Contacts of the strand formed by residues 420 - 430 (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 LEU 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ARG* 5.0 1.6 + - - -
288B LEU* 4.8 6.1 - - + +
291B ARG* 4.6 15.0 - - + +
292B GLY 3.6 22.0 + - - +
293B PRO* 3.6 19.0 - - + +
296B ALA* 3.9 15.3 - - + -
297B PHE* 3.4 38.4 - - + -
411B VAL* 3.3 34.3 - - + -
412B VAL 3.8 2.5 - - - +
413B THR* 3.8 9.0 - - + -
418B GLN 3.6 2.4 + - - -
419B GLU* 1.3 76.8 - - - +
421B LEU* 1.3 62.8 - - - +
422B LEU 3.8 14.4 - - - +
423B CYS* 4.1 7.4 - - + -
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Residues in contact with LEU 421 (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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225B THR* 3.9 12.5 + - - +
227B ARG* 3.5 50.9 - - + +
228B LEU* 4.0 19.4 - - + +
296B ALA* 3.7 12.7 - - - +
339B MET* 4.0 19.7 - - + -
341B LEU* 3.5 31.9 - - + -
412B VAL* 2.7 10.0 + - + +
413B THR* 3.8 2.5 - - - -
414B ASN* 3.7 15.9 - - - +
419B GLU* 4.0 9.0 - - + +
420B LEU* 1.3 77.9 - - - +
422B LEU* 1.3 72.2 + - - +
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Residues in contact with LEU 422 (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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223B LEU* 3.8 22.4 - - + -
224B GLY* 3.9 16.2 - - - -
225B THR* 3.9 6.7 - - + -
228B LEU* 4.0 14.8 - - + +
230B LEU* 4.8 4.9 - - + +
296B ALA* 3.7 3.6 - - - +
298B PHE* 3.7 27.4 - - + -
333B TYR* 4.0 30.7 - - + -
410B GLN 3.8 1.1 - - - +
411B VAL* 3.7 0.9 - - - -
412B VAL* 2.9 41.8 + - + +
420B LEU* 3.8 3.9 - - - +
421B LEU* 1.3 85.0 - - - +
423B CYS* 1.3 63.0 + - - +
424B THR* 4.2 7.6 - - - +
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Residues in contact with CYS 423 (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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285B LEU* 4.5 2.7 - - - -
288B LEU* 4.0 7.2 - - - -
296B ALA 2.9 10.8 + - - +
297B PHE* 3.4 39.4 - - + -
298B PHE* 2.9 25.6 + - - +
409B LEU* 3.7 25.4 - - - -
410B GLN 3.3 7.9 - - - +
411B VAL* 4.0 11.4 - - + -
420B LEU* 4.1 12.6 - - + -
422B LEU* 1.3 74.8 - - - +
424B THR* 1.3 64.9 + - - +
425B ALA 4.2 0.2 - - - -
444B LEU* 5.5 0.4 - - - +
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Residues in contact with THR 424 (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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223B LEU* 3.7 25.4 - - + +
298B PHE* 3.3 8.5 - - - +
300B VAL* 3.7 24.2 - - + -
409B LEU* 3.4 6.4 - - - +
410B GLN* 2.8 44.4 + - - -
422B LEU* 4.2 8.5 - - - +
423B CYS* 1.3 77.7 + - - +
425B ALA* 1.3 62.6 + - - +
426B TYR* 3.5 36.2 + - + +
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Residues in contact with ALA 425 (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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274B ILE* 4.2 7.9 - - + -
278B PHE* 3.5 28.7 - - + -
285B LEU* 4.8 2.0 - - + -
298B PHE 2.8 12.4 + - - +
299B LEU* 3.3 15.5 - - + +
300B VAL* 2.7 31.7 + - - -
408B ILE 3.5 4.9 - - - -
409B LEU* 4.0 10.5 - - + +
423B CYS* 5.2 0.4 - - - -
424B THR* 1.3 73.1 - - - +
426B TYR* 1.3 58.0 + - - +
444B LEU* 4.4 5.8 - - + +
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Residues in contact with TYR 426 (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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223B LEU* 4.9 0.7 - - - +
230B LEU* 4.9 8.0 - - - +
233B PHE* 4.7 11.4 - + - -
254B ILE* 4.5 6.9 - - + +
300B VAL* 3.4 23.8 - - + +
302B PHE* 3.2 36.1 - + + -
407B THR* 3.5 6.4 - - - -
408B ILE* 2.7 43.7 + - + +
410B GLN* 3.0 35.0 + - + -
424B THR* 3.5 28.5 + - + +
425B ALA* 1.3 72.9 - - - +
427B VAL* 1.3 67.2 + - - +
428B PHE* 3.7 19.6 - - + -
501B 5E4 3.5 21.1 - - + -
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Residues in contact with VAL 427 (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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274B ILE* 6.0 0.2 - - + -
278B PHE* 4.3 6.5 - - + -
299B LEU* 4.2 19.7 - - + -
300B VAL 3.0 9.1 + - - +
301B LYS* 3.4 26.8 - - + -
302B PHE* 2.9 26.9 + - - +
406B PHE 4.8 1.8 - - - -
407B THR* 4.0 10.3 - - + -
425B ALA 4.2 0.2 - - - -
426B TYR* 1.3 78.6 - - - +
428B PHE* 1.3 67.3 + - - +
502B 5E4 3.5 57.2 - - + +
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Residues in contact with PHE 428 (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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252B VAL* 4.4 10.3 - - + -
302B PHE* 3.5 35.4 - + + -
304B ALA* 4.8 8.5 - - + -
400B ASN 5.0 0.9 - - - +
403B LEU* 3.5 42.9 - - + +
406B PHE* 4.3 14.6 + - + -
407B THR* 4.9 0.2 - - - -
408B ILE* 4.0 32.5 - - + -
426B TYR* 3.7 32.5 - - + -
427B VAL* 1.3 78.0 - - - +
429B GLU* 1.3 69.3 + - - +
501B 5E4 4.3 13.9 - + - -
502B 5E4 3.7 16.2 - - - -
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Residues in contact with GLU 429 (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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302B PHE 3.0 6.4 + - - +
303B TRP* 3.3 29.1 + - + -
304B ALA* 2.8 28.2 + - - +
396B ARG* 4.6 4.3 + - - -
400B ASN* 3.5 30.2 + - + +
403B LEU* 4.0 3.8 - - - -
428B PHE* 1.3 79.6 - - - +
430B VAL* 1.3 66.3 + - - +
502B 5E4 3.1 48.1 - - + +
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Residues in contact with VAL 430 (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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303B TRP* 4.4 2.5 - - - -
304B ALA* 3.5 7.2 - - + +
306B LEU* 3.9 28.3 - - + -
390B LEU* 4.5 0.9 - - + -
396B ARG* 2.7 61.7 + - + -
399B MET* 3.8 29.8 - - + -
400B ASN* 2.8 17.0 + - - +
403B LEU* 3.5 23.6 - - + -
429B GLU* 1.3 76.6 - - - +
431B SER* 1.3 59.5 + - - +
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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