Contacts of the strand formed by residues 385 - 389 (chain A) in PDB entry 6BHG
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 CYS 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A GLU* 4.3 1.8 - - - -
376A ARG* 3.5 43.3 - - + -
377A ILE 3.1 10.5 - - - +
378A LEU* 4.0 24.0 - - - -
379A PHE* 5.0 0.9 - - - -
383A LYS 4.2 1.3 + - - -
384A ARG* 1.3 77.2 - - - +
386A GLU* 1.3 62.5 + - - +
387A TRP* 6.2 0.4 - - + -
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Residues in contact with GLU 386 (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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301A TYR* 6.4 3.1 - - + -
358A TRP* 3.9 5.4 - - - -
375A VAL 3.4 1.2 - - - +
376A ARG* 4.4 1.8 - - - -
377A ILE* 2.9 32.2 + - - +
379A PHE* 3.7 22.3 - - + -
385A CYS* 1.3 77.4 - - - +
387A TRP* 1.3 73.2 + - - +
388A ILE* 3.6 7.7 + - + +
394A ARG* 2.8 44.2 + - - -
10B SER 4.4 4.4 - - - +
11B THR* 3.7 14.0 + - - -
12B GLY 3.0 16.6 + - - -
14B ALY 3.8 4.9 - - - +
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Residues in contact with TRP 387 (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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301A TYR* 5.7 4.2 - + + -
302A ALA* 4.5 7.5 + - - +
369A GLU* 3.6 37.0 - - + -
371A ASP* 3.6 34.5 - - + -
374A LEU* 3.7 30.1 - - + -
375A VAL 3.4 10.1 - - - -
376A ARG* 3.4 49.9 - - + +
385A CYS* 6.2 0.4 - - + -
386A GLU* 1.3 76.2 - - - +
388A ILE* 1.3 62.8 + - - +
532A UNX 3.5 27.6 - - - -
14B ALY 3.6 15.2 - - - +
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Residues in contact with ILE 388 (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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356A THR* 3.6 30.5 - - + -
374A LEU* 3.4 3.9 - - - -
375A VAL* 2.8 44.0 + - + +
377A ILE* 4.1 13.0 - - + -
379A PHE* 4.6 0.9 - - + -
386A GLU* 3.8 34.1 - - + +
387A TRP* 1.3 79.9 - - - +
389A TYR* 1.3 75.9 + - - +
392A SER* 3.8 15.3 - - - +
394A ARG* 3.9 16.4 - - + +
395A LEU* 4.1 16.2 - - + -
14B ALY 3.5 10.8 - - - +
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Residues in contact with TYR 389 (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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294A LEU* 4.6 2.2 - - + -
296A PHE* 3.9 19.1 - + + -
332A PHE* 4.5 8.7 - + - -
336A TYR* 3.4 23.8 - + - -
343A ARG* 3.4 41.5 - - - +
344A PRO 4.6 0.7 + - - -
345A MET* 3.7 18.7 - - + +
373A SER* 3.4 24.9 - - - -
374A LEU* 3.6 10.2 - - + +
388A ILE* 1.3 72.3 - - - +
390A ARG* 1.3 58.1 + - - +
391A GLY* 3.4 33.1 - - - -
392A SER* 2.9 37.8 + - - -
395A LEU* 3.4 6.1 - - - +
512A UNX 4.4 7.2 - - - -
14B ALY 2.8 27.1 + - + +
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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