Contacts of the strand formed by residues 363 - 369 (chain A) in PDB entry 4X8G
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 THR 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A TYR* 4.4 3.6 - - + -
357A ILE 3.7 5.6 - - - +
358A GLN* 3.2 32.9 + - + +
359A ALA 3.8 6.1 + - - -
362A LYS* 1.3 86.9 + - - +
364A LEU* 1.3 65.8 + - - +
365A PRO* 4.7 0.5 - - - +
388A ASP* 4.8 4.9 - - - +
653A PRO* 4.4 24.2 - - + -
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Residues in contact with LEU 364 (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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151A LEU* 5.2 6.1 - - + -
152A VAL 5.5 1.3 - - - +
154A CYS* 5.1 1.8 - - - -
155A ASP* 4.3 12.8 - - + +
179A ASP* 3.3 32.8 - - + +
356A TYR* 3.4 5.0 - - - +
357A ILE* 3.1 48.5 + - + +
362A LYS* 4.2 13.5 - - + +
363A THR* 1.3 75.4 - - - +
365A PRO* 1.3 76.1 - - + +
366A VAL* 3.7 22.0 - - + -
388A ASP* 4.2 18.4 - - + +
389A PHE 5.1 1.1 - - - +
390A GLY* 4.4 8.1 - - - +
653A PRO* 6.2 0.7 - - - -
703A CA 4.3 3.1 - - - -
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Residues in contact with PRO 365 (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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306A GLN* 5.7 1.1 - - - +
354A ILE* 4.6 4.9 - - + -
355A GLY 3.3 12.1 - - - +
356A TYR* 3.9 3.8 - - + -
363A THR 4.7 0.7 - - - +
364A LEU* 1.3 86.9 - - - +
366A VAL* 1.3 52.9 + - - +
388A ASP* 3.3 24.9 - - + +
389A PHE* 3.4 22.5 - - + -
390A GLY 2.7 29.1 + - - -
650A ARG* 4.2 29.2 - - + +
653A PRO* 6.2 1.1 - - + -
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Residues in contact with VAL 366 (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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154A CYS* 3.8 16.4 - - - -
256A PHE* 4.6 2.5 - - + -
296A TRP* 3.2 18.3 + - + -
354A ILE* 4.7 2.5 - - - -
355A GLY 2.7 42.8 + - - +
356A TYR* 4.4 0.7 - - - -
357A ILE* 3.8 17.7 - - + +
364A LEU* 3.7 17.7 - - + +
365A PRO* 1.3 79.7 - - - +
367A VAL* 1.3 58.0 + - - +
390A GLY* 3.5 26.9 - - - -
391A TYR* 3.6 4.3 - - - +
392A VAL* 4.0 25.1 - - + -
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Residues in contact with VAL 367 (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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352A MET* 3.7 39.9 - - + -
353A GLU 3.5 11.0 - - - +
354A ILE* 4.3 9.4 - - + +
366A VAL* 1.3 74.2 - - - +
368A PHE* 1.3 63.5 + - - +
369A ASP* 3.6 4.4 + - + +
384A VAL* 4.6 9.6 - - + +
389A PHE* 4.2 24.1 - - + -
390A GLY 3.0 17.5 + - - +
391A TYR* 3.6 20.8 - - + -
392A VAL 3.3 20.1 + - - +
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Residues in contact with PHE 368 (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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296A TRP* 3.4 44.6 - + + +
352A MET* 3.5 0.5 - - - -
353A GLU 2.8 35.9 + - - +
366A VAL 3.8 2.2 + - - -
367A VAL* 1.3 71.4 - - - +
369A ASP* 1.3 67.6 + - - +
371A PRO* 6.1 0.2 - - + -
392A VAL* 3.1 27.6 - - + -
393A THR* 4.0 0.9 - - - -
394A ARG* 3.5 31.6 - - + -
407A PHE* 3.1 27.4 - + + -
410A LEU* 4.9 1.1 - - + -
447A LEU* 3.7 24.9 - - + -
450A PHE* 3.5 32.3 - + - -
451A LEU* 4.6 5.6 - - + -
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Residues in contact with ASP 369 (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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351A GLU* 3.4 18.1 - - - +
352A MET* 3.9 19.6 - - + +
367A VAL* 3.6 1.8 + - + +
368A PHE* 1.3 88.7 - - - +
370A SER* 1.3 82.4 + - - +
371A PRO* 3.7 2.8 - - - +
382A LYS 4.7 6.7 - - - +
391A TYR* 3.3 39.5 + - + +
392A VAL 3.4 4.6 + - - -
393A THR* 4.2 13.9 + - - +
407A PHE* 3.8 2.2 - - - -
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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