Contacts of the helix formed by residues 377 - 386 (chain A) in PDB entry 1BFD
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 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLU* 3.6 5.2 + - - -
376A SER* 1.3 74.4 - - - +
378A SER* 1.3 58.1 + - - +
379A THR 3.4 0.7 + - - -
380A THR* 3.6 16.9 + - - -
397A PHE* 4.5 20.9 - - + -
403A LEU* 4.1 19.5 - - + -
460A ALA* 3.5 13.1 - - - +
530A TPP 2.9 56.7 + - - -
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Residues in contact with SER 378 (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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377A THR* 1.3 72.7 + - - +
379A THR* 1.3 68.5 + - - +
380A THR 3.7 0.7 - - - -
382A GLN* 3.7 10.6 + - - +
455A ASN* 4.6 7.4 + - - -
459A GLY* 4.1 4.5 - - - -
460A ALA* 3.7 26.2 - - - +
463A TRP* 6.0 1.6 - - - -
530A TPP 2.8 29.2 + - - -
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Residues in contact with THR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PRO* 3.6 33.0 - - + -
359A PHE* 3.6 20.7 - - - -
374A ASN* 4.9 0.9 + - - -
376A SER* 2.8 34.8 + - - +
378A SER* 1.3 93.7 - - - +
380A THR* 1.3 63.4 + - - +
381A ALA 3.4 2.7 - - - -
382A GLN* 3.3 14.4 + - - +
383A MET* 3.0 21.8 + - - +
453A MET* 4.7 2.9 - - + -
530A TPP 4.9 0.4 - - - +
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Residues in contact with THR 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.2 11.4 - - + -
374A ASN* 3.0 31.9 + - - +
376A SER 3.7 4.9 + - - -
377A THR* 3.6 17.4 + - - -
378A SER 3.7 2.0 - - - -
379A THR* 1.3 76.5 - - - +
381A ALA* 1.3 63.3 + - - +
383A MET* 3.3 3.9 + - - +
384A TRP* 3.1 39.5 + - + +
395A TYR* 4.0 3.6 - - - +
397A PHE* 4.3 12.1 - - + -
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Residues in contact with ALA 381 (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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252A LEU* 5.2 6.1 - - + -
379A THR 3.4 0.6 - - - -
380A THR* 1.3 79.5 - - - +
382A GLN* 1.3 70.8 + - + +
384A TRP* 3.4 5.8 + - - +
385A GLN* 3.3 37.9 + - - +
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Residues in contact with GLN 382 (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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355A PRO* 4.5 9.5 - - - +
356A GLU* 3.4 42.1 + - + +
359A PHE* 4.1 14.1 - - + -
378A SER 3.7 11.7 + - - +
379A THR* 3.3 26.8 + - - +
381A ALA* 1.3 80.5 + - + +
383A MET* 1.3 66.4 + - - +
385A GLN* 3.2 10.2 + - - +
386A ARG* 3.0 32.1 + - - +
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Residues in contact with MET 383 (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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359A PHE* 3.8 29.7 - - + -
372A TYR* 3.8 21.3 - - + -
373A LEU 4.1 8.3 - - - +
374A ASN* 3.5 43.1 - - + +
379A THR* 3.0 13.6 + - - +
380A THR* 3.5 9.4 - - - +
382A GLN* 1.3 77.5 - - - +
384A TRP* 1.3 63.5 + - + +
387A LEU* 3.2 52.8 + - + +
389A MET* 5.2 1.2 - - + +
395A TYR* 4.1 12.8 - - + -
425A VAL* 4.1 17.0 - - + -
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Residues in contact with TRP 384 (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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233A VAL* 4.0 17.5 - - + -
237A ALA* 3.9 18.6 + - + +
239A ARG 4.1 0.2 - - - -
240A CYS* 3.7 41.7 - - + -
244A THR* 4.0 11.4 - - + +
245A ARG* 4.7 4.7 + - - -
249A PHE* 3.9 32.4 - + - -
251A GLY* 6.2 0.7 - - - -
252A LEU* 3.5 42.1 - - + +
380A THR* 3.1 32.1 + - + +
381A ALA* 3.8 5.2 - - - +
382A GLN 3.3 0.2 - - - -
383A MET* 1.3 78.2 - - + +
385A GLN* 1.3 59.2 + - + +
387A LEU 4.3 9.2 - - - +
389A MET* 4.4 10.0 - - + +
395A TYR* 3.3 46.9 + + - -
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Residues in contact with GLN 385 (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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245A ARG* 2.8 25.0 + - - +
343A PRO* 3.6 22.3 - - + +
381A ALA* 3.3 26.2 + - - +
382A GLN* 3.2 11.3 + - - +
384A TRP* 1.3 78.5 - - + +
386A ARG* 1.3 68.7 + - + +
387A LEU 3.7 0.7 - - - -
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Residues in contact with ARG 386 (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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245A ARG* 4.0 6.2 + - - +
343A PRO* 3.9 25.9 + - + +
344A ALA* 2.8 32.9 + - - +
345A LYS* 4.7 0.6 - - - +
346A VAL* 4.1 8.1 - - - +
356A GLU* 3.4 48.9 - - - +
359A PHE* 3.8 15.8 - - + +
360A ASP* 3.0 39.5 + - - +
363A ASN* 3.3 27.4 + - - +
382A GLN* 3.0 22.4 + - - +
383A MET 3.3 0.2 + - - -
385A GLN* 1.3 89.5 + - + +
387A LEU* 1.3 62.1 + - - +
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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