Contacts of the strand formed by residues 2039 - 2047 (chain C) in PDB entry 1Y1S
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 ASP2039 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2038C MET* 1.3 77.7 - - - +
2040C LYS* 1.3 92.4 + - + +
2041C PRO* 3.2 1.3 - - - -
2055C ALA* 3.4 2.3 - - - +
2056C GLU* 2.6 49.6 + - + +
2057C LEU* 4.8 2.3 - - - +
2058C ASP 4.6 9.0 + - - -
2059C GLY 5.6 0.7 + - - -
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Residues in contact with LYS2040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2039C ASP* 1.3 95.6 + - + +
2041C PRO* 1.3 71.3 - - - +
2042C VAL* 3.2 17.5 + - + +
2054C ARG* 3.6 10.2 + - - +
2055C ALA* 4.0 2.3 - - - -
2056C GLU* 4.2 25.4 + - + +
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Residues in contact with PRO2041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2035C ALA* 3.4 25.6 - - + +
2036C ALA* 4.4 7.9 - - - +
2038C MET 3.4 11.2 - - - +
2039C ASP* 3.2 6.0 - - - -
2040C LYS* 1.3 87.7 - - - +
2042C VAL* 1.3 61.0 + - - +
2053C TRP* 3.2 25.7 - - + -
2054C ARG 3.3 8.5 - - - +
2055C ALA* 4.1 2.2 - - + -
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Residues in contact with VAL2042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040C LYS* 3.3 18.8 - - + +
2041C PRO* 1.3 75.9 - - - +
2043C LYS* 1.3 74.2 + - - +
2044C LEU* 5.5 2.5 - - + -
2053C TRP* 3.4 7.0 - - - -
2054C ARG* 2.8 57.3 + - - +
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Residues in contact with LYS2043 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2042C VAL* 1.3 86.9 - - - +
2044C LEU* 1.3 66.1 + - - +
2045C ALA* 4.1 11.9 - - - +
2046C SER* 3.6 32.5 - - - +
2051C THR* 5.5 4.3 - - - -
2052C SER 3.8 4.9 - - - +
2053C TRP* 3.5 42.4 - - + +
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Residues in contact with LEU2044 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2010C GLY 5.2 0.2 - - - +
2011C LEU* 3.5 30.7 - - + +
2015C ASP* 3.5 38.2 - - - +
2016C LEU* 4.5 0.7 - - + -
2042C VAL* 3.5 3.3 + - + +
2043C LYS* 1.3 80.4 - - - +
2045C ALA* 1.3 66.3 + - - +
2052C SER* 2.9 15.7 + - - +
2053C TRP 4.3 3.1 - - - -
2054C ARG* 3.6 34.8 - - + +
2063C ILE* 3.5 31.6 - - + -
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Residues in contact with ALA2045 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009C LEU 3.7 6.7 - - - +
2010C GLY 3.6 24.0 - - - +
2011C LEU* 3.6 3.4 - - + -
2043C LYS* 3.9 10.8 - - - +
2044C LEU* 1.3 82.6 - - - +
2046C SER* 1.3 63.5 + - - +
2047C HIS* 4.0 7.9 - - + +
2050C PHE 4.5 0.9 - - - -
2051C THR* 3.5 0.5 - - - -
2052C SER* 2.7 41.9 + - - +
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Residues in contact with SER2046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2043C LYS* 3.6 25.6 - - - +
2045C ALA* 1.3 80.5 - - - +
2047C HIS* 1.3 73.6 + - - +
2048C ARG 4.8 2.4 + - - -
2050C PHE 3.5 6.3 - - - -
2051C THR* 3.1 24.0 - - - +
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Residues in contact with HIS2047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008C HIS 3.6 15.3 - - - +
2009C LEU 3.5 25.1 - - - -
2010C GLY* 3.4 23.7 + - - -
2045C ALA* 4.0 9.6 - - + +
2046C SER* 1.3 86.3 + - - +
2048C ARG* 1.3 76.7 + - + +
2049C GLU 3.1 0.3 + - - -
2050C PHE* 2.8 27.5 + - - +
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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