Contacts of the helix formed by residues 348 - 363 (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 HIS 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ALA* 3.8 22.0 - - + +
343A PHE* 3.4 33.4 - + + -
344A ASP* 3.0 28.4 + - - +
345A LEU 2.9 10.5 + - - +
347A SER* 1.3 84.3 + - - +
349A HIS* 1.3 64.9 + - - +
350A HIS 3.3 2.9 - - - -
351A VAL* 3.2 21.0 + - + +
352A LYS* 3.1 23.6 + - - +
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Residues in contact with HIS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA 3.4 24.0 + - - -
347A SER* 3.5 12.1 + - - -
348A HIS* 1.3 72.1 - - - +
350A HIS* 1.3 63.4 + - + +
352A LYS* 3.3 5.3 + - + +
353A PHE* 2.9 27.4 + - - +
378A MET* 3.7 34.6 - - + +
389A MET* 4.3 11.1 - - + +
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Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 4.0 14.6 - - + -
348A HIS 3.3 0.4 - - - -
349A HIS* 1.3 80.8 - - + +
351A VAL* 1.3 64.1 + - - +
353A PHE* 3.3 6.8 + - + +
354A HIS* 3.0 37.1 + - + +
389A MET* 4.1 18.6 - - + +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA* 4.9 5.2 - - + -
314A VAL* 4.1 27.1 - - + -
315A ILE* 3.7 26.5 - - + -
318A LEU* 4.2 11.0 - - + +
334A VAL* 4.2 11.0 - - + -
337A LEU* 4.8 4.0 - - + -
343A PHE* 4.8 5.4 - - + -
345A LEU* 3.6 20.4 - - + -
348A HIS* 3.2 28.1 + - + +
350A HIS* 1.3 75.1 - - - +
352A LYS* 1.3 58.7 + - - +
354A HIS* 3.3 2.9 + - - +
355A TYR* 3.0 26.2 + - - +
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.4 41.7 - - + +
346A ALA* 3.9 26.1 + - - +
348A HIS 3.1 15.7 + - - +
349A HIS* 3.6 7.4 - - - +
351A VAL* 1.3 72.4 - - - +
353A PHE* 1.3 66.5 + - - +
355A TYR* 3.2 8.6 + - + +
356A ALA* 3.0 25.5 + - - +
374A ILE* 3.9 35.3 + - + +
378A MET* 4.1 26.7 - - + +
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Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 5.1 4.9 - - - -
349A HIS 2.9 13.9 + - - +
350A HIS* 3.4 13.2 - - + +
351A VAL 3.2 0.2 - - - -
352A LYS* 1.3 77.1 - - - +
354A HIS* 1.3 80.5 + + - +
356A ALA 3.3 0.2 + - - -
357A PHE* 2.9 48.4 + + + +
375A MET* 4.2 11.0 - - + -
378A MET* 4.2 0.4 - - - +
388A ASP* 3.5 39.3 - - + -
389A MET* 4.0 28.7 - - + -
392A LEU* 3.6 27.5 - - + +
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Residues in contact with HIS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 4.0 19.9 - - + +
318A LEU* 3.8 31.9 - - + +
319A LEU* 3.7 32.2 - - + +
322A ARG* 4.0 24.9 + - - +
330A ILE* 4.0 6.7 - - + +
350A HIS* 3.0 36.0 + - + +
351A VAL 3.3 0.4 + - - +
353A PHE* 1.3 92.0 - + - +
355A TYR* 1.3 56.5 - - - +
357A PHE* 3.6 7.9 - - - +
358A ALA* 3.0 29.1 + - - +
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Residues in contact with TYR 355 (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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318A LEU* 5.0 0.2 - - - +
330A ILE* 4.6 1.3 - - - +
331A VAL* 4.1 26.5 - - + -
334A VAL* 3.4 39.3 - - + -
335A GLU* 3.6 22.9 + - + +
338A GLU* 6.0 1.9 - - + +
345A LEU* 4.4 15.0 - - + -
351A VAL 3.0 17.5 + - - +
352A LYS* 3.4 9.2 - - + +
354A HIS* 1.3 74.2 - - - +
356A ALA* 1.3 53.6 + - - +
358A ALA* 3.2 5.4 + - - +
359A LEU* 2.8 62.1 + - + +
370A LYS* 4.2 16.9 - - - +
374A ILE* 3.5 27.6 - - + -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS 3.0 15.2 + - - +
353A PHE 3.7 3.8 - - - +
355A TYR* 1.3 73.1 - - - +
357A PHE* 1.3 61.6 + - - +
359A LEU* 3.2 7.1 + - - +
360A ASN* 2.9 31.8 + - - +
371A ALA* 3.6 24.0 - - + +
374A ILE* 4.4 5.4 - - + -
375A MET* 3.5 33.0 - - + -
392A LEU* 4.0 4.0 - - + -
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Residues in contact with PHE 357 (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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322A ARG* 4.0 19.3 - - - -
327A TYR* 3.8 32.5 - + - -
330A ILE* 6.3 0.4 - - + -
353A PHE* 2.9 35.0 + + + +
354A HIS* 3.6 11.0 - - - +
356A ALA* 1.3 78.0 - - - +
358A ALA* 1.3 56.3 + - - +
360A ASN* 3.3 4.6 + - - +
361A ARG* 3.0 33.3 + - + +
392A LEU* 3.8 28.1 - - + +
395A ARG* 3.3 31.0 - - - -
509A TRP* 3.7 31.2 - + + -
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Residues in contact with ALA 358 (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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327A TYR* 3.7 31.2 - - + +
330A ILE* 3.6 30.1 - - + -
331A VAL* 4.0 5.6 - - + -
354A HIS 3.0 18.4 + - - +
355A TYR 3.6 4.7 - - - +
357A PHE* 1.3 75.2 - - - +
359A LEU* 1.3 59.4 + - - +
361A ARG 3.3 0.5 + - - -
362A ARG* 2.8 32.1 + - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 3.8 29.2 - - + -
335A GLU* 5.6 0.4 - - - +
355A TYR* 2.8 36.1 + - + +
356A ALA* 3.2 5.6 + - - +
358A ALA* 1.3 71.1 - - - +
360A ASN* 1.3 58.9 + - - +
362A ARG* 3.2 2.4 + - - +
363A ASN* 2.9 28.2 + - - -
367A ASP* 3.3 43.1 - - + +
370A LYS* 3.6 19.7 - - + -
371A ALA* 3.9 9.4 - - + +
374A ILE* 3.5 31.6 - - + -
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Residues in contact with ASN 360 (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 2.9 18.1 + - - +
357A PHE* 3.6 6.2 + - - +
358A ALA 3.3 0.2 - - - -
359A LEU* 1.3 77.2 - - - +
361A ARG* 1.3 67.3 + - - +
363A ASN* 3.6 2.1 - - - +
368A ARG* 2.8 70.2 + - + +
371A ALA* 4.4 1.9 - - + +
392A LEU* 5.2 3.2 - - + +
395A ARG* 4.2 9.7 + - - +
396A ILE* 3.6 36.6 - - + +
399A ASP* 2.8 27.3 + - - +
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Residues in contact with ARG 361 (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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327A TYR* 3.5 46.4 - - + +
357A PHE* 3.0 26.2 + - + +
359A LEU 3.3 0.2 - - - -
360A ASN* 1.3 80.0 - - - +
362A ARG* 1.3 65.1 + - - +
363A ASN* 4.0 3.1 - - - +
368A ARG* 3.6 14.9 + - - +
395A ARG* 3.6 26.2 - - - +
399A ASP* 2.7 33.1 + - - -
403A ASP* 5.0 3.4 + - - -
512A LYS* 3.4 35.9 - - - +
516A GLU* 3.1 13.4 + - - -
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Residues in contact with ARG 362 (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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327A TYR* 4.3 8.7 - - + +
328A ASP* 2.9 46.6 + - + +
331A VAL* 3.6 35.4 - - + +
332A LYS* 4.5 10.5 - - - +
335A GLU* 4.6 6.5 + - - -
358A ALA 2.8 22.5 + - - +
359A LEU* 3.8 2.3 - - - +
361A ARG* 1.3 72.5 - - - +
363A ASN* 1.3 71.5 + - - +
364A LEU* 3.2 35.3 + - + +
367A ASP* 2.8 36.1 + - - +
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Residues in contact with ASN 363 (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 2.9 15.2 + - - -
360A ASN 3.6 13.9 - - - +
361A ARG 4.0 3.1 - - - +
362A ARG* 1.3 78.6 - - - +
364A LEU* 1.3 68.5 + - - +
365A PRO* 4.6 1.0 - - - +
367A ASP* 3.2 5.8 + - - -
368A ARG* 3.3 46.1 + - - +
403A ASP* 4.1 7.9 + - - +
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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
------------------------------------------------------------
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