 70.4 - - - +
367B ASP* 1.3 64.9 + - - +
368B ARG 3.5 2.0 - - - -
369B ALA* 3.4 14.8 + - - +
370B LYS* 3.0 24.4 + - - +
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Residues in contact with ASP 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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359B LEU* 3.3 39.7 - - - +
362B ARG* 2.8 44.7 + - - +
363B ASN* 3.2 7.3 + - - -
364B LEU* 2.7 38.4 + - - +
365B PRO 4.6 2.1 - - - +
366B GLY* 1.3 77.4 - - - +
368B ARG* 1.3 59.0 + - - +
370B LYS* 3.1 6.7 + - - +
371B ALA 2.9 23.6 + - - -
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Residues in contact with ARG 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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359B LEU 4.7 0.7 - - - +
360B ASN* 2.8 51.2 + - - +
361B ARG* 3.6 21.2 + - - +
363B ASN* 3.3 37.4 + - - +
364B LEU 4.6 0.6 + - - -
366B GLY 3.5 0.6 - - - +
367B ASP* 1.3 72.7 - - - +
369B ALA* 1.3 65.6 + - - +
371B ALA* 3.3 6.6 + - - +
372B LEU* 3.1 30.0 + - - +
396B ILE* 4.1 8.9 - - + +
399B ASP* 3.7 18.6 + - - +
400B MET* 4.0 27.3 - - + +
403B ASP* 2.8 37.4 + - - +
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Residues in contact with ALA 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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366B GLY* 3.4 16.6 + - - +
367B ASP 3.3 0.4 - - - -
368B ARG* 1.3 77.8 - - - +
370B LYS* 1.3 58.0 + - - +
372B LEU* 3.4 9.3 + - - +
373B ASP* 3.0 35.1 + - - +
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Residues in contact with LYS 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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355B TYR* 4.2 16.6 - - - +
359B LEU* 3.6 20.0 - - + -
366B GLY 3.0 17.4 + - - +
367B ASP* 3.1 6.0 + - - +
369B ALA* 1.3 74.2 - - - +
371B ALA* 1.3 59.4 + - - +
373B ASP* 3.2 11.9 + - + +
374B ILE* 2.9 49.5 + - + +
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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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356B ALA* 3.6 31.4 - - + +
359B LEU* 3.9 10.9 - - + +
360B ASN 4.4 2.2 - - - +
367B ASP 2.9 13.1 + - - +
368B ARG* 3.6 12.1 - - - +
370B LYS* 1.3 76.3 - - - +
372B LEU* 1.3 56.9 + - - +
374B ILE* 3.3 2.6 + - - +
375B MET* 2.9 33.8 + - - +
396B ILE* 3.9 17.3 - - + -
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Residues in contact with LEU 372 (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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368B ARG 3.1 23.0 + - - +
369B ALA* 3.7 7.9 - - - +
371B ALA* 1.3 75.4 - - - +
373B ASP* 1.3 58.5 + - - +
375B MET* 4.4 2.9 - - - +
376B ILE* 2.8 46.3 + - + +
393B VAL* 4.0 16.2 - - + -
396B ILE* 3.7 30.1 - - + -
397B TYR* 3.8 46.9 - - + +
400B MET* 4.3 11.9 - - + -
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Residues in contact with ASP 373 (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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369B ALA* 3.0 19.2 + - - +
370B LYS* 3.4 20.4 - - + +
372B LEU* 1.3 78.7 - - - +
374B ILE* 1.3 57.1 + - - +
377B PRO* 3.1 25.0 - - - +
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Residues in contact with ILE 374 (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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352B LYS* 3.9 51.1 + - + +
355B TYR* 3.5 35.0 - - + -
356B ALA* 4.4 6.3 - - + -
359B LEU* 3.6 18.2 - - + -
370B LYS* 2.9 36.1 + - - +
371B ALA* 3.5 6.7 - - - +
373B ASP* 1.3 78.5 - - - +
375B MET* 1.3 67.4 + - - +
377B PRO* 3.6 4.3 - - - +
378B MET* 3.6 21.1 + - + +
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Residues in contact with MET 375 (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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353B PHE* 4.2 7.0 - - + -
356B ALA* 3.5 20.4 - - + -
371B ALA 2.9 21.2 + - - +
372B LEU* 4.3 2.5 - - - +
374B ILE* 1.3 78.3 - - - +
376B ILE* 1.3 64.2 + - - +
378B MET* 3.1 24.7 + - + +
379B VAL* 3.1 25.4 + - + +
389B MET* 3.8 51.1 - - + +
392B LEU* 3.8 26.5 - - + -
393B VAL* 3.6 17.9 - - + -
396B ILE* 4.5 4.9 - - + -
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Residues in contact with ILE 376 (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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372B LEU* 2.8 39.1 + - + +
375B MET* 1.3 71.3 - - - +
377B PRO* 1.3 61.4 - - + +
379B VAL* 3.3 1.2 + - - +
380B GLN* 2.8 59.0 + - - +
393B VAL* 4.1 13.2 - - + -
397B TYR* 3.7 24.0 - - - +
418B TRP* 4.0 23.6 - - + +
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Residues in contact with PRO 377 (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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372B LEU 3.8 0.2 - - - +
373B ASP* 3.1 30.7 - - - +
374B ILE 3.6 5.6 - - - +
376B ILE* 1.3 96.9 - - + +
378B MET* 1.3 57.8 + - - +
380B GLN* 4.8 0.9 - - + -
381B SER* 2.7 47.0 + - - +
382B GLU* 3.1 5.0 + - - +
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Residues in contact with MET 378 (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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349B HIS* 3.8 55.0 - - + +
352B LYS* 4.1 31.0 - - + +
353B PHE 4.2 1.3 - - - +
374B ILE* 3.6 13.4 + - + +
375B MET* 3.1 44.0 + - + +
377B PRO* 1.3 77.2 - - - +
379B VAL* 1.3 65.0 + - + +
382B GLU* 3.3 27.8 - - + +
385B VAL 5.0 3.6 + - - -
389B MET* 3.9 13.5 - - - +
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Residues in contact with VAL 379 (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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375B MET* 3.1 15.0 + - + +
376B ILE 3.7 4.9 - - - +
378B MET* 1.3 77.3 - - + +
380B GLN* 1.3 71.3 + - + +
382B GLU 4.3 4.9 + - - +
385B VAL 4.5 13.7 + - - +
389B MET* 4.0 36.3 - - + +
390B TYR* 3.3 38.4 - - + +
393B VAL* 4.5 2.7 - - + -
418B TRP* 3.6 24.0 - - + -
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Residues in contact with GLN 380 (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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376B ILE* 2.8 36.3 + - - +
377B PRO* 4.8 1.1 - - + +
379B VAL* 1.3 80.2 - - + +
381B SER* 1.3 64.5 + - - +
382B GLU* 3.3 1.6 + - - -
418B TRP* 3.8 29.8 - - + -
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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