Contacts of the helix formed by residues 354 - 366 (chain X) in PDB entry 3F6E
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 HIS 354 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346X VAL* 4.1 14.8 - - + +
347X ASP 3.4 25.9 + - - -
348X GLN* 2.9 32.7 + - - +
349X ASP* 5.4 1.6 + - - -
352X ARG 4.8 0.2 - - - -
353X LEU* 1.3 73.0 - - - +
355X PRO* 1.3 72.9 - - - +
356X GLU* 3.6 15.1 + - - +
357X THR* 2.9 20.4 + - - +
358X VAL* 3.2 10.9 + - - +
524X VAL* 3.6 29.6 - - + +
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Residues in contact with PRO 355 (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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353X LEU 3.6 5.1 - - - +
354X HIS* 1.3 82.6 - - + +
356X GLU* 1.3 71.1 + - - +
358X VAL* 3.0 4.6 + - + +
359X PHE* 3.0 30.4 + - + -
379X THR* 3.5 37.9 - - + -
382X GLN* 4.6 9.6 - - - +
453X MET* 3.9 21.5 - - + -
523X THR* 5.0 4.7 - - + -
524X VAL* 3.9 17.3 - - + +
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Residues in contact with GLU 356 (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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346X VAL* 3.6 37.2 - - + +
354X HIS* 3.6 17.9 + - + +
355X PRO* 1.3 80.2 - - - +
357X THR* 1.3 56.9 + - - +
359X PHE* 3.4 1.6 + - - -
360X ASP* 3.0 36.3 + - - +
382X GLN* 3.5 34.0 + - + +
386X ARG* 3.4 35.4 - - - +
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Residues in contact with THR 357 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346X VAL* 4.6 6.6 + - - +
348X GLN* 2.7 42.4 + - + +
353X LEU* 3.9 10.1 - - + -
354X HIS* 2.9 15.3 + - - +
356X GLU* 1.3 75.3 - - - +
358X VAL* 1.3 67.0 + - - +
360X ASP* 3.4 6.2 + - + +
361X THR* 2.8 30.9 + - - +
500X LEU* 3.8 30.3 - - + -
503X LEU* 5.0 0.2 - - + -
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Residues in contact with VAL 358 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353X LEU* 3.8 25.4 - - + -
354X HIS 3.6 12.6 - - - +
355X PRO* 3.0 6.4 + - + +
357X THR* 1.3 79.9 - - - +
359X PHE* 1.3 61.0 + - + +
361X THR* 3.3 1.7 + - - -
362X LEU* 2.9 44.0 + - + +
451X VAL* 4.3 13.0 - - + -
453X MET* 3.9 32.5 - - + -
503X LEU* 4.0 17.9 - - + +
521X VAL* 4.1 13.7 - - + -
523X THR* 4.5 1.3 - - + -
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Residues in contact with PHE 359 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355X PRO* 3.0 33.0 + - + +
356X GLU* 4.1 2.5 - - - +
358X VAL* 1.3 75.3 - - + +
360X ASP* 1.3 58.6 + - - +
362X LEU* 3.3 15.0 + - + +
363X ASN* 2.8 31.7 + - - +
376X SER* 5.2 0.2 - - - -
379X THR* 3.7 39.7 - - - -
382X GLN* 4.2 6.5 - - + -
383X MET* 3.6 44.9 - - + -
386X ARG* 3.7 21.8 - - + -
387X LEU* 3.6 11.7 - - + +
425X VAL* 3.8 34.8 - - + -
453X MET* 4.5 5.8 - - + -
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Residues in contact with ASP 360 (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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343X PRO* 4.9 2.6 - - - +
344X ALA 4.9 0.2 - - - -
345X LYS* 4.3 22.0 + - + +
346X VAL 5.0 0.7 + - - -
356X GLU 3.0 19.3 + - - +
357X THR* 3.7 6.8 - - - +
358X VAL 3.3 0.2 - - - -
359X PHE* 1.3 77.8 - - - +
361X THR* 1.3 57.4 + - - +
363X ASN* 3.4 6.2 + - - +
364X ASP* 3.0 35.8 + - - +
386X ARG* 2.9 44.9 + - - +
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Residues in contact with THR 361 (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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357X THR* 2.8 22.3 + - - +
358X VAL 3.7 3.4 - - - -
360X ASP* 1.3 75.0 - - - +
362X LEU* 1.3 65.4 + - - +
364X ASP* 3.2 8.6 + - + +
365X MET* 3.0 38.8 + - + +
500X LEU* 3.7 17.0 - - - +
503X LEU* 4.0 12.6 - - + -
504X LYS* 4.2 23.1 + - + +
507X LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 362 (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 VAL* 2.9 32.7 + - + +
359X PHE* 3.5 20.2 - - + +
361X THR* 1.3 76.4 - - - +
363X ASN* 1.3 59.0 + - - +
365X MET* 4.6 1.1 - - - +
366X ALA* 2.8 37.8 + - + +
372X TYR* 4.3 10.8 - - + -
387X LEU* 4.1 6.5 - - + -
423X ILE* 4.0 27.1 - - + -
425X VAL* 3.8 28.9 - - + -
451X VAL* 4.6 6.1 - - + -
507X LEU* 3.7 33.7 - - + -
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Residues in contact with ASN 363 (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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245X ARG* 5.3 4.0 - - - +
342X GLU* 5.9 0.6 + - - -
359X PHE 2.8 12.7 + - - +
360X ASP* 3.6 5.8 - - - +
361X THR 3.2 0.2 - - - -
362X LEU* 1.3 77.2 - - - +
364X ASP* 1.3 67.4 + - - +
365X MET 3.4 0.3 + - - -
366X ALA* 4.2 9.2 + - - +
372X TYR* 4.4 8.8 + - - -
386X ARG 3.3 26.2 + - - +
387X LEU* 3.8 3.9 - - + +
388X ASN* 2.9 37.7 + - - +
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Residues in contact with ASP 364 (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 ASP* 3.0 25.4 + - - +
361X THR* 3.5 14.0 + - + +
362X LEU 3.2 0.6 - - - -
363X ASN* 1.3 82.3 + - - +
365X MET* 1.3 66.4 + - + +
366X ALA 4.8 1.2 - - - +
504X LYS* 4.9 8.9 + - - +
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Residues in contact with MET 365 (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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361X THR* 3.0 34.2 + - + +
362X LEU* 4.9 1.6 - - - -
364X ASP* 1.3 86.0 - - + +
366X ALA* 1.3 67.0 + - - +
367X PRO* 3.8 0.9 - - - +
504X LYS* 3.6 32.5 - - + +
507X LEU* 3.9 18.2 - - + -
508X GLN* 3.7 28.9 - - + +
511X LEU* 3.5 23.1 - - + +
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Residues in contact with ALA 366 (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 LEU* 2.8 23.9 + - + +
363X ASN 4.2 7.7 - - - +
364X ASP 4.8 1.2 - - - +
365X MET* 1.3 77.6 - - - +
367X PRO* 1.3 78.9 - - + +
368X GLU* 3.7 2.1 + - - +
370X ALA* 4.0 2.0 - - + -
372X TYR* 3.4 20.2 - - - +
423X ILE* 3.8 20.9 - - + -
511X LEU* 4.4 6.2 - - - +
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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