Contacts of the strand formed by residues 322 - 329 (chain A) in PDB entry 2G19
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 ARG 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR* 4.6 6.3 - - - -
315A ASP* 2.8 31.1 + - - +
316A ASN* 2.8 26.3 + - + +
320A ASP* 2.8 33.6 + - - +
321A GLY* 1.3 76.5 - - - +
323A CYS* 1.3 60.1 + - - +
368A SER* 3.6 15.2 - - - +
369A ASP* 4.9 1.6 + - - +
389A TRP* 3.3 64.7 - - + +
390A TYR 3.5 7.4 - - - +
391A PHE* 3.6 22.2 - - + -
395A GLU* 4.1 2.3 - - - +
801A 4HG 5.5 7.1 - - - +
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Residues in contact with CYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A TYR* 3.6 46.8 + - + -
292A ILE* 3.9 23.1 - - - -
321A GLY 3.3 0.8 + - - -
322A ARG* 1.3 73.9 - - - +
324A VAL* 1.3 73.3 + - - +
367A TRP* 3.5 13.0 - - - +
368A SER* 3.0 21.5 + - - -
369A ASP* 4.8 1.7 + - - +
390A TYR 2.8 14.2 + - - -
392A ASP* 3.8 20.9 - - + -
395A GLU* 5.2 2.2 - - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A MET* 4.6 4.0 - - + -
280A ILE* 4.7 4.0 - - + -
287A LEU* 4.5 8.5 - - + -
290A TYR* 5.2 0.7 - - + -
292A ILE* 4.3 10.8 - - + -
323A CYS* 1.3 94.3 - - - +
325A THR* 1.3 73.4 + - - +
326A CYS 4.0 0.5 + - - -
365A PHE* 4.0 25.8 - - + -
366A PHE 3.6 6.7 - - - +
367A TRP* 3.7 25.4 - - + -
368A SER* 3.1 4.8 + - - -
389A TRP* 3.4 4.5 - - - +
390A TYR* 2.9 48.1 + - + +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ASP* 2.9 28.3 + - - +
324A VAL* 1.3 73.8 - - - +
326A CYS* 1.3 62.0 + - - +
327A ILE* 3.9 15.5 - - + -
364A LEU 3.6 0.3 - - - +
365A PHE* 3.2 6.9 - - - -
366A PHE* 2.8 63.2 + - + -
368A SER* 2.8 20.8 + - - -
387A THR* 3.9 7.9 - - + -
389A TRP* 3.2 16.7 - - + +
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Residues in contact with CYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A MET* 3.5 35.8 - - - +
324A VAL 4.0 0.2 + - - -
325A THR* 1.3 73.7 - - - +
327A ILE* 1.3 61.7 + - - +
363A LEU* 3.5 16.6 - - - -
364A LEU 3.2 3.6 - - - -
365A PHE* 3.5 32.1 - - + -
386A ILE 3.7 0.9 - - - +
387A THR* 3.2 4.7 - - - +
388A VAL* 2.9 48.1 + - + +
390A TYR* 4.0 7.6 - - + -
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A THR* 3.9 13.7 - - + -
326A CYS* 1.3 78.4 - - - +
328A TYR* 1.3 63.6 + - - +
329A TYR* 3.7 33.3 + - + +
343A LEU* 4.7 0.2 - - + -
362A ARG 3.8 1.0 - - - +
363A LEU* 3.4 5.3 - - - -
364A LEU* 2.7 46.1 + - + +
366A PHE* 3.9 24.0 - - + -
385A ALA* 3.8 17.9 - - + -
386A ILE 3.3 4.5 - - - +
387A THR* 3.5 22.7 - - + +
801A 4HG 3.7 30.7 - - - +
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Residues in contact with TYR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 4.2 18.8 - + - -
214A LEU* 4.0 9.1 - - + +
219A GLY* 3.5 21.5 - - - -
222A ILE* 3.8 25.6 - - + -
272A LEU* 3.5 27.4 - - + -
276A MET* 3.7 20.4 - - + +
327A ILE* 1.3 74.9 - - - +
329A TYR* 1.3 68.4 + - - +
330A LEU* 3.8 16.9 - - + +
360A PHE* 5.4 0.3 - - - -
361A ASP* 2.7 47.9 + - - -
362A ARG 3.4 13.0 - - - -
363A LEU* 4.2 3.4 - - + -
385A ALA* 3.4 3.5 - - - -
386A ILE* 2.8 39.1 + - + +
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Residues in contact with TYR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ILE* 3.7 22.2 - - + +
328A TYR* 1.3 77.6 - - - +
330A LEU* 1.3 62.6 + - - +
331A ASN* 4.3 0.2 - - - +
343A LEU* 3.4 21.1 - - + +
356A ILE* 4.7 4.7 - - + -
358A PRO* 3.4 42.8 - - + +
359A LYS 3.1 18.6 - - - +
361A ASP* 2.9 25.6 + - - -
362A ARG* 2.9 32.2 + - + +
364A LEU* 3.6 21.6 - - + +
383A ARG* 3.9 4.0 - - - -
384A TYR 4.0 5.4 - - - -
385A ALA* 3.8 16.8 - - + -
801A 4HG 2.6 29.9 + - - -
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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