Contacts of the helix formed by residues 383 - 402 (chain N) in PDB entry 2DYS
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 MET 383 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344N PHE* 4.3 0.7 - - - -
347N LEU* 3.5 37.2 - - + -
378N HIS 3.2 2.7 + - - +
379N TYR* 2.9 65.7 - - + +
382N SER* 1.3 86.5 - - - +
384N GLY* 1.3 59.2 + - - +
387N PHE* 2.8 38.5 + - - +
421N VAL* 3.3 46.0 - - + +
422N ASN* 3.8 7.4 - - - +
425N PHE* 3.7 11.4 - - + -
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Residues in contact with GLY 384 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247N ILE* 4.5 0.9 - - - -
344N PHE* 2.9 39.1 - - - -
347N LEU* 5.2 0.4 - - - +
348N PHE* 4.6 9.0 - - - -
379N TYR 2.7 15.4 + - - -
380N VAL* 3.0 12.2 + - - -
383N MET* 1.3 78.1 - - - +
385N ALA* 1.3 64.8 + - - +
388N ALA 3.0 8.1 + - - -
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Residues in contact with ALA 385 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N VAL* 4.5 11.7 - - + -
74N MET* 3.5 26.1 - - + +
246N LEU 4.2 8.5 - - - +
247N ILE* 3.6 10.7 - - + +
380N VAL 2.8 9.3 + - - +
381N LEU* 3.2 34.3 + - + +
384N GLY* 1.3 70.0 - - - +
386N VAL* 1.3 62.8 + - - +
388N ALA* 3.2 2.8 + - - -
389N ILE* 3.0 21.7 + - - +
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Residues in contact with VAL 386 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N MET* 3.8 18.6 - - + -
70N VAL* 5.3 0.2 - - + -
340N TRP* 5.3 0.7 - - + -
381N LEU 2.9 20.3 + - - +
382N SER* 3.5 17.0 - - - +
384N GLY 3.3 0.4 - - - -
385N ALA* 1.3 75.7 - - + +
387N PHE* 1.3 68.5 + - + +
389N ILE* 3.1 10.7 + - + +
390N MET* 2.9 38.4 + - + +
417N MET* 5.4 6.5 - - + -
604N HEA 3.6 51.6 - - + -
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Residues in contact with PHE 387 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N ILE* 5.1 0.2 - - - +
340N TRP* 3.4 68.0 - + + +
343N GLY* 4.0 3.6 - - - -
344N PHE* 4.0 16.2 - - + -
347N LEU* 3.6 26.0 - - + -
382N SER 4.0 6.5 - - - -
383N MET* 2.8 39.6 + - - +
384N GLY 3.7 1.8 - - - +
386N VAL* 1.3 81.5 - - + +
388N ALA* 1.3 57.3 + - - +
390N MET 3.4 0.2 + - - -
391N GLY* 2.9 24.3 + - - -
414N PHE* 4.2 13.5 - + - -
417N MET* 4.2 11.0 - - + -
418N PHE* 4.2 15.5 - + - -
421N VAL* 4.1 15.7 - - + -
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Residues in contact with ALA 388 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N MET* 4.3 2.2 - - + -
250N GLY* 3.6 38.1 - - - +
253N MET* 3.5 13.7 - - + +
254N ILE* 4.2 13.5 - - + -
257N ILE* 4.7 0.9 - - - +
344N PHE* 4.0 10.5 - - + -
384N GLY 3.0 12.0 + - - +
385N ALA* 3.5 9.0 - - - +
387N PHE* 1.3 76.7 - - - +
389N ILE* 1.3 57.3 + - - +
391N GLY* 3.5 0.7 + - - -
392N GLY* 2.9 24.1 + - - -
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Residues in contact with ILE 389 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N MET* 3.9 27.8 - - + -
70N VAL* 4.2 21.1 - - + -
73N ILE* 4.1 28.0 - - + -
74N MET* 3.8 26.0 - - + -
78N PHE* 4.1 4.4 - - + -
253N MET* 4.1 6.5 - - + -
385N ALA 3.0 17.6 + - - +
386N VAL* 3.1 10.3 + - + +
388N ALA* 1.3 77.8 - - - +
390N MET* 1.3 62.3 + - - +
392N GLY 3.4 0.3 + - - -
393N PHE* 2.8 27.5 + - - +
604N HEA 4.1 24.5 - - + -
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Residues in contact with MET 390 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340N TRP* 3.6 40.2 - - + -
386N VAL* 2.9 26.9 + - + +
387N PHE 4.0 0.2 - - - +
389N ILE* 1.3 76.8 - - - +
391N GLY* 1.3 66.2 + - - +
393N PHE* 3.3 11.2 + - + +
394N VAL* 3.0 37.2 + - + +
413N HIS* 3.5 25.4 - - + +
417N MET* 5.6 3.6 - - + -
468N MET* 3.6 26.0 - - + +
604N HEA 3.7 34.1 - - + -
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Residues in contact with GLY 391 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N ILE* 6.1 0.4 - - - -
257N ILE* 3.3 16.1 - - - +
337N ALA* 3.6 9.1 - - - +
340N TRP* 3.6 24.8 - - - +
341N ALA* 6.1 0.2 - - - -
387N PHE 2.9 13.2 + - - -
388N ALA* 4.0 0.4 - - - -
390N MET* 1.3 73.1 - - - +
392N GLY* 1.3 64.1 + - - +
395N HIS* 3.0 27.2 + - - +
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Residues in contact with GLY 392 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 3.5 14.5 - - - -
253N MET* 4.2 3.8 - - - -
257N ILE* 3.4 12.8 - - - +
388N ALA 2.9 17.6 + - - -
389N ILE 3.8 0.7 - - - -
391N GLY* 1.3 76.3 - - - +
393N PHE* 1.3 62.4 + - - +
396N TRP* 3.0 42.4 + - - -
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Residues in contact with PHE 393 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N LEU* 5.5 6.3 - - + -
78N PHE* 3.5 16.1 - + + -
389N ILE 2.8 18.5 + - - +
390N MET* 3.6 16.4 - - + +
391N GLY 3.2 0.4 - - - -
392N GLY* 1.3 76.3 - - - +
394N VAL* 1.3 64.2 + - + +
397N PHE* 2.8 63.2 + + + +
400N PHE* 5.7 4.7 - + - -
405N LEU* 5.4 5.6 - - + -
468N MET* 5.4 1.1 - - + -
472N ILE* 3.8 27.8 - - + -
604N HEA 3.7 39.9 - - + -
606N TGL 3.9 35.0 - - + -
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Residues in contact with VAL 394 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336N PRO* 4.1 10.3 - - + -
337N ALA* 3.5 37.5 - - + +
340N TRP* 4.3 11.9 - - + +
390N MET* 3.0 22.9 + - + +
391N GLY* 3.7 3.1 - - - +
393N PHE* 1.3 82.8 - - + +
395N HIS* 1.3 67.2 + - - +
396N TRP 3.6 0.2 + - - -
398N PRO* 3.6 15.6 - - - +
405N LEU* 3.9 27.0 - - + +
410N ALA* 5.1 11.0 - - + -
413N HIS* 5.8 1.8 - - - +
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Residues in contact with HIS 395 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256N HIS* 5.5 1.8 + - - +
257N ILE* 4.4 10.3 - - + -
260N TYR* 3.7 39.4 - + + +
261N TYR* 2.8 34.4 + + - -
337N ALA* 3.8 9.0 - - + -
391N GLY 3.0 21.0 + - - +
392N GLY 3.9 2.0 - - - +
394N VAL* 1.3 82.0 - - - +
396N TRP* 1.3 103.6 + + - +
398N PRO* 3.7 4.2 - - - +
491N ASN* 5.2 1.4 + - - -
493N GLU* 4.7 0.8 + - - -
494N TRP* 3.4 37.3 + + - -
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Residues in contact with TRP 396 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 4.0 4.3 - + - -
82N LEU* 3.9 26.2 - - + +
86N MET* 3.9 14.8 - - + -
184N PHE* 5.6 1.8 - + - -
253N MET* 4.2 23.3 - - + -
256N HIS* 4.1 24.7 - + + -
257N ILE* 4.8 2.5 - - + -
392N GLY* 3.0 39.8 + - - +
395N HIS* 1.3 96.1 - + - +
397N PHE* 1.3 66.7 + - - +
398N PRO* 3.2 3.1 - - - -
399N LEU* 2.8 38.2 + - + +
400N PHE* 3.0 32.3 + - + -
491N ASN* 5.9 0.2 - - - -
493N GLU* 2.6 33.6 + - - +
494N TRP* 3.6 15.9 - + - +
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Residues in contact with PHE 397 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393N PHE* 2.8 51.4 + + + +
394N VAL 4.2 0.2 - - - +
396N TRP* 1.3 71.3 - - - +
398N PRO* 1.3 59.8 - - + +
400N PHE* 3.0 8.9 + - - +
401N SER* 2.7 57.1 + - - -
403N TYR* 3.6 15.5 - - + -
405N LEU* 3.6 30.7 - - + -
472N ILE* 4.4 7.0 - - + -
475N ALA* 3.6 31.4 - - + -
476N PHE* 4.1 31.6 - + - -
606N TGL 4.1 14.8 - - + -
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Residues in contact with PRO 398 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394N VAL 3.6 13.9 - - - +
395N HIS 3.7 6.5 - - - +
396N TRP 3.5 2.9 - - - -
397N PHE* 1.3 95.9 - - + +
399N LEU* 1.3 55.0 + - - +
402N GLY* 2.8 30.0 + - - -
403N TYR 3.0 22.4 - - - +
404N THR* 4.1 11.7 - - + -
405N LEU* 4.8 3.6 - - + +
482N VAL* 3.8 16.2 - - + -
494N TRP* 4.1 9.2 - - + -
498N CYS* 3.3 6.6 - - - +
1Z ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N TRP* 4.9 1.1 - - + -
82N LEU* 4.1 4.0 - - + -
85N LEU* 4.7 4.5 - - + -
396N TRP* 2.8 33.4 + - + +
398N PRO* 1.3 79.6 - - - +
400N PHE* 1.3 77.4 + - + +
493N GLU* 3.6 40.6 - - + +
494N TRP* 3.4 31.8 - - + -
497N GLY 3.6 20.6 - - - +
498N CYS* 3.9 2.5 - - - -
499N PRO* 3.3 19.1 - - - +
500N PRO* 3.5 12.4 - - + +
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Residues in contact with PHE 400 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N LEU* 4.0 25.4 - - + -
78N PHE* 3.7 34.8 - + - -
81N TRP* 3.4 45.7 - + + -
82N LEU* 3.8 21.8 - - + -
393N PHE* 5.7 5.2 - + - -
396N TRP* 3.0 31.4 + - + -
397N PHE* 3.7 6.5 - - - +
399N LEU* 1.3 86.4 - - + +
401N SER* 1.3 58.4 + - - +
499N PRO* 3.5 2.3 - - - +
606N TGL 3.4 30.2 - - + +
10Y ASN* 2.8 28.4 + - - -
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Residues in contact with SER 401 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397N PHE* 2.7 41.3 + - - -
400N PHE* 1.3 76.4 - - - +
402N GLY* 1.3 55.2 + - - +
403N TYR* 3.0 21.2 + - - +
476N PHE* 3.8 27.3 - - - -
499N PRO* 3.7 5.0 - - - +
606N TGL 3.9 12.6 - - - -
7Y PRO* 3.5 21.8 - - - +
8Y GLY 4.0 3.5 + - - -
10Y ASN* 4.5 3.6 - - - +
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Residues in contact with GLY 402 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398N PRO 2.8 20.7 + - - -
400N PHE 3.7 0.8 - - - -
401N SER* 1.3 72.3 - - - +
403N TYR* 1.3 61.0 + - - +
481N GLU* 3.4 7.3 - - - +
482N VAL* 2.9 32.6 + - - +
498N CYS* 3.3 28.1 - - - +
499N PRO* 3.6 3.2 - - - +
7Y PRO* 4.2 3.7 - - - +
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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
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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