Contacts of the strand formed by residues 2046 - 2051 (chain B) in PDB entry 1CVU
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 GLU2046 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A GLN* 4.0 2.3 - - - +
546A LYS* 3.0 33.0 + - + +
548A SER* 3.0 25.9 + - - +
2041B CYS* 3.8 2.9 - - - -
2044B ARG 3.9 7.8 - - - +
2045B GLY* 1.3 74.2 - - - -
2047B CYS* 1.3 62.1 + - - +
2048B MET* 3.8 0.3 + - - +
2056B LYS 3.4 2.1 - - - +
2057B CYS* 3.2 4.3 - - - -
2058B ASP* 2.7 38.2 + - + +
2130B TYR* 3.7 17.8 + - - +
2137B LYS* 3.0 34.2 + - - +
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Residues in contact with CYS2047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A SER* 5.9 0.2 - - - -
2036B CYS* 2.0 55.8 - - + +
2039B ASN* 5.9 1.3 - - - -
2040B PRO* 3.7 19.5 - - + -
2041B CYS* 3.4 15.6 - - + -
2045B GLY 4.0 1.0 + - - -
2046B GLU* 1.3 74.4 - - - +
2048B MET* 1.3 60.6 + - - +
2055B TYR* 3.7 20.2 - - - -
2056B LYS 3.5 0.7 - - - -
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Residues in contact with MET2048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A HIS* 3.8 10.3 - - + -
323A TRP* 4.3 10.3 - - + +
327A GLN* 5.9 0.7 - - - +
548A SER* 4.3 26.0 - - - +
551A GLY* 3.4 38.8 - - - +
552A GLY* 3.7 12.6 - - - -
2036B CYS* 3.9 4.5 - - - -
2047B CYS* 1.3 75.6 - - - +
2049B SER* 1.3 70.3 + - - +
2050B THR* 4.1 23.3 - - + -
2055B TYR* 3.1 1.7 - - - -
2056B LYS* 2.8 49.7 + - + +
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Residues in contact with SER2049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A HIS* 2.9 28.6 + - - -
322A GLU* 2.6 29.0 + - - -
323A TRP* 3.3 14.6 + - - -
2034B ASN* 4.4 8.7 + - - -
2035B PRO* 3.6 26.0 - - - -
2036B CYS* 4.1 3.6 - - - -
2048B MET* 1.3 76.1 - - - +
2050B THR* 1.3 59.8 + - - +
2051B GLY 3.9 1.1 - - - -
2054B GLN 3.4 6.1 - - - -
2055B TYR* 4.1 1.6 - - - +
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Residues in contact with THR2050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLU 3.9 11.2 - - - +
320A HIS* 4.4 4.9 - - + -
321A PRO* 5.2 0.5 - - - +
322A GLU* 3.2 6.4 - - - +
2048B MET* 3.6 13.0 + - + +
2049B SER* 1.3 77.5 - - - +
2051B GLY* 1.3 58.1 + - - +
2054B GLN* 2.9 38.7 + - - +
2055B TYR* 3.4 4.2 + - - -
2056B LYS* 3.5 33.9 - - + -
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Residues in contact with GLY2051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PRO* 4.9 6.7 - - - -
322A GLU* 2.9 25.3 + - - +
2035B PRO* 3.9 4.9 - - - +
2049B SER* 3.9 0.5 - - - -
2050B THR* 1.3 78.8 + - - +
2052B PHE* 1.3 69.4 + - - +
2053B ASP 3.2 3.0 + - - -
2054B GLN* 3.4 24.9 + - - +
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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