Contacts of the strand formed by residues 2072 - 2076 (chain C) in PDB entry 1KY5
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 GLU2072 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2047C ALA 2.9 14.5 + - - +
2048C ARG* 3.6 9.3 - - + +
2049C ILE* 2.9 26.2 + - - +
2067C VAL* 5.2 0.7 - - - -
2070C GLY 5.5 1.1 - - - +
2071C ALA* 1.3 75.5 - - - +
2073C VAL* 1.3 62.5 + - - +
2119C PHE* 4.3 6.1 - - + -
2120C LYS* 2.9 34.3 + - - +
2121C ASP* 2.9 34.9 - - - +
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Residues in contact with VAL2073 (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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2049C ILE* 3.5 11.2 - - + +
2063C ILE* 4.2 17.9 - - + +
2066C LEU* 4.1 26.7 - - + -
2067C VAL* 4.0 23.3 - - + +
2071C ALA* 4.1 6.0 - - + -
2072C GLU* 1.3 80.4 - - - +
2074C ARG* 1.3 65.4 + - - +
2075C TRP* 3.1 38.6 - - + +
2096C ILE* 3.6 6.2 - - + +
2097C PRO* 3.3 24.3 - - - +
2119C PHE* 4.3 3.3 - - - -
2120C LYS* 4.8 2.9 + - - +
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Residues in contact with ARG2074 (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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2003C LYS* 2.8 32.2 - - - +
2004C LEU 3.9 10.9 + - - -
2005C PRO* 4.6 2.6 + - - +
2049C ILE 3.1 6.2 + - - +
2050C ALA* 3.6 2.3 - - - -
2051C GLY 3.3 21.8 + - - -
2073C VAL* 1.3 76.1 - - - +
2075C TRP* 1.3 60.8 + - - +
2097C PRO* 3.7 26.6 - - + +
2099C PHE* 3.1 25.4 - - + -
2115C GLN 2.6 26.8 + - - -
2116C THR* 3.6 30.6 - - - +
2118C HIS 3.4 18.2 + - - -
2119C PHE* 4.0 14.4 - - + -
2120C LYS* 3.8 23.5 - - - +
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Residues in contact with TRP2075 (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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2049C ILE* 4.9 2.5 - - + -
2051C GLY* 3.8 24.5 - - - -
2053C LEU* 3.2 40.6 + - + -
2055C MET* 3.7 18.4 - - + -
2059C THR* 3.3 20.4 - - + +
2062C LEU* 4.2 8.3 - - + -
2063C ILE* 3.5 27.1 - - + -
2066C LEU* 4.4 11.2 - - + -
2073C VAL* 3.1 36.1 - - + -
2074C ARG* 1.3 72.5 - - - +
2076C SER* 1.3 79.5 + - - +
2096C ILE* 5.3 2.0 - - + +
2097C PRO 3.2 8.8 + - - +
2098C VAL* 4.3 13.2 - - + -
2099C PHE* 3.2 26.0 + - - -
2116C THR* 3.4 10.4 - - - +
2128C LEU* 3.8 34.3 - - + -
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Residues in contact with SER2076 (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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2051C GLY 3.1 14.3 + - - +
2052C CYS* 3.3 17.5 - - - +
2053C LEU 2.9 28.0 + - - +
2055C MET* 4.9 0.2 - - - -
2075C TRP* 1.3 81.7 - - - +
2077C SER* 1.3 57.7 + - - +
2099C PHE 3.9 11.2 - - - -
2100C ALA* 4.6 2.7 - - - -
2112C CYS* 4.1 13.9 - - - -
2113C ILE* 3.8 15.5 - - - +
2116C THR* 3.9 14.7 + - - +
2134C LEU* 5.7 0.3 - - - +
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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