Contacts of the strand formed by residues 389 - 394 (chain C) in PDB entry 6BW4
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 VAL 389 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.5 9.4 - - + -
49C TRP* 4.2 5.6 - - + -
86C LEU* 4.3 10.3 - - + -
382C TRP* 3.6 2.8 - - - -
383C ASN* 2.8 42.5 + - + +
386C GLU* 3.1 28.6 + - + +
387C PRO 3.2 0.2 - - - -
388C TRP* 1.3 77.1 - - - +
390C ILE* 1.3 66.3 + - - +
401C VAL* 3.7 28.5 - - + -
402C TRP 3.4 5.8 - - - +
403C GLN* 3.6 29.2 - - + +
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Residues in contact with ILE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TRP* 4.5 0.2 - - - -
334C ALA* 4.8 1.3 - - + -
342C LEU* 4.1 15.3 - - + -
344C VAL* 4.7 2.9 - - + -
380C PHE* 4.1 14.8 - - + -
381C SER 3.5 7.9 - - - +
382C TRP* 3.6 45.1 - - + -
383C ASN 4.7 0.2 - - - +
388C TRP 4.3 2.9 - - - +
389C VAL* 1.3 83.4 - - - +
391C CYS* 1.3 76.0 + - - +
400C GLN 3.6 1.2 - - - +
401C VAL* 3.2 3.7 - - - +
402C TRP* 2.8 79.2 + - + +
404C MET* 6.1 0.9 - - + -
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Residues in contact with CYS 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA* 4.6 5.5 - - - +
49C TRP* 3.6 29.9 - - + +
66C LEU* 3.9 25.4 - - + -
68C LEU* 5.2 0.4 - - - -
380C PHE* 3.1 5.5 - - - +
381C SER* 2.9 33.9 + - - +
390C ILE* 1.3 73.9 - - - +
392C SER* 1.3 63.1 + - - +
393C VAL* 4.4 8.7 - - - -
399C MET* 3.6 29.8 - - - -
400C GLN 3.2 5.6 - - - -
401C VAL* 4.2 4.0 - - + +
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Residues in contact with SER 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU* 3.9 15.0 - - - -
370C HIS* 4.2 0.9 + - - -
373C HIS* 2.7 31.8 + - - -
377C ILE* 4.5 4.5 - - - -
379C ASP 3.6 5.6 - - - -
380C PHE* 3.8 13.5 - - - -
391C CYS* 1.3 76.0 - - - +
393C VAL* 1.3 63.4 + - - +
399C MET* 3.5 1.7 - - - +
400C GLN 2.8 32.4 + - - -
402C TRP* 3.1 21.9 + - - -
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Residues in contact with VAL 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.9 2.7 - - + -
44C SER* 3.5 29.8 - - - +
46C THR 4.1 14.1 - - - +
47C ALA* 4.1 17.0 - - + -
68C LEU* 4.3 12.6 - - + -
373C HIS* 4.3 1.3 - - - -
377C ILE* 3.6 4.0 - - - +
378C SER 2.8 23.2 + - - -
379C ASP* 3.1 25.0 + - + +
391C CYS* 4.4 1.6 - - - -
392C SER* 1.3 79.6 - - - +
394C SER* 1.3 61.4 + - - +
398C ILE 3.4 5.2 - - - +
399C MET* 3.9 24.7 - - + -
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Residues in contact with SER 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO* 3.9 8.1 - - - +
44C SER 4.6 4.7 + - - +
373C HIS* 2.9 29.3 + - - +
375C ALA 3.8 12.1 - - - -
376C LYS 3.0 16.6 - - - -
377C ILE* 4.2 0.7 - - - -
378C SER* 4.2 3.8 - - - +
393C VAL* 1.3 74.4 - - - +
395C GLU* 1.3 64.1 + - - +
396C ASP* 2.6 23.5 + - - -
397C ASN* 3.2 15.1 + - - -
398C ILE* 3.0 13.5 + - - +
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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