Contacts of the strand formed by residues 437 - 442 (chain B) in PDB entry 4ZCH
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 PHE 437 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B PHE* 3.8 22.9 - + + -
255B SER* 3.5 16.8 - - - -
256B ALA 3.1 28.5 - - - -
307B GLN* 5.0 5.6 - - + -
308B LEU 3.3 13.9 - - - +
309B ILE* 4.1 11.7 - - + -
327B TRP* 3.7 8.5 - - - -
355B TYR* 4.1 22.4 - + - -
356B GLY* 3.3 1.9 - - - -
357B GLN* 3.0 64.1 + - + +
405B TYR* 4.3 4.5 - + - -
420B LEU* 4.5 0.9 - - - +
433B GLY 3.8 12.1 - - - -
434B ASP 3.6 14.4 - - - -
435B VAL 4.1 0.2 - - - -
436B THR* 1.4 77.6 - - - +
438B PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 438 (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 LEU* 2.7 46.6 + - + +
327B TRP* 3.7 38.4 - + + -
342B ASN 5.4 1.8 - - - -
344B ILE* 3.7 22.7 - - + +
354B ILE* 3.8 23.6 - - + -
355B TYR* 3.3 20.0 - - - -
371B ILE* 4.2 13.7 - - + -
418B LEU* 3.8 37.0 - - + -
419B GLN* 3.8 13.7 - - - -
420B LEU* 3.9 22.7 - - + -
437B PHE* 1.3 78.1 - - - +
439B GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU 3.1 12.8 - - - -
307B GLN* 4.0 0.7 - - - -
344B ILE* 4.1 7.9 - - - -
354B ILE* 3.5 8.5 - - - +
355B TYR* 3.1 55.6 + - - +
438B PHE* 1.3 75.8 - - - +
440B ALA* 1.3 59.3 + - - -
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Residues in contact with ALA 440 (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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258B ILE* 4.8 1.7 - - - +
305B CYS* 3.2 7.1 - - - +
306B LEU 2.9 28.5 + - - +
337B LEU* 3.7 31.6 - - + -
344B ILE* 4.4 11.4 - - + +
352B PHE* 4.6 4.3 - - + -
353B PHE 3.4 7.4 - - - +
354B ILE* 4.5 12.1 - - + -
355B TYR* 4.1 2.4 - - - -
418B LEU* 4.5 5.4 - - + -
439B GLY* 1.3 73.7 - - - +
441B LEU* 1.3 59.8 + - - +
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Residues in contact with LEU 441 (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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56B LEU* 6.4 1.6 - - + -
202B PHE* 5.2 8.1 - - + -
258B ILE* 4.1 16.2 - - + -
290B LEU* 6.0 0.4 - - + -
292B LEU* 3.8 41.1 - - + -
303B GLN* 3.9 29.2 - - + +
304B ASP 3.7 12.6 - - - +
305B CYS* 3.9 5.8 - - + -
352B PHE* 3.4 5.7 - - - -
353B PHE* 2.8 58.2 + - + +
355B TYR* 5.1 1.3 - - + -
440B ALA* 1.3 76.1 - - - +
442B LYS* 1.3 63.8 + - - +
443B LEU* 3.4 6.4 + - + +
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Residues in contact with LYS 442 (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 GLN* 3.4 30.1 + - - +
304B ASP* 2.8 33.9 + - + +
336B ALA* 3.8 18.2 - - + -
337B LEU* 4.6 0.2 - - - +
348B GLU* 3.7 25.1 + - - +
349B THR 3.8 21.9 + - - -
350B GLY* 4.4 9.6 - - - -
351B TYR 3.9 5.6 - - - +
352B PHE* 3.8 27.1 - - + -
441B LEU* 1.3 71.1 - - - +
443B LEU* 1.4 69.4 + - - +
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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