Contacts of the helix formed by residues 380 - 393 (chain B) in PDB entry 5DQE
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 CYS 380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A LYS* 5.0 9.0 - - - -
353A GLN* 5.6 8.3 - - - -
355B VAL* 4.6 19.3 - - + -
357B LYS* 5.6 0.4 - - - +
378B PRO 3.3 4.6 + - - -
379B MET* 1.3 72.7 - - - +
381B GLU* 1.3 62.3 + - - +
382B TYR* 3.5 26.0 - - - -
383B LEU* 2.9 25.9 + - + +
384B VAL* 3.1 8.8 + - - +
501B 5E4 2.9 34.6 + - + +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS* 3.0 63.9 - - + +
379B MET 3.3 5.1 + - - +
380B CYS* 1.3 74.8 - - - +
382B TYR* 1.3 56.3 + - - +
384B VAL* 3.4 9.8 + - + +
385B ASN* 2.9 53.0 + - - +
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Residues in contact with TYR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS* 5.0 7.5 - - - +
347B VAL* 4.4 18.6 - - + -
354B VAL* 4.8 13.0 - - + +
355B VAL* 4.9 15.7 - - + -
380B CYS* 3.5 17.1 - - - -
381B GLU* 1.3 80.1 + - - +
383B LEU* 1.3 75.4 + - + +
385B ASN* 3.6 7.3 + - - +
386B PHE* 3.0 43.1 + + + +
406B PHE* 2.9 37.6 - + - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B VAL* 4.5 11.0 - - + -
379B MET* 4.0 13.0 - - + -
380B CYS* 2.9 13.6 + - + +
382B TYR* 1.3 92.6 - - + +
384B VAL* 1.3 67.9 + - - +
386B PHE* 3.1 19.6 + - + +
387B LEU* 2.9 36.5 + - + +
408B ILE* 4.6 8.7 - - + -
501B 5E4 3.7 63.3 - - + +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B TYR* 3.7 48.2 - - + -
379B MET* 3.9 17.7 - - + +
380B CYS 3.1 13.6 + - - +
381B GLU* 3.4 12.3 + - + +
383B LEU* 1.3 77.8 - - - +
385B ASN* 1.3 66.4 + - - +
387B LEU* 3.2 7.3 + - - +
388B HIS* 3.1 45.4 + - + +
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Residues in contact with ASN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B GLU* 2.9 46.8 + - - +
382B TYR* 3.9 7.3 - - + +
384B VAL* 1.3 80.0 - - - +
386B PHE* 1.3 63.6 + - - +
388B HIS* 3.2 9.0 + - - +
389B LYS* 3.1 42.7 + - - +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B TYR* 3.0 38.6 + + + +
383B LEU* 3.6 21.1 - - + +
385B ASN* 1.3 77.0 - - - +
387B LEU* 1.3 63.8 + - + +
389B LYS* 3.2 15.3 + - + +
390B LEU* 2.9 45.1 + - + +
402B VAL* 3.9 16.8 - - + -
403B LEU* 4.0 24.7 - - + -
406B PHE* 3.8 42.0 - + + -
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 3.9 38.1 - - + -
306B LEU* 3.9 27.5 - - + +
308B TRP* 4.1 15.3 - - + -
327B TYR* 4.8 4.5 - - + -
379B MET* 4.1 21.3 - - + -
383B LEU* 2.9 21.7 + - + +
384B VAL* 3.5 8.3 - - - +
386B PHE* 1.3 87.2 - - + +
388B HIS* 1.3 64.3 + - + +
390B LEU* 3.8 7.4 - - + +
391B ARG* 3.0 24.6 + - - +
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B TRP* 3.7 18.9 - + - -
327B TYR* 2.6 35.5 + + - -
384B VAL* 3.1 36.7 + - + +
385B ASN* 3.2 10.3 + - - +
387B LEU* 1.3 76.1 - - + +
389B LYS* 1.3 63.7 + - + +
391B ARG* 3.4 30.4 + - - +
392B GLN* 3.4 17.3 + - - +
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Residues in contact with LYS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ASN* 3.1 29.6 + - - +
386B PHE* 3.6 14.3 - - + +
388B HIS* 1.3 75.0 - - + +
390B LEU* 1.3 65.0 + - - +
392B GLN* 3.1 33.2 + - - +
393B LEU* 3.3 14.1 - - + +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B LEU* 3.7 23.8 - - + -
386B PHE* 2.9 39.8 + - + +
387B LEU* 3.8 10.5 - - + +
389B LYS* 1.3 75.7 - - - +
391B ARG* 1.3 63.5 + - - +
392B GLN 3.0 1.2 + - - -
393B LEU* 3.2 37.5 + - + +
399B MET* 3.3 35.4 - - + +
402B VAL* 4.1 21.8 - - + -
403B LEU* 4.0 22.4 - - + -
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B LEU* 3.7 25.8 + - + +
307B ASN* 5.6 0.2 - - - +
308B TRP* 2.3 84.7 + - + +
387B LEU 3.0 16.4 + - - +
388B HIS* 3.4 23.4 + - - +
389B LYS 3.2 0.2 - - - -
390B LEU* 1.3 77.9 - - - +
392B GLN* 1.3 58.7 + - + +
393B LEU 3.4 1.8 + - - +
399B MET* 3.8 13.8 - - - +
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B HIS* 3.4 15.9 + - - +
389B LYS* 3.1 27.5 + - - +
390B LEU 3.0 1.2 + - - -
391B ARG* 1.3 77.2 - - + +
393B LEU* 1.3 70.5 + - + +
394B PRO* 3.5 4.5 - - - +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B LYS* 3.3 20.6 - - + +
390B LEU* 3.2 23.2 + - + +
391B ARG 4.1 1.7 - - - +
392B GLN* 1.3 82.6 - - + +
394B PRO* 1.3 74.6 - - + +
395B GLU 3.3 5.6 + - - +
398B MET* 4.0 11.4 - - + -
399B MET* 3.5 50.8 - - + +
402B VAL* 4.0 13.7 - - + -
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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