Contacts of the helix formed by residues 355 - 369 (chain A) in PDB entry 4I6J
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 PHE 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A THR* 3.0 17.4 + - - +
354A GLY* 1.3 79.5 - - - +
356A PRO* 1.3 70.8 - - + +
357A TRP 3.2 1.1 - - - -
358A ILE* 2.9 17.8 + - + -
359A ASP* 2.8 21.8 + - - -
382A PHE* 3.8 24.7 - + - -
433A PRO* 3.3 35.4 - - + +
434A VAL* 4.1 10.1 - - + -
466A TRP* 3.9 26.2 - + - -
484A TYR* 3.2 3.1 - - - -
487A PRO* 3.9 7.9 - - + -
488A ILE* 4.1 14.8 - - + -
489A VAL* 3.6 36.6 - - + -
491A HIS* 4.9 7.0 - - + -
317B ARG* 6.2 0.2 - - - -
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Residues in contact with PRO 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLY 3.0 8.3 - - - +
355A PHE* 1.3 80.9 - - - +
357A TRP* 1.3 56.8 + - - +
360A ALA* 2.6 37.2 + - - +
447A ILE* 3.3 32.3 - - + -
451A LEU* 3.4 7.6 - - + -
454A LEU* 4.2 5.2 - - + -
462A ILE 3.0 22.0 - - - +
463A TYR* 4.1 8.7 - - - +
465A PRO* 3.6 20.9 - - + -
466A TRP* 4.3 0.7 - - + -
484A TYR* 3.0 22.7 - - + +
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Residues in contact with TRP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.6 16.8 - - + -
355A PHE 3.2 0.2 - - - -
356A PRO* 1.3 79.8 - - - +
358A ILE* 1.3 76.7 + - + +
360A ALA* 3.6 2.4 - - - +
361A ILE* 3.0 44.9 + - + +
374A LEU* 5.4 0.9 - - + -
375A ALA* 4.7 6.3 - - + -
378A ALA* 3.4 22.3 - - + +
432A CYS 4.2 6.5 - - - -
433A PRO* 3.4 24.0 + - + +
436A PHE* 3.7 13.8 - + - -
437A GLY* 3.4 35.4 - - - +
440A THR* 4.1 27.4 - - + -
441A ASP* 5.4 2.0 - - + -
446A TYR* 3.8 29.2 - + + -
447A ILE* 3.5 6.6 - - - +
463A TYR* 4.0 24.1 + + + +
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TRP* 4.3 9.0 - - + -
353A THR* 3.6 29.6 - - + +
355A PHE* 2.9 22.0 + - + +
357A TRP* 1.3 89.0 - - + +
359A ASP* 1.3 61.8 + - - +
361A ILE* 3.1 8.8 + - + +
362A MET* 3.0 24.1 + - + +
378A ALA* 3.9 27.6 - - + +
379A VAL* 4.2 13.2 - - + -
382A PHE* 4.0 32.3 - - + -
433A PRO* 4.3 8.7 - - + -
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Residues in contact with ASP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLY* 3.0 34.6 - - - +
352A LYS* 4.3 0.2 - - - -
353A THR* 2.3 57.8 + - - +
355A PHE 2.8 11.1 + - - +
358A ILE* 1.3 69.1 - - - +
360A ALA* 1.3 66.5 + - - +
362A MET* 4.2 0.3 - - - +
363A THR* 2.8 32.0 + - - +
451A LEU* 3.7 20.0 - - + -
484A TYR* 2.9 18.7 + - - -
485A PRO* 5.3 0.5 - - - +
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Residues in contact with ALA 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 PRO 2.6 24.7 + - - +
357A TRP 3.6 1.8 - - - +
359A ASP* 1.3 73.2 - - - +
361A ILE* 1.3 64.3 + - - +
363A THR* 3.6 1.4 - - - -
364A GLN* 3.0 20.4 + - - +
446A TYR* 3.3 33.5 + - + -
447A ILE* 4.2 15.9 - - + -
450A TYR* 3.9 11.0 - - + +
451A LEU* 3.6 14.2 - - + +
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Residues in contact with ILE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TRP* 3.0 38.2 + - + +
358A ILE* 3.1 1.3 + - - +
360A ALA* 1.3 77.5 - - - +
362A MET* 1.3 58.9 + - - +
363A THR 3.1 0.7 + - - -
364A GLN* 3.1 2.8 + - - +
365A LEU* 2.9 26.0 + - - +
371A ILE* 3.4 31.8 - - + +
375A ALA* 3.4 30.1 - - + +
378A ALA* 5.1 1.1 - - + -
379A VAL* 3.4 32.8 - - + -
446A TYR* 3.2 30.5 - - + +
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Residues in contact with MET 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TRP* 3.2 53.2 - - + +
349A ALA* 4.1 14.1 - - - +
350A GLU 5.9 0.9 - - - -
351A GLY* 4.1 14.8 - - - +
358A ILE* 3.0 22.8 + - + +
359A ASP 3.3 2.0 + - - +
361A ILE* 1.3 77.0 - - - +
363A THR* 1.3 61.8 + - - +
365A LEU* 3.3 31.0 - - + +
366A ARG* 3.1 24.1 + - - +
379A VAL* 3.6 35.7 - - + -
398A VAL* 4.3 5.4 - - + -
402A LEU* 5.2 1.7 - - + +
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Residues in contact with THR 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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350A GLU 5.1 2.0 + - - -
351A GLY* 4.8 6.9 + - - -
359A ASP* 2.8 23.4 + - - -
360A ALA 3.6 3.4 - - - -
362A MET* 1.3 75.8 - - - +
364A GLN* 1.3 68.4 + - - +
365A LEU 3.1 0.2 + - - -
366A ARG* 3.2 4.7 + - - +
367A GLN* 2.8 58.3 + - + +
450A TYR* 3.7 24.7 - - + +
451A LEU* 4.2 9.5 - - - +
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Residues in contact with GLN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.2 22.3 + - - +
263A LEU* 4.3 1.4 - - - +
264A ALA 4.1 10.3 - - - +
360A ALA 3.0 13.1 + - - +
361A ILE 3.6 6.1 - - - +
363A THR* 1.3 76.9 - - - +
365A LEU* 1.3 63.9 + - - +
367A GLN* 4.4 1.3 - - - -
368A GLU* 2.9 38.0 + - - +
369A GLY 3.9 0.5 + - - -
370A TRP* 3.7 19.7 + - - +
371A ILE* 3.9 10.7 - - - +
372A HIS 5.1 0.5 + - - -
446A TYR* 2.9 22.6 + - - +
450A TYR* 3.4 47.6 + - + +
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Residues in contact with LEU 365 (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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68A ASN* 4.5 0.2 + - - -
361A ILE 2.9 13.1 + - - +
362A MET* 3.3 39.5 - - + +
363A THR 3.1 0.2 - - - -
364A GLN* 1.3 75.2 - - - +
366A ARG* 1.3 59.4 + - - +
369A GLY* 2.9 34.5 + - - -
370A TRP 4.7 0.7 - - - -
371A ILE* 3.6 23.2 - - + +
398A VAL* 5.0 0.2 - - + -
399A PHE* 3.6 27.8 - - + -
402A LEU* 3.7 38.1 - - + +
403A LEU* 4.2 18.6 - - + +
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Residues in contact with ARG 366 (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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67A ILE* 4.8 8.3 - - + +
68A ASN* 3.2 13.3 + - - -
349A ALA* 2.9 36.4 + - - +
350A GLU* 3.3 24.4 + - - +
362A MET 3.1 12.0 + - - +
363A THR* 3.9 4.5 - - - +
365A LEU* 1.3 78.9 - - - +
367A GLN* 1.3 63.6 + - + +
398A VAL* 4.9 2.0 - - - +
401A GLU* 5.9 1.2 + - - -
402A LEU* 3.6 48.1 - - + +
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Residues in contact with GLN 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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68A ASN* 3.1 14.4 + - - +
227A VAL* 5.4 0.7 - - - +
363A THR* 2.8 43.0 + - + +
364A GLN* 3.8 2.9 - - - +
366A ARG* 1.3 80.0 - - + +
368A GLU* 1.3 69.1 + - + +
450A TYR* 3.7 23.7 + - - +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 3.6 10.6 + - - +
227A VAL* 3.3 46.1 + - + +
228A TRP* 3.6 18.8 + - - +
264A ALA* 4.1 8.1 + - - +
364A GLN* 2.9 31.0 + - + +
367A GLN* 1.3 82.1 - - + +
369A GLY* 1.3 62.0 + - - +
370A TRP 3.5 5.3 - - - +
404A LEU* 3.9 5.0 - - - +
449A ARG* 4.9 5.9 + - - -
450A TYR* 2.6 38.8 + - - -
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Residues in contact with GLY 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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68A ASN* 3.6 7.0 - - - +
365A LEU* 2.9 12.1 + - - -
368A GLU* 1.3 78.1 - - - +
370A TRP* 1.3 60.0 + - - +
402A LEU 3.4 20.6 - - - -
403A LEU* 3.3 8.5 - - - +
404A LEU* 2.8 39.7 + - - +
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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