Contacts of the helix formed by residues 352 - 373 (chain A) in PDB entry 4RG1
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 ARG 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASN* 5.3 16.0 + - - +
87A ALA* 5.7 4.6 - - - +
96A LEU* 4.5 14.8 - - - +
350A THR* 5.2 2.9 - - - +
351A ILE* 1.3 74.4 - - - +
353A THR* 1.3 67.3 + - - +
354A GLU* 2.6 42.6 + - - +
355A GLU* 2.8 30.6 + - - +
356A ALA* 2.8 21.6 + - - +
401A SAH 4.9 1.3 - - - -
95B TYR* 3.5 12.1 + - - -
102B ARG* 4.1 10.5 - - - +
173B ASN* 3.0 41.2 + - - +
402B PGO 4.7 0.6 - - - -
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Residues in contact with THR 353 (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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79A LEU* 4.2 7.9 - - + -
83A ILE* 3.6 37.0 - - + +
311A PHE* 4.2 12.1 - - + -
312A GLY 2.8 28.3 + - - +
313A GLY* 3.7 2.8 - - - -
351A ILE 3.8 1.2 + - - -
352A ARG* 1.3 71.2 - - - +
354A GLU* 1.3 60.1 + - - +
356A ALA* 3.2 3.5 + - - +
357A ILE* 3.0 43.4 + - + +
401A SAH 3.5 18.0 - - - +
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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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83A ILE* 4.9 2.4 - - - +
96A LEU* 3.5 30.1 - - + +
99A GLN* 3.6 32.9 + - + +
100A ILE* 3.7 19.9 - - + +
103A ALA* 5.0 2.6 - - - +
352A ARG* 2.6 51.8 + - - +
353A THR* 1.3 79.4 + - - +
355A GLU* 1.3 67.7 + - + +
357A ILE* 3.7 9.4 + - - +
358A LEU* 3.7 18.9 + - - +
95B TYR* 4.1 5.5 + - - -
402B PGO 5.7 0.7 - - - -
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Residues in contact with GLU 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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351A ILE* 3.7 9.1 - - + -
352A ARG* 2.8 34.5 + - + +
354A GLU* 1.3 80.1 - - + +
356A ALA* 1.3 65.8 + - - +
358A LEU* 3.2 5.2 + - - +
359A ILE* 3.0 27.2 + - + +
99B GLN* 5.5 0.3 - - - +
102B ARG* 2.8 56.7 + - - +
106B ILE* 3.6 15.6 - - + +
358B LEU* 4.1 23.4 - - + +
402B PGO 4.0 7.1 + - - -
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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
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311A PHE* 3.8 6.3 - - + -
351A ILE* 3.6 10.9 - - + +
352A ARG 2.8 12.6 + - - +
353A THR 3.5 4.5 - - - +
355A GLU* 1.3 78.8 - - - +
357A ILE* 1.3 56.9 + - - +
359A ILE* 4.4 5.4 - - - -
360A SER* 2.7 37.1 + - - +
401A SAH 3.5 45.5 - - + +
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Residues in contact with ILE 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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77A VAL* 4.6 6.5 - - + -
79A LEU* 4.0 15.3 - - + -
100A ILE* 3.7 35.9 - - + -
103A ALA* 3.8 19.1 - - + -
104A CYS* 4.6 8.7 - - - -
311A PHE* 3.6 33.9 - - + -
353A THR* 3.0 21.8 + - + +
354A GLU 4.1 5.2 - - - +
355A GLU 3.2 0.8 - - - -
356A ALA* 1.3 76.3 - - - +
358A LEU* 1.3 64.1 + - - +
361A LEU* 3.0 46.6 + - + +
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Residues in contact with LEU 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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99A GLN 5.9 0.7 - - - +
103A ALA* 3.6 34.1 - - + -
106A ILE* 4.5 7.6 - - + -
107A PHE* 3.9 23.1 - - + -
354A GLU 3.7 10.0 + - - +
355A GLU 3.2 7.6 + - - +
357A ILE* 1.3 78.8 - - - +
359A ILE* 1.3 62.0 + - - +
362A ALA* 3.1 26.0 + - - +
355B GLU* 4.1 27.6 - - + +
358B LEU* 3.8 31.9 - - + -
359B ILE* 4.0 16.8 - - + +
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Residues in contact with ILE 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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342A THR* 3.6 28.3 - - - +
343A CYS* 4.1 6.5 - - + -
351A ILE* 4.1 20.9 - - + -
355A GLU 3.0 17.4 + - - +
356A ALA* 4.0 3.6 - - - +
358A LEU* 1.3 75.7 - - - +
360A SER* 1.3 60.3 + - - +
362A ALA* 3.4 2.1 + - - +
363A ALA* 2.9 27.4 + - - +
106B ILE* 3.9 19.1 - - + -
107B PHE* 3.8 40.4 - - + -
358B LEU* 4.0 18.6 - - + +
362B ALA* 3.8 11.5 - - + +
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Residues in contact with SER 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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289A THR* 4.0 9.4 - - - +
311A PHE* 3.6 23.4 - - - -
342A THR* 2.7 36.3 + - - +
356A ALA* 2.7 28.6 + - - -
359A ILE* 1.3 69.7 - - - +
361A LEU* 1.3 60.5 + - - +
363A ALA* 3.3 1.0 + - - +
364A LEU* 2.9 39.6 + - - +
401A SAH 4.1 4.7 + - - -
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Residues in contact with LEU 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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75A LEU* 4.5 12.6 - - + -
77A VAL* 4.1 13.0 - - + -
103A ALA 4.3 2.9 - - - +
104A CYS* 4.9 0.2 - - - -
107A PHE* 3.6 41.6 - - + -
109A VAL* 3.9 17.9 - - + -
309A VAL* 4.3 30.1 - - + -
311A PHE* 4.7 2.7 - - + -
357A ILE* 3.0 41.2 + - + +
360A SER* 1.3 74.1 - - - +
362A ALA* 1.3 59.5 + - - +
364A LEU* 3.7 4.8 - - + +
365A GLN* 2.9 31.5 + - - +
368A LEU* 5.2 4.8 - - + +
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Residues in contact with ALA 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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107A PHE* 3.6 19.6 - - + -
358A LEU 3.1 21.2 + - - +
359A ILE 3.6 3.8 - - - +
361A LEU* 1.3 76.4 - - - +
363A ALA* 1.3 63.2 + - - +
364A LEU 3.3 0.5 + - - -
365A GLN* 3.3 12.5 + - - +
366A PRO* 3.5 10.6 - - - +
342B THR 5.7 0.7 - - - +
359B ILE* 3.8 17.5 - - + +
362B ALA* 3.8 17.9 - - + -
363B ALA* 4.6 10.2 - - + +
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Residues in contact with ALA 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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296A VAL* 4.2 19.1 - - + +
342A THR* 4.0 27.8 - - + +
359A ILE 2.9 19.1 + - - +
360A SER 3.3 3.8 + - - +
362A ALA* 1.3 78.3 - - - +
364A LEU* 1.3 60.0 + - - +
365A GLN 3.7 0.3 + - - -
366A PRO* 3.9 7.4 - - - +
367A GLY 5.2 0.9 + - - -
362B ALA* 4.7 10.3 - - + +
363B ALA* 6.1 0.7 - - - +
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Residues in contact with LEU 364 (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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287A ILE* 4.3 31.6 - - + -
289A THR* 5.4 0.4 - - + -
296A VAL* 3.8 24.9 - - + -
301A LEU* 4.4 19.0 - - + +
309A VAL* 4.2 31.9 - - + -
340A VAL* 4.9 2.9 - - + -
342A THR* 4.9 5.2 - - + -
360A SER* 2.9 27.7 + - - +
361A LEU* 3.7 4.0 - - + +
363A ALA* 1.3 76.1 - - - +
365A GLN* 1.3 60.1 + - - +
366A PRO* 3.4 1.8 - - - -
367A GLY* 3.2 5.1 + - - +
368A LEU* 2.9 42.5 + - + +
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Residues in contact with GLN 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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106A ILE 5.5 0.6 + - - -
107A PHE* 3.7 32.7 + - + +
361A LEU 2.9 18.2 + - - +
362A ALA* 3.6 6.2 - - - +
364A LEU* 1.3 77.1 - - - +
366A PRO* 1.3 63.8 - - + +
368A LEU* 3.9 7.1 - - - +
369A THR* 2.7 44.3 + - - +
342B THR 4.1 3.8 - - - +
343B CYS* 4.0 8.6 - - - -
344B PRO* 3.3 52.0 + - + +
345B GLY 5.6 0.2 - - - -
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Residues in contact with PRO 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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362A ALA 3.5 10.5 - - - +
363A ALA 3.9 7.2 - - - +
364A LEU 3.6 3.1 - - - -
365A GLN* 1.3 97.2 - - + +
367A GLY* 1.3 60.9 + - - +
369A THR* 3.4 6.6 + - - -
370A GLN* 3.1 23.6 + - - +
297B ALA* 6.0 8.1 - - + -
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Residues in contact with GLY 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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301A LEU* 3.5 17.4 - - - +
363A ALA 5.2 0.4 + - - -
364A LEU* 3.2 6.9 + - - -
366A PRO* 1.3 77.5 - - - +
368A LEU* 1.3 61.0 + - - +
370A GLN* 3.9 4.9 - - - +
371A ALA* 2.9 33.4 + - - +
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Residues in contact with LEU 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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73A TYR* 3.9 11.9 - - + +
75A LEU* 3.9 30.7 - - + -
285A LEU* 4.4 1.6 - - + -
287A ILE* 4.4 11.7 - - + -
301A LEU* 3.6 17.7 - - + +
304A PHE* 3.5 29.7 - - + -
307A ALA* 4.0 16.8 - - + -
309A VAL* 4.9 5.2 - - + -
361A LEU* 5.2 4.9 - - + +
364A LEU* 2.9 36.3 + - + +
365A GLN* 3.9 4.7 - - - +
367A GLY* 1.3 75.5 - - - +
369A THR* 1.3 63.7 + - - +
372A GLY* 2.9 22.2 + - - -
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Residues in contact with THR 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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73A TYR* 3.7 20.6 + - + +
365A GLN* 2.7 31.0 + - - +
366A PRO* 3.6 6.7 - - - +
367A GLY 3.3 0.2 - - - -
368A LEU* 1.3 79.4 - - - +
370A GLN* 1.3 62.1 + - - +
372A GLY 4.2 0.5 - - - -
373A ALA* 3.4 20.6 + - - +
344B PRO* 6.0 0.9 - - - +
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Residues in contact with GLN 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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301A LEU* 4.5 5.9 - - - +
303A ASN* 4.4 9.8 + - - +
366A PRO 3.1 16.3 + - - +
367A GLY* 3.9 5.4 - - - +
369A THR* 1.3 78.0 - - - +
371A ALA* 1.3 78.7 + - - +
372A GLY 3.4 0.5 + - - -
373A ALA* 3.5 18.0 + - - +
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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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301A LEU* 3.8 17.7 - - + +
302A PRO 3.4 23.3 - - - +
303A ASN* 3.3 14.8 - - - +
304A PHE* 3.3 28.1 + - + +
367A GLY 2.9 18.4 + - - +
370A GLN* 1.3 90.1 - - - +
372A GLY* 1.3 58.6 + - - +
373A ALA 4.4 3.0 - - - +
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Residues in contact with GLY 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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72A PRO* 3.7 12.5 - - - +
73A TYR* 3.5 27.2 - - - +
304A PHE* 3.3 27.9 - - - +
368A LEU 2.9 13.8 + - - -
371A ALA* 1.3 75.4 - - - +
373A ALA* 1.3 66.6 + - - +
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Residues in contact with ALA 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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72A PRO* 4.7 5.2 - - - -
73A TYR* 5.0 1.6 - - - -
303A ASN* 6.0 1.2 - - - -
369A THR 3.4 17.3 + - - +
370A GLN* 3.7 12.2 - - - +
371A ALA 3.4 5.0 - - - +
372A GLY* 1.3 81.4 - - - +
374A ARG* 1.3 68.4 + - - +
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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