Contacts of the strand formed by residues 381 - 386 (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 381 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354R HIS* 3.6 4.9 - - - -
374R GLY* 3.4 5.4 - - - -
375R GLY 3.3 21.5 + - - -
379R ASP* 3.0 39.4 + - - +
380R ARG* 1.3 81.0 - - - +
382R ILE* 1.3 61.1 + - - +
383R ARG* 4.4 23.6 - - + +
395R ALA* 4.9 8.5 - - + -
396R VAL* 3.3 28.0 - - - -
397R ASP* 3.8 29.5 + - - +
402R VAL* 4.3 2.3 - - - +
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Residues in contact with ILE 382 (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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372R ALA* 5.3 0.2 - - + -
373R THR 3.5 7.6 - - - +
381R HIS* 1.3 73.1 - - - +
383R ARG* 1.3 66.3 + - - +
384R ILE* 4.5 14.2 + - + +
394R SER 4.0 0.5 - - - +
395R ALA* 3.3 3.8 - - - -
396R VAL* 3.0 44.3 + - + +
398R ALA* 4.0 11.7 - - + -
402R VAL* 4.1 20.9 - - + -
405R ILE* 4.2 13.0 - - + -
414R LEU* 5.1 7.4 - - + -
416R SER* 3.6 15.5 - - - +
418R HIS* 4.5 0.2 - - + -
428R TRP* 3.5 43.7 - - + +
433R MET* 4.8 6.9 - - + +
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Residues in contact with ARG 383 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353R GLN* 3.8 38.5 + - - +
354R HIS* 3.5 34.0 + - + +
371R LEU 3.6 1.0 - - - +
372R ALA* 3.3 5.2 - - - -
373R THR* 2.9 31.3 + - - +
379R ASP* 5.0 2.0 + - - -
381R HIS* 4.4 20.7 - - + +
382R ILE* 1.3 79.6 - - - +
384R ILE* 1.3 64.1 + - - +
385R TRP* 3.7 28.6 - - + +
392R CYS* 3.7 22.0 - - - +
394R SER 3.4 4.9 - - - +
395R ALA* 4.0 18.4 - - + +
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Residues in contact with ILE 384 (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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370R VAL* 3.7 26.9 - - + -
371R LEU 3.4 1.6 - - - +
372R ALA* 3.8 16.6 - - + -
382R ILE* 4.7 7.9 - - + +
383R ARG* 1.3 75.2 - - - +
385R TRP* 1.3 60.1 + - - +
392R CYS* 3.5 5.9 - - - -
393R LEU* 2.8 42.5 + - + -
394R SER* 2.8 37.4 + - - +
407R TRP* 4.2 5.2 - - + -
414R LEU* 3.8 31.4 - - + -
430R TYR* 4.4 14.8 - - + +
433R MET* 4.9 11.2 - - + -
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Residues in contact with TRP 385 (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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333R VAL* 5.2 0.2 - - - +
351R PHE* 3.7 57.1 - + + -
353R GLN* 3.5 47.6 - - + -
354R HIS* 4.0 9.9 - + - -
369R ASN 3.3 0.6 - - - +
370R VAL* 3.3 13.3 - - - +
371R LEU* 2.7 46.4 + - + +
373R THR* 2.6 35.0 + - + +
383R ARG* 3.7 33.5 + - + +
384R ILE* 1.3 74.7 - - - +
386R ASN* 1.3 59.6 + - - +
387R VAL* 4.0 8.3 - - + -
390R GLY 4.1 8.3 - - - -
391R ALA 3.9 3.1 - - - -
392R CYS* 3.9 22.0 - - + -
393R LEU* 4.3 5.2 - - - +
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Residues in contact with ASN 386 (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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347J GLU* 4.4 9.5 + - - +
349J GLU* 3.4 24.6 + - - +
351R PHE* 4.7 0.3 - - - -
369R ASN* 3.5 10.4 - - - +
370R VAL* 5.1 1.6 - - + +
385R TRP* 1.3 73.6 - - - +
387R VAL* 1.3 62.3 + - - +
388R CYS* 3.4 20.8 - - - -
389R SER* 3.2 23.6 + - - +
390R GLY* 2.9 31.4 + - - -
391R ALA* 3.1 13.4 + - + +
393R LEU* 4.1 18.3 - - + +
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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