Contacts of the strand formed by residues 2060 - 2065 (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 LYS2060 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2056C GLU* 3.3 1.8 - - - -
2057C LEU* 2.7 42.7 + - - +
2058C ASP* 3.6 23.7 + - - +
2059C GLY* 1.3 76.2 - - - +
2061C ALA* 1.3 64.5 + - - +
2062C VAL* 4.8 0.2 - - - -
2250C ARG 5.7 1.0 + - - -
2253C LEU* 4.0 45.9 - - + +
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Residues in contact with ALA2061 (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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2016C LEU 4.1 11.7 - - - +
2017C GLN* 3.7 31.0 - - + +
2018C GLY 4.8 1.8 + - - +
2019C ALA* 3.2 21.5 - - + +
2020C GLN 4.2 2.8 + - - -
2021C LEU 4.9 0.9 + - - +
2054C ARG* 4.5 6.1 - - - +
2055C ALA 3.2 9.4 - - - +
2056C GLU* 4.2 8.5 - - + +
2059C GLY 3.8 2.0 + - - -
2060C LYS* 1.3 74.7 - - - +
2062C VAL* 1.3 63.9 + - - +
2253C LEU* 5.3 1.2 - - - +
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Residues in contact with VAL2062 (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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2019C ALA* 4.2 0.4 - - - -
2021C LEU* 3.8 23.6 - - + +
2023C ILE* 4.3 6.3 - - + -
2038C MET* 4.2 27.4 - - + -
2054C ARG* 3.4 3.1 - - - +
2055C ALA* 2.5 42.7 + - - +
2057C LEU* 4.0 23.8 - - + -
2060C LYS 4.3 0.2 - - - +
2061C ALA* 1.3 79.6 - - - +
2063C ILE* 1.3 78.4 + - - +
2064C VAL* 4.9 0.5 - - - +
2253C LEU* 3.9 28.0 - - + -
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Residues in contact with ILE2063 (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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2011C LEU* 5.7 0.7 - - + -
2016C LEU* 3.5 42.4 - - + -
2019C ALA* 3.6 10.5 - - + -
2021C LEU 3.2 9.7 + - - +
2022C ALA* 3.1 11.8 - - + -
2023C ILE 2.8 24.8 + - - -
2044C LEU* 3.5 24.5 - - + -
2052C SER* 5.3 2.5 - - - -
2053C TRP 3.5 5.2 - - - +
2054C ARG* 3.8 17.3 - - + -
2062C VAL* 1.3 77.2 - - - +
2064C VAL* 1.3 74.5 + - - +
2065C CYS* 4.2 8.3 - - + +
2081C LEU* 4.1 20.0 - - + -
2086C ILE* 4.0 4.3 - - + -
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Residues in contact with VAL2064 (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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2023C ILE* 3.3 20.4 - - + +
2025C PRO* 4.2 10.3 - - + -
2031C VAL* 3.2 40.6 - - + +
2034C ILE* 4.2 14.4 - - + -
2035C ALA* 4.3 10.8 - - + -
2038C MET* 3.7 30.1 - - + -
2053C TRP* 2.8 41.8 + - + +
2055C ALA* 5.6 0.4 - - + -
2062C VAL* 4.6 1.8 - - + +
2063C ILE* 1.3 77.9 - - - +
2065C CYS* 1.3 61.0 + - - +
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Residues in contact with CYS2065 (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* 4.4 22.4 - - - -
2011C LEU* 5.9 0.2 - - - -
2023C ILE 3.0 5.7 + - - -
2024C VAL* 3.1 30.8 - - + +
2025C PRO* 3.2 5.0 - - - +
2031C VAL* 4.3 0.9 - - - -
2050C PHE* 4.4 7.0 - - - -
2051C THR 3.4 10.1 - - - +
2052C SER* 4.3 11.9 - - - -
2063C ILE* 4.1 8.7 - - + +
2064C VAL* 1.3 75.3 - - - +
2066C SER* 1.3 75.0 + - - +
2077C ALA* 4.5 5.6 - - - -
2081C LEU* 4.1 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