Contacts of the helix formed by residues 379 - 387 (chain X) in PDB entry 3F6B
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 THR 379 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355X PRO* 3.5 33.4 - - + -
359X PHE* 3.7 20.6 - - - -
374X ASN* 5.0 0.6 + - - -
376X SER* 2.7 34.9 + - - +
378X SER* 1.4 93.1 - - - +
380X THR* 1.3 63.4 + - - +
382X GLN* 3.2 18.5 + - - +
383X MET* 3.0 21.1 + - - +
453X MET* 4.7 2.7 - - + -
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Residues in contact with THR 380 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252X LEU* 4.2 12.6 - - + -
374X ASN* 2.9 32.6 + - - +
376X SER 3.7 6.6 + - - -
377X THR 3.8 7.4 + - - -
378X SER 3.7 2.2 - - - -
379X THR* 1.3 76.7 - - - +
381X ALA* 1.3 65.4 + - - +
383X MET* 3.2 3.8 + - - +
384X TRP* 3.0 41.3 + - + +
395X TYR* 4.0 2.2 - - - +
397X PHE* 3.3 24.4 - - + -
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Residues in contact with ALA 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252X LEU* 5.4 5.2 - - + -
379X THR 3.3 0.6 - - - -
380X THR* 1.3 80.0 - - - +
382X GLN* 1.3 70.4 + - + +
384X TRP* 3.4 6.9 + - - +
385X GLN* 3.2 39.0 + - - +
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Residues in contact with GLN 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355X PRO* 4.5 5.0 - - + +
356X GLU* 3.5 44.3 + - + +
359X PHE* 4.2 9.0 - - + -
378X SER 3.7 12.3 + - - +
379X THR* 3.3 32.2 - - - +
381X ALA* 1.3 84.7 + - + +
383X MET* 1.3 63.6 + - - +
385X GLN* 3.2 9.0 + - - +
386X ARG* 3.0 36.8 + - - +
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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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359X PHE* 3.5 37.8 - - + -
372X TYR* 3.9 15.7 - - + -
373X LEU 3.8 22.0 - - - +
374X ASN* 3.6 35.2 - - + +
379X THR* 3.0 12.8 + - - +
380X THR* 3.2 10.3 + - - +
382X GLN* 1.3 75.7 - - - +
384X TRP* 1.3 63.6 + - + +
386X ARG 3.3 0.2 + - - -
387X LEU* 3.2 51.4 + - + +
389X MET* 5.4 2.0 - - + +
395X TYR* 4.1 12.1 - - + -
425X VAL* 4.3 9.0 - - + -
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Residues in contact with TRP 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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233X VAL* 4.1 14.1 - - + -
237X ALA* 3.8 20.2 + - + +
239X ARG 4.0 1.8 - - - -
240X CYS* 3.7 43.5 - - + -
244X THR* 3.9 8.2 - - + -
245X ARG* 4.9 4.0 + - - -
249X PHE* 3.9 30.7 - + - -
251X GLY* 6.1 0.7 - - - -
252X LEU* 3.7 44.9 - - + +
380X THR* 3.0 30.6 + - + +
381X ALA* 3.8 5.8 - - - +
382X GLN 3.3 0.2 - - - -
383X MET* 1.3 77.5 - - + +
385X GLN* 1.3 62.7 + - + +
387X LEU 4.4 8.3 - - - +
389X MET* 4.1 13.9 - - + +
395X TYR* 3.3 43.9 + + - -
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Residues in contact with GLN 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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245X ARG* 3.0 23.9 + - - +
343X PRO* 3.4 27.0 - - + +
381X ALA* 3.2 30.4 + - - +
382X GLN* 3.2 9.7 + - - +
384X TRP* 1.3 80.3 - - + +
386X ARG* 1.3 66.4 + - + +
387X LEU 3.7 0.4 - - - -
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Residues in contact with ARG 386 (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* 3.9 5.5 + - - +
343X PRO* 3.8 25.6 + - + +
344X ALA* 3.0 31.3 + - - +
345X LYS* 4.9 0.4 - - - +
346X VAL* 4.1 6.1 - - - +
356X GLU* 3.5 47.7 - - - +
359X PHE* 3.6 19.9 - - + +
360X ASP* 2.8 58.4 + - - +
363X ASN* 3.5 23.7 + - - +
382X GLN* 3.0 25.4 + - - +
383X MET 3.3 0.2 + - - -
385X GLN* 1.3 87.7 + - - +
387X LEU* 1.4 59.6 + - - +
388X ASN 3.9 0.2 + - - -
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Residues in contact with LEU 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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244X THR* 3.0 16.8 + - - -
245X ARG* 4.3 5.0 + - - -
359X PHE* 3.5 38.8 - - + +
362X LEU* 4.2 5.6 - - + -
363X ASN* 3.7 10.3 - - + +
372X TYR* 3.6 52.5 - - + +
383X MET* 3.2 42.8 + - + +
384X TRP 4.4 3.5 - - - +
385X GLN 3.7 0.4 - - - -
386X ARG* 1.4 73.2 - - - +
388X ASN* 1.3 61.0 + - - +
389X MET* 3.3 18.7 + - + +
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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