Contacts of the helix formed by residues 346 - 360 (chain A) in PDB entry 5JAJ
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 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ARG* 3.6 19.9 + - - +
294A ASN 3.3 6.1 + - - -
295A ASP* 3.0 26.5 + - - +
296A THR 3.4 9.7 + - - -
297A VAL* 2.8 28.8 + - - +
298A ARG* 5.3 1.5 - - - +
345A GLU* 1.3 74.1 - - - +
347A PRO* 1.4 67.7 - - - +
348A ARG* 3.0 25.6 + - - +
349A LEU* 2.9 32.1 + - + +
350A SER* 3.1 11.6 + - - -
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Residues in contact with PRO 347 (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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221A CYS* 3.9 11.5 - - + +
222A GLN* 3.3 31.0 - - + +
223A GLU 4.3 0.7 - - - +
224A ARG* 3.8 30.3 - - + +
345A GLU 3.3 9.8 - - - +
346A ASN* 1.4 89.4 - - - +
348A ARG* 1.3 54.8 + - - +
350A SER* 3.6 11.1 - - - +
351A LYS* 3.0 29.6 + - - +
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Residues in contact with ARG 348 (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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221A CYS* 3.6 22.2 - - - -
295A ASP* 2.8 46.7 + - - -
296A THR* 3.9 15.7 + - - +
346A ASN* 3.0 13.2 + - - +
347A PRO* 1.3 77.3 - - - +
349A LEU* 1.3 57.7 + - - +
351A LYS* 3.4 3.5 + - - +
352A LEU* 3.0 26.5 + - - +
454A TYR* 3.3 25.0 - - + +
455A GLY* 4.0 24.2 + - - -
480A LEU* 3.9 11.7 + - + +
481A ALA* 4.4 3.6 - - - +
482A LYS* 3.6 41.4 - - + +
487A GLU* 5.7 5.5 + - - -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.7 22.9 - - + +
298A ARG* 3.6 32.1 - - + -
345A GLU* 4.1 8.5 - - + +
346A ASN* 2.9 19.1 + - + +
348A ARG* 1.3 74.6 - - - +
350A SER* 1.3 60.6 + - - +
351A LYS 3.2 0.2 - - - -
352A LEU* 3.2 3.9 + - + +
353A GLU* 2.8 26.5 + - - +
381A LEU* 3.5 24.9 - - + -
384A TRP* 3.4 41.0 - - + +
454A TYR* 3.4 21.3 - - + +
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Residues in contact with SER 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU* 3.1 33.9 + - - +
346A ASN 3.1 7.9 + - - -
347A PRO* 3.4 15.1 + - - +
349A LEU* 1.3 76.6 - - - +
351A LYS* 1.3 60.9 + - - +
353A GLU* 3.4 8.2 + - - +
354A GLU* 3.1 30.4 + - - +
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Residues in contact with LYS 351 (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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219A ASP* 4.0 31.4 + - + +
220A LEU 3.6 22.1 + - - +
221A CYS* 4.5 5.4 - - + +
347A PRO 3.0 17.7 + - - +
348A ARG 3.7 4.5 - - - +
349A LEU 3.2 0.2 - - - -
350A SER* 1.3 74.9 - - - +
352A LEU* 1.3 66.1 + - - +
354A GLU* 2.9 34.0 + - + +
355A ILE* 3.1 22.1 + - + +
480A LEU* 3.9 24.9 - - + -
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG 3.0 17.3 + - - +
349A LEU* 3.2 6.2 + - + +
351A LYS* 1.3 76.3 - - - +
353A GLU* 1.3 62.0 + - - +
355A ILE* 3.1 6.2 + - + +
356A LEU* 3.0 38.7 + - + +
370A VAL* 4.3 19.1 - - + -
381A LEU* 4.1 22.7 - - + -
384A TRP* 3.7 26.0 - - + -
434A PHE* 4.5 11.9 - - + -
452A VAL* 4.4 13.9 - - + -
454A TYR* 4.1 11.7 - - + -
480A LEU* 3.6 18.8 - - + +
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU* 4.4 12.6 - - - +
349A LEU 2.8 16.9 + - - +
350A SER* 3.6 7.2 - - - +
352A LEU* 1.3 75.9 - - - +
354A GLU* 1.3 58.2 + - + +
356A LEU* 3.3 0.3 + - - -
357A GLN* 2.8 62.5 + - - +
384A TRP* 3.7 15.7 - - + -
388A THR* 3.5 19.8 - - - +
390A GLY* 3.4 18.5 + - - -
391A LEU* 4.0 15.9 - - + +
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Residues in contact with GLU 354 (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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350A SER* 3.1 17.9 + - - +
351A LYS* 2.9 44.4 + - + +
353A GLU* 1.3 74.8 - - - +
355A ILE* 1.3 63.5 + - + +
357A GLN* 3.5 12.1 + - - +
358A GLU* 3.0 26.1 + - - +
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Residues in contact with ILE 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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217A GLN* 4.9 2.5 - - - +
219A ASP* 3.5 35.9 - - + +
351A LYS* 3.1 13.0 + - + +
352A LEU* 3.1 7.8 + - + +
354A GLU* 1.3 76.1 - - + +
356A LEU* 1.3 70.3 + - + +
358A GLU* 3.3 3.1 + - - -
359A HIS* 3.0 46.1 + - + +
450A ILE* 5.4 2.5 - - + -
452A VAL* 4.2 23.3 - - + -
476A MET* 4.4 10.1 - - + -
478A SER* 3.5 11.7 - - - +
480A LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 356 (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 LEU* 3.0 43.2 + - + +
355A ILE* 1.3 83.0 - - + +
357A GLN* 1.3 57.4 + - - +
360A PHE* 2.9 63.5 + - + +
370A VAL* 4.7 5.2 - - + -
384A TRP* 4.2 15.5 - - + -
385A LEU* 4.4 6.1 - - + -
391A LEU* 3.8 24.2 - - + -
394A GLN* 4.1 0.5 - - - +
396A ILE* 4.5 3.6 - - + -
432A LEU* 4.2 29.6 - - + -
434A PHE* 4.9 2.9 - - + -
450A ILE* 6.4 1.1 - - + -
452A VAL* 5.5 2.2 - - + -
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Residues in contact with GLN 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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353A GLU* 2.8 50.3 + - + +
354A GLU* 3.7 13.1 - - - +
356A LEU* 1.3 74.0 - - - +
358A GLU* 1.3 61.8 + - - +
360A PHE 4.2 0.2 + - - -
361A GLN* 3.2 32.2 - - - +
390A GLY* 3.1 22.2 + - - -
391A LEU* 3.7 13.4 - - + +
394A GLN* 3.4 19.2 - - - +
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Residues in contact with GLU 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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217A GLN* 5.9 1.0 + - - -
354A GLU 3.0 18.2 + - - +
355A ILE* 3.7 5.0 - - - +
357A GLN* 1.3 79.8 - - - +
359A HIS* 1.3 85.5 + - + +
361A GLN* 4.5 7.8 + - - +
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Residues in contact with HIS 359 (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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217A GLN* 4.6 6.6 + - - -
355A ILE* 3.0 32.3 + - + +
358A GLU* 1.3 106.3 + - + +
360A PHE* 1.3 63.5 + - + +
361A GLN 3.4 4.0 + - - +
365A SER* 3.8 7.6 + - - -
366A SER* 2.5 26.5 + - - -
450A ILE* 3.4 28.7 - - + +
476A MET* 3.2 39.3 - - + +
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Residues in contact with PHE 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 LEU* 2.9 47.2 + - + +
359A HIS* 1.3 80.7 - - + +
361A GLN* 1.3 58.2 + - - +
364A GLY 4.6 11.0 - - - +
365A SER* 4.8 3.4 - - - -
366A SER* 3.4 38.8 - - - -
368A GLY* 3.9 12.6 - - - -
394A GLN* 3.0 33.0 - - - +
396A ILE* 3.9 28.7 - - + -
431A ASN* 3.5 32.3 - - - -
432A LEU* 4.0 14.6 - - + -
450A ILE* 4.1 12.6 - - + -
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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