Contacts of the helix formed by residues 378 - 395 (chain X) in PDB entry 2DE0
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 PRO 378 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366X ARG* 3.7 9.9 - - - +
374X ALA 4.9 2.9 - - - +
375X ALA* 3.8 19.3 - - + -
377X HIS* 1.4 94.3 - - + +
379X ILE* 1.3 66.8 + - - +
380X GLU* 3.1 16.7 + - + +
381X GLU* 3.2 32.7 + - + +
382X TYR* 3.3 7.3 - - - -
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Residues in contact with ILE 379 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362X VAL* 6.1 1.3 - - + -
364X VAL* 5.4 2.2 - - + -
366X ARG* 4.4 5.0 - - - +
377X HIS 3.8 0.8 + - - -
378X PRO* 1.3 73.7 - - - +
380X GLU* 1.3 81.0 + - - +
382X TYR* 3.0 24.7 + - + +
383X MET* 3.1 24.7 + - + +
406X LEU* 6.1 2.9 - - + -
413X LEU* 4.0 27.6 - - + -
416X GLU* 3.7 20.5 + - - +
417X ALA* 3.7 31.9 - - + -
420X LYS* 4.5 3.4 - - + -
421X TYR* 4.0 22.0 - - + -
426X PHE* 5.4 0.7 - - + -
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Residues in contact with GLU 380 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378X PRO* 3.1 17.5 + - + +
379X ILE* 1.3 85.1 + - - +
381X GLU* 1.3 57.2 + - - +
383X MET* 2.9 3.3 + - - +
384X VAL* 2.9 36.4 + - + +
420X LYS* 2.9 39.5 + - - +
421X TYR* 3.2 21.8 + - + +
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Residues in contact with GLU 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375X ALA* 2.8 20.4 - - + +
376X PHE* 2.6 47.5 - - - +
377X HIS 2.7 11.2 + - - -
378X PRO* 3.2 18.3 + - + +
380X GLU* 1.3 79.6 - - - +
382X TYR* 1.3 57.1 + - - +
384X VAL* 4.1 8.6 - - + +
385X HIS* 3.1 29.4 + - + -
493X LEU* 3.9 17.9 - - + +
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Residues in contact with TYR 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362X VAL* 3.8 31.4 - - + -
363X HIS 3.8 18.0 + - - -
364X VAL* 3.6 31.7 - - + +
365X ARG 4.5 5.2 + - - -
366X ARG* 5.7 0.2 - - - -
376X PHE 4.5 2.8 + - - -
377X HIS* 3.2 33.7 + - - -
378X PRO 3.3 18.8 - - - -
379X ILE* 3.0 15.9 + - + +
381X GLU* 1.3 78.2 - - - +
383X MET* 1.3 63.2 + - + +
384X VAL 3.2 2.6 + - - -
385X HIS* 3.3 13.5 + - - +
386X VAL* 3.3 16.3 + - - +
464X VAL* 3.8 18.9 - - + +
465X CYS* 4.4 8.1 - - - -
466X THR* 4.8 8.5 - - - +
493X LEU* 3.7 26.6 - - + +
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Residues in contact with MET 383 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362X VAL* 3.6 25.6 - - + -
379X ILE* 3.1 20.0 + - + +
380X GLU 2.9 2.3 + - - +
382X TYR* 1.3 75.2 - - + +
384X VAL* 1.3 63.0 + - - +
385X HIS 3.3 0.4 - - - -
386X VAL* 3.2 41.0 - - + +
387X GLU* 3.1 23.6 + - - +
404X VAL* 4.3 2.0 - - + -
406X LEU* 6.3 0.7 - - + -
421X TYR* 3.5 47.2 - - + +
424X TYR* 4.4 16.6 + - - -
426X PHE* 4.2 30.3 - - + -
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Residues in contact with VAL 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380X GLU* 2.9 17.1 + - + +
381X GLU* 4.1 6.3 - - + +
382X TYR 3.2 0.2 - - - -
383X MET* 1.3 77.2 - - - +
385X HIS* 1.3 85.4 + - + +
387X GLU* 3.3 6.5 + - - +
388X GLU* 3.1 32.6 + - - +
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Residues in contact with HIS 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381X GLU* 3.1 30.1 + - + -
382X TYR 3.3 5.6 + - - +
384X VAL* 1.3 88.8 - - + +
386X VAL* 1.3 65.8 + - - +
388X GLU* 3.8 15.7 - - - +
389X HIS* 3.0 25.5 + - - +
462X PHE* 4.4 5.0 - - + -
464X VAL* 4.2 16.1 - - + +
491X HIS* 3.1 50.3 + + + -
493X LEU* 4.0 9.1 - - + +
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Residues in contact with VAL 386 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360X ILE* 3.6 17.3 - - + +
362X VAL* 3.8 13.2 - - + -
382X TYR 3.3 14.6 - - - +
383X MET* 3.2 34.5 - - + +
384X VAL 3.3 0.8 - - - -
385X HIS* 1.3 78.7 - - - +
387X GLU* 1.3 58.1 + - - +
390X PHE* 2.9 42.6 + - + -
404X VAL* 3.6 28.0 - - + -
424X TYR* 3.6 6.7 - - + +
464X VAL* 4.0 11.4 - - + -
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Residues in contact with GLU 387 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383X MET 3.1 17.2 + - - +
384X VAL* 3.6 5.4 - - - +
385X HIS 3.2 0.2 - - - -
386X VAL* 1.3 74.0 - - - +
388X GLU* 1.3 56.8 + - - +
390X PHE* 3.0 2.6 + - - +
391X GLN* 2.7 58.7 + - - +
402X LYS* 3.4 23.3 + - - +
423X ASN* 5.3 1.7 - - - +
424X TYR* 2.9 34.1 + - - +
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Residues in contact with GLU 388 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X GLU* 5.0 10.8 - - - +
161X ARG* 3.9 17.7 - - + +
384X VAL* 3.1 20.0 + - - +
385X HIS* 3.8 16.2 - - - +
387X GLU* 1.3 79.7 - - - +
389X HIS* 1.3 57.5 + - - +
391X GLN* 3.2 14.4 - - - +
392X LEU* 2.9 27.5 + - + +
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Residues in contact with HIS 389 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360X ILE* 3.8 13.0 - - + -
385X HIS 3.0 17.9 + - - +
388X GLU* 1.3 73.2 - - - +
390X PHE* 1.3 60.5 + - - +
392X LEU* 3.1 27.1 + - + +
393X LEU* 2.7 60.1 + - + +
396X ARG* 4.8 4.7 + - - -
461X ASP* 4.5 4.0 + - - +
462X PHE* 3.3 57.6 - + + +
489X ASN* 4.8 4.7 + - - -
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Residues in contact with PHE 390 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358X PRO* 4.2 23.8 - - + -
359X VAL* 4.5 0.2 - - - -
360X ILE* 3.5 25.6 - - + -
386X VAL* 2.9 29.2 + - + +
387X GLU* 3.0 3.8 + - - +
389X HIS* 1.3 77.8 - - - +
391X GLN* 1.3 62.5 + - - +
393X LEU* 3.2 10.2 + - + +
394X ALA* 3.0 25.0 + - - +
399X VAL* 4.1 26.9 - - + +
402X LYS* 3.9 25.4 - - + -
403X ARG* 3.3 41.3 - - - -
424X TYR* 3.4 30.5 - + - -
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Residues in contact with GLN 391 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X HIS* 4.1 15.7 + - - +
161X ARG* 3.6 42.1 + - - +
387X GLU* 2.7 40.8 + - - +
388X GLU* 3.2 17.0 + - - +
390X PHE* 1.3 70.3 - - - +
392X LEU* 1.3 63.0 + - - +
394X ALA* 3.1 22.5 + - - +
395X ARG* 3.4 9.9 + - - +
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Residues in contact with LEU 392 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X GLU* 5.5 0.2 - - - +
161X ARG* 3.5 34.6 - - + +
164X MET* 3.6 33.2 - - + -
165X THR* 3.9 10.3 + - - +
388X GLU* 2.9 16.5 + - + +
389X HIS* 3.1 33.6 + - + +
391X GLN* 1.3 73.2 - - - +
393X LEU* 1.3 63.2 + - - +
395X ARG* 3.1 20.2 + - - +
396X ARG* 4.1 25.0 + - - +
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Residues in contact with LEU 393 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358X PRO* 4.5 21.8 - - + -
360X ILE* 5.2 2.0 - - + -
389X HIS* 2.7 46.0 + - + +
390X PHE* 3.2 17.5 + - + +
392X LEU* 1.3 74.8 - - - +
394X ALA* 1.3 56.4 + - - +
396X ARG* 2.9 59.6 + - - +
397X MET* 3.2 32.8 + - + +
399X VAL* 4.6 6.3 - - + -
461X ASP* 4.5 14.6 - - + -
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Residues in contact with ALA 394 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390X PHE 3.0 12.4 + - - +
391X GLN* 3.1 16.8 + - - +
393X LEU* 1.3 72.7 - - - +
395X ARG* 1.3 64.7 + - - +
397X MET 3.4 18.2 + - - +
399X VAL* 4.2 14.9 - - + +
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Residues in contact with ARG 395 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X HIS* 3.3 43.1 + - - +
161X ARG* 3.6 25.9 - - + +
162X SER* 3.3 21.7 - - - +
165X THR* 3.4 32.2 - - + +
169X TYR* 4.0 6.4 + - - -
391X GLN 3.4 8.3 + - - +
392X LEU* 3.1 13.2 + - - +
394X ALA* 1.3 80.6 - - - +
396X ARG* 1.3 56.8 + - - +
397X MET 3.8 0.2 - - - -
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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