Contacts of the strand formed by residues 422 - 427 (chain B) in PDB entry 4P22
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 GLN 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B PHE* 3.5 9.4 - - - -
200B CYS 3.2 34.5 + - - -
303B PHE* 4.1 6.2 - - - -
304B LYS* 3.5 29.0 + - + +
309B SER* 3.4 19.7 + - - +
312B GLU 5.2 0.7 - - - +
314B ASP* 2.5 59.4 - - + +
420B ILE* 2.8 25.1 + - - +
421B MET* 1.3 82.2 - - + +
423B TRP* 1.3 70.1 + - + +
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Residues in contact with TRP 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 6.3 0.7 - - + -
172B GLN* 5.9 2.9 - - - -
188B VAL* 6.0 1.6 - - + -
197B GLN* 3.8 24.5 - - + -
198B LEU 3.2 4.9 - - - +
199B PHE* 3.2 26.2 - + + -
306B LEU* 3.3 30.1 - - + -
309B SER* 3.0 26.3 + - - -
310B LEU* 3.6 42.4 - - + -
313B PRO* 3.7 15.9 - - + +
314B ASP 3.0 3.6 + - - -
315B PHE* 3.2 14.4 - + + +
316B VAL 3.1 23.0 + - - +
330B HIS* 3.6 13.9 - + - -
420B ILE* 4.1 2.7 - - - -
422B GLN* 1.3 92.9 - - + +
424B LEU* 1.3 59.4 + - - +
425B TYR* 3.6 31.2 - + + -
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Residues in contact with LEU 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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322A LYS* 5.1 8.5 - - - +
196B GLY 4.1 0.5 - - - +
197B GLN* 3.6 2.3 - - - -
198B LEU* 2.7 43.2 + - + +
316B VAL* 3.9 22.4 - - + +
317B VAL* 3.6 30.1 - - + -
401B ILE* 6.0 2.1 - - + +
404B LEU* 4.2 23.1 - - + -
420B ILE* 3.8 32.9 - - + +
423B TRP* 1.3 72.5 - - - +
425B TYR* 1.3 75.4 + - - +
426B PHE* 4.2 7.2 + - + +
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Residues in contact with TYR 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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196B GLY 3.6 11.4 - - - -
197B GLN* 2.9 39.6 + - + -
315B PHE* 3.6 28.0 - + - -
316B VAL 5.2 1.5 + - - +
317B VAL* 5.8 0.3 - - - +
325B ARG* 5.5 6.1 + - - -
326B PRO* 3.9 22.1 - - + +
329B LEU* 3.7 30.0 - - + +
330B HIS* 2.6 49.6 + - + -
333B PHE* 3.8 21.2 - + - +
423B TRP* 3.6 16.1 + + + -
424B LEU* 1.3 83.4 - - - +
426B PHE* 1.3 61.1 + - - +
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Residues in contact with PHE 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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404A LEU* 5.3 4.5 - - + -
407A GLN* 4.6 8.3 - - - -
194B LEU 3.9 8.1 - - - -
195B PHE* 3.2 9.3 - - - +
196B GLY* 2.8 48.8 + - - +
329B LEU* 4.4 4.2 - - - +
397B ILE* 4.8 8.1 - - + -
400B PHE* 3.2 44.9 - + + -
401B ILE* 4.5 11.2 - - + -
424B LEU* 5.4 8.7 - - + +
425B TYR* 1.3 75.6 - - - +
427B ASP* 1.3 89.4 + - - +
428B ALA* 3.3 17.5 - - + -
429B LEU 4.7 5.4 - - - -
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Residues in contact with ASP 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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194B LEU* 3.7 7.3 - - - +
195B PHE* 3.7 28.5 - - + -
325B ARG* 5.5 9.8 - - - +
329B LEU* 5.2 3.6 - - + -
382B LEU* 5.5 1.7 - - - +
385B LYS* 3.8 10.3 + - - +
426B PHE* 1.3 96.0 - - - +
428B ALA* 1.3 82.1 + - - +
429B LEU* 2.6 48.0 + - + +
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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