Contacts of the strand formed by residues 323 - 328 (chain R) in PDB entry 5G04
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 HIS 323 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351J ASP* 5.7 1.8 - - - -
317R TRP* 3.3 10.2 - - - -
318R ALA* 2.8 34.9 + - + +
320R ASP* 5.2 0.6 + - - -
321R GLY 3.5 0.2 - - - -
322R ARG* 1.3 99.8 + - + +
324R LEU* 1.3 60.5 + - - +
335R VAL* 3.9 18.2 - - + -
336R TRP 3.5 4.3 - - - -
348R LEU* 3.8 28.3 - - + +
363R TRP* 3.7 25.5 - + + -
368R SER* 5.1 3.8 + - - -
369R ASN* 3.6 23.4 + - - -
387R VAL* 4.0 18.7 + - + +
388R CYS* 5.2 5.5 - - + -
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Residues in contact with LEU 324 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275R SER* 4.5 0.2 - - - -
282R SER* 4.1 4.5 - - - +
290R ILE* 4.4 1.8 - - + -
292R HIS* 3.6 30.1 - - + -
305R LEU* 4.1 16.4 - - + -
315R LEU* 3.9 35.4 - - + -
316R ARG 3.6 25.8 - - - +
317R TRP* 3.7 35.7 - - + +
323R HIS* 1.3 73.7 - - - +
325R ALA* 1.3 58.1 + - - +
335R VAL* 3.5 1.4 - - - -
336R TRP* 2.7 52.4 + - + +
337R PRO 5.2 0.9 - - - +
363R TRP* 4.6 1.3 - - - -
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Residues in contact with ALA 325 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315R LEU* 3.4 5.7 - - - +
316R ARG 2.8 35.1 + - - -
324R LEU* 1.3 74.1 - - - +
326R SER* 1.3 61.3 + - - +
333R VAL* 5.4 1.8 - - + -
334R ASN 3.3 8.3 - - - +
335R VAL* 4.5 2.0 - - + +
361R VAL* 3.6 25.5 - - + +
363R TRP* 3.6 25.6 - - + +
371R LEU* 4.0 12.3 - - + -
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Residues in contact with SER 326 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290R ILE* 3.8 15.3 - - - -
308R HIS* 2.8 27.4 + - - -
312R VAL* 4.4 1.6 - - - -
314R GLY 3.2 10.5 - - - -
315R LEU* 3.8 6.5 - - - -
324R LEU 4.2 0.2 + - - -
325R ALA* 1.3 74.7 - - - +
327R GLY* 1.3 58.6 + - - +
333R VAL* 3.4 6.3 - - - +
334R ASN* 2.8 38.4 + - - +
336R TRP* 2.9 27.6 + - - -
361R VAL* 4.7 4.5 - - - -
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Residues in contact with GLY 327 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308R HIS* 3.8 4.0 - - - -
312R VAL* 3.6 4.2 - - - -
313R CYS 3.0 22.5 + - - -
314R GLY* 2.8 19.4 + - - +
326R SER* 1.3 75.1 - - - +
328R GLY* 1.3 57.7 + - - -
332R LEU 3.5 6.1 - - - -
333R VAL* 4.7 0.2 - - - -
358R VAL* 3.2 29.6 - - - -
361R VAL* 4.3 3.0 - - - +
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Residues in contact with GLY 328 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308R HIS* 3.5 8.2 - - - -
311R GLU 3.3 10.5 - - - -
312R VAL* 4.4 0.2 - - - -
313R CYS* 4.0 6.5 - - - -
327R GLY* 1.3 74.0 - - - -
329R ASN* 1.3 59.5 + - - -
330R ASP* 3.0 22.1 + - - +
331R ASN* 3.4 10.2 + - - -
332R LEU 3.1 11.6 + - - -
357R ALA* 3.7 0.2 - - - -
358R VAL* 3.2 19.8 + - - +
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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