Contacts of the helix formed by residues 213 - 218 (chain C) in PDB entry 3SKU
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 THR 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C ALA 4.3 17.0 - - - +
43C GLY* 4.3 5.6 - - - -
44C LEU 4.6 0.4 - - - +
211C GLY 5.3 1.6 - - - -
212C VAL* 1.3 87.6 - - - +
214C VAL* 1.3 57.0 + - - +
215C ASP* 3.7 8.5 + - - +
216C SER* 2.5 58.5 + - - +
217C ILE 3.6 2.4 + - - -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 4.6 7.9 - - + +
43C GLY* 5.3 0.6 - - - -
44C LEU* 3.8 25.2 - - + +
112C VAL* 4.1 4.9 - - + -
114C GLU* 6.1 0.2 - - - +
134C ARG* 3.7 45.3 - - + +
213C THR* 1.3 70.2 - - - +
215C ASP* 1.3 68.4 + - - +
216C SER 3.3 0.9 + - - -
217C ILE* 3.5 4.2 + - - -
218C GLY 3.4 4.0 + - - -
219C MET* 3.3 60.4 + - + +
77E ASN* 4.4 0.2 - - - -
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Residues in contact with ASP 215 (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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39C HIS* 2.9 31.4 + - - -
134C ARG* 3.4 21.2 + - - -
213C THR* 2.7 10.6 + - - +
214C VAL* 1.3 79.0 - - - +
216C SER* 1.3 60.4 + - - +
220C LEU* 5.8 0.2 - - - +
76E GLN* 4.1 2.3 - - - +
77E ASN* 2.7 39.0 + - - +
80E ILE* 4.3 4.2 - - - +
90E LEU* 3.1 46.1 - - + +
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Residues in contact with SER 216 (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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212C VAL* 4.5 3.4 - - - -
213C THR* 2.5 49.6 + - - +
215C ASP* 1.3 74.1 - - - +
217C ILE* 1.3 68.2 + - - -
218C GLY 3.3 1.2 + - - -
75E LYS 3.3 12.0 - - - +
76E GLN* 3.7 10.4 + - - +
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Residues in contact with ILE 217 (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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44C LEU* 5.3 0.7 - - + -
108C ILE* 5.8 0.9 - - + -
109C PRO* 3.4 48.5 - - + +
136C ASN* 3.4 16.4 + - - +
137C TYR* 4.4 7.3 + - + -
201C ALA* 5.6 3.1 - - - +
203C LEU* 3.8 25.6 - - + -
212C VAL* 3.2 31.4 - - + -
213C THR 3.6 0.2 + - - -
214C VAL* 3.5 6.7 + - - +
216C SER* 1.3 78.8 - - - +
218C GLY* 1.3 56.4 + - - +
219C MET* 3.5 26.9 - - + -
75E LYS* 3.6 8.6 + - - +
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Residues in contact with GLY 218 (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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136C ASN* 2.9 20.0 - - - +
214C VAL 3.4 2.4 + - - -
216C SER 3.2 5.1 + - - -
217C ILE* 1.3 77.8 - - - +
219C MET* 1.3 66.9 - - - +
220C LEU* 4.6 0.2 - - - +
68E GLN* 3.3 16.4 + - - -
75E LYS* 3.6 20.8 - - - +
76E GLN 4.5 0.2 - - - -
77E ASN* 3.3 15.1 - - - +
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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