Contacts of the helix formed by residues 366 - 380 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A LEU 3.0 1.0 + - - -
365A PRO* 1.3 70.8 - - - +
367A ASP* 1.3 64.6 + - - +
368A ARG 3.4 2.4 - - - +
369A ALA* 3.5 14.1 + - - +
370A LYS* 3.0 25.5 + - - +
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Residues in contact with ASP 367 (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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359A LEU* 3.3 38.5 - - + +
362A ARG* 2.8 45.4 + - - +
363A ASN* 3.2 6.8 + - - -
364A LEU* 2.8 39.9 + - - +
365A PRO 3.4 2.3 - - - +
366A GLY* 1.3 77.5 - - - +
368A ARG* 1.3 59.2 + - - +
370A LYS* 3.2 6.0 + - - +
371A ALA 2.9 23.9 + - - -
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Residues in contact with ARG 368 (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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359A LEU 4.7 0.7 - - - +
360A ASN* 2.8 52.3 + - - +
361A ARG* 3.6 20.8 + - - +
363A ASN* 3.3 35.6 + - - +
364A LEU 4.6 0.6 + - - -
366A GLY 3.4 0.4 - - - -
367A ASP* 1.3 71.9 - - - +
369A ALA* 1.3 64.7 + - - +
371A ALA* 3.3 7.3 + - - +
372A LEU* 3.1 29.8 + - - +
396A ILE* 4.1 8.6 - - + +
399A ASP* 3.7 18.3 + - - +
400A MET* 4.0 27.8 - - + +
403A ASP* 2.8 37.2 + - - +
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Residues in contact with ALA 369 (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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366A GLY* 3.5 17.1 + - - +
367A ASP 3.3 0.4 - - - -
368A ARG* 1.3 78.0 - - - +
370A LYS* 1.3 56.9 + - - +
372A LEU* 3.4 9.9 + - - +
373A ASP* 3.0 28.6 + - - +
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Residues in contact with LYS 370 (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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355A TYR* 4.2 16.8 - - - +
359A LEU* 3.6 19.7 - - + -
366A GLY 3.0 18.3 + - - +
367A ASP* 3.5 5.4 - - - +
369A ALA* 1.3 73.0 - - - +
371A ALA* 1.3 60.4 + - - +
373A ASP* 3.2 11.2 + - + +
374A ILE* 2.9 49.4 + - + +
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Residues in contact with ALA 371 (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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356A ALA* 3.6 30.3 - - + +
359A LEU* 3.9 11.2 - - + +
360A ASN 4.4 2.2 - - - +
367A ASP 2.9 12.9 + - - +
368A ARG* 3.6 12.6 - - - +
369A ALA 3.3 0.2 - - - -
370A LYS* 1.3 77.3 - - - +
372A LEU* 1.3 56.7 + - - +
374A ILE* 3.3 3.8 + - - +
375A MET* 2.9 35.1 + - - +
396A ILE* 3.9 16.4 - - + -
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Residues in contact with LEU 372 (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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368A ARG 3.1 20.8 + - - +
369A ALA* 3.7 8.1 - - - +
371A ALA* 1.3 76.0 - - - +
373A ASP* 1.3 58.4 + - - +
375A MET* 4.4 2.2 - - - +
376A ILE* 2.8 45.8 + - + +
393A VAL* 4.0 16.4 - - + -
396A ILE* 3.7 30.3 - - + -
397A TYR* 3.8 46.7 - - + +
400A MET* 4.3 11.7 - - + -
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Residues in contact with ASP 373 (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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369A ALA 3.0 15.3 + - - +
370A LYS* 3.2 17.2 + - + +
372A LEU* 1.3 75.6 - - - +
374A ILE* 1.3 58.2 + - - +
376A ILE* 5.5 0.2 - - - -
377A PRO* 3.1 27.7 - - - +
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Residues in contact with ILE 374 (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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352A LYS* 3.9 50.2 + - + +
355A TYR* 3.5 34.8 - - + -
356A ALA* 4.4 6.7 - - + -
359A LEU* 3.5 17.9 - - + -
370A LYS* 2.9 36.1 + - - +
371A ALA* 3.5 7.0 - - - +
373A ASP* 1.3 78.4 - - - +
375A MET* 1.3 66.8 + - - +
377A PRO* 3.6 4.0 - - - +
378A MET* 3.6 21.9 + - + +
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Residues in contact with MET 375 (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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353A PHE* 4.2 7.4 - - + -
356A ALA* 3.5 20.0 - - + -
371A ALA 2.9 23.4 + - - +
372A LEU* 4.3 2.5 - - - +
374A ILE* 1.3 74.4 - - - +
376A ILE* 1.3 65.0 + - - +
378A MET* 3.1 24.5 + - + +
379A VAL* 3.1 26.8 + - + +
389A MET* 3.8 50.5 - - + +
392A LEU* 3.8 25.4 - - + -
393A VAL* 3.6 18.4 - - + -
396A ILE* 4.5 5.6 - - + -
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Residues in contact with ILE 376 (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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372A LEU* 2.8 40.2 + - + +
373A ASP* 5.5 0.2 - - - -
375A MET* 1.3 72.4 - - - +
377A PRO* 1.4 62.1 - - + +
379A VAL* 3.3 0.9 + - - +
380A GLN* 2.8 58.2 + - + +
393A VAL* 4.1 14.8 - - + -
397A TYR* 3.7 23.8 - - - +
418A TRP* 4.1 21.8 - - + +
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Residues in contact with PRO 377 (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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372A LEU 3.7 0.2 - - - +
373A ASP* 3.1 33.4 - - - +
374A ILE 3.6 5.4 - - - +
376A ILE* 1.4 96.8 - - + +
378A MET* 1.3 60.8 + - - +
379A VAL 3.5 0.3 + - - -
380A GLN* 3.6 19.7 - - + +
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Residues in contact with MET 378 (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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349A HIS* 3.7 54.5 - - + +
352A LYS* 4.1 31.0 - - + +
353A PHE 4.2 1.3 - - - +
374A ILE* 3.6 12.8 + - + +
375A MET* 3.1 44.6 + - + +
377A PRO* 1.3 78.3 - - - +
379A VAL* 1.3 64.0 + - + +
380A GLN 4.8 0.2 - - - -
385A VAL* 4.7 5.5 - - - +
389A MET* 3.9 14.6 - - - +
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Residues in contact with VAL 379 (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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375A MET* 3.1 15.5 + - + +
376A ILE 3.7 4.7 - - - +
378A MET* 1.3 78.2 - - + +
380A GLN* 1.3 69.8 + - + +
385A VAL* 3.6 36.9 - - + +
389A MET* 4.0 27.1 - - + +
390A TYR* 3.3 34.3 - - + +
393A VAL* 4.5 2.7 - - + -
418A TRP* 3.6 23.8 - - + -
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Residues in contact with GLN 380 (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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376A ILE* 2.8 37.8 + - - +
377A PRO* 3.6 16.6 - - + +
378A MET 4.8 0.4 - - - -
379A VAL* 1.3 82.4 - - + +
418A TRP* 3.8 28.2 - - + -
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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