Contacts of the helix formed by residues 2058 - 2064 (chain C) in PDB entry 5Y3R
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 ASP2058 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2056C SER* 4.6 1.4 + - - +
2057C GLN* 1.3 76.2 - - - +
2059C PRO* 1.3 74.4 - - + +
2061C PRO* 3.6 0.9 - - - +
2062C ALA* 3.7 9.7 - - - +
2104C MET* 3.4 28.7 - - - +
2107C SER* 3.0 42.5 + - - -
2108C LEU* 4.2 7.9 + - + +
2123C PRO 4.8 2.1 - - - +
2124C SER* 5.8 0.3 - - - -
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Residues in contact with PRO2059 (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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2057C GLN* 3.4 22.2 - - + +
2058C ASP* 1.3 94.7 - - + +
2060C ARG* 1.3 63.0 + - - +
2062C ALA* 3.2 4.5 + - + +
2063C THR* 2.8 41.0 + - + +
2123C PRO 4.8 4.7 - - - +
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Residues in contact with ARG2060 (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 ALA* 4.1 28.0 + - - +
2015C ALA* 5.7 2.2 - - - +
2052C TYR* 3.0 62.4 + - - +
2055C SER* 2.9 34.1 + - - -
2056C SER* 3.0 5.4 - - - +
2057C GLN* 3.3 36.3 + - + +
2058C ASP 3.4 0.2 - - - -
2059C PRO* 1.3 81.0 - - - +
2061C PRO* 1.3 71.5 - - + +
2063C THR* 3.6 3.6 + - - -
2064C GLY* 3.0 20.6 + - - -
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Residues in contact with PRO2061 (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 VAL* 4.9 19.3 - - + +
2052C TYR* 4.4 11.9 - - + -
2056C SER* 3.4 28.5 - - - -
2057C GLN 3.0 22.2 - - - +
2060C ARG* 1.3 101.6 - - + +
2062C ALA* 1.3 65.2 + - - +
2064C GLY* 3.6 3.0 + - - -
2065C ARG* 3.6 20.1 + - - +
2100C LEU* 5.5 1.8 - - + -
2104C MET* 3.5 18.4 - - + -
2125C TRP* 4.5 1.1 - - - -
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Residues in contact with ALA2062 (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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2058C ASP 3.7 9.1 + - - +
2059C PRO 3.2 7.3 + - - +
2061C PRO* 1.3 84.0 - - - +
2063C THR* 1.3 63.4 + - - +
2065C ARG* 3.1 15.6 - - - +
2066C PHE* 3.6 6.0 - - - -
2104C MET* 4.6 3.7 - - + +
2123C PRO 3.7 10.5 - - - +
2124C SER* 3.4 9.4 - - - +
2125C TRP* 3.2 47.8 - - + +
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Residues in contact with THR2063 (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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2059C PRO* 2.8 31.3 + - + +
2060C ARG* 3.6 4.2 + - - -
2062C ALA* 1.3 73.7 - - + +
2064C GLY* 1.3 58.8 + - - +
2065C ARG 2.8 13.3 + - - -
2066C PHE* 3.1 33.4 + - + +
2122C LEU 5.2 6.3 - - - +
2123C PRO* 4.4 10.5 - - + +
2124C SER 5.3 0.4 - - - +
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Residues in contact with GLY2064 (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 SER* 4.7 9.9 - - - -
2045C PHE* 3.9 14.3 - - - -
2060C ARG 3.0 18.0 + - - -
2061C PRO* 3.6 2.9 + - - -
2062C ALA 3.2 2.4 - - - -
2063C THR* 1.3 76.5 + - - +
2065C ARG* 1.3 63.3 + - - +
2066C PHE 3.4 4.1 + - - +
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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