Contacts of the helix formed by residues 214 - 219 (chain A) in PDB entry 2C17
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 ASN 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU 5.6 0.2 + - - -
81A ALA* 4.9 7.5 - - - +
85A PHE* 2.8 37.2 + - - +
86A ALA* 4.1 11.5 - - - +
94A LYS* 3.4 20.8 - - - +
135A ILE* 4.7 8.6 - - + +
136A CYS* 3.9 22.1 - - - +
213A THR* 1.3 75.4 - - - +
215A MET* 1.3 55.1 + - - +
217A ASP* 4.4 6.5 - - - +
218A THR* 2.6 32.9 + - - +
400A LEU* 3.9 14.2 - - - +
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Residues in contact with MET 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE 3.3 24.5 - - - +
136A CYS 3.4 19.7 - - - +
137A PHE* 3.9 8.5 - - - -
138A ASN* 4.0 2.7 - - + +
203A TYR* 3.7 43.7 - - + -
208A ARG 5.9 0.2 - - - +
210A ASP* 3.8 24.0 - - + +
212A ILE* 2.9 28.4 + - + +
213A THR 3.3 1.4 + - - -
214A ASN* 1.3 76.3 - - - +
216A LEU* 1.3 73.8 + - + +
218A THR* 3.4 2.5 - - - +
219A LEU* 2.9 37.9 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PHE 5.4 0.2 - - - +
208A ARG 3.6 22.7 - - - +
209A SER* 3.7 24.5 - - - +
210A ASP 3.7 21.8 - - - +
211A SER* 4.6 5.4 - - - -
212A ILE 2.8 18.0 + - - +
215A MET* 1.3 80.9 - - + +
217A ASP* 1.3 62.9 + - - +
219A LEU* 3.1 8.5 + - + +
220A MET* 2.8 61.9 + - + +
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 5.3 0.4 - - - -
85A PHE* 4.1 30.3 - - + -
212A ILE 4.4 0.6 + - - -
213A THR* 3.4 37.1 + - + -
214A ASN* 4.4 2.4 - - - +
216A LEU* 1.3 82.9 - - - +
218A THR* 1.3 60.5 + - - +
220A MET* 4.3 7.2 - - - -
221A GLN* 2.8 39.6 + - + +
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Residues in contact with THR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.8 32.7 + - + +
81A ALA* 6.2 0.5 - - - +
136A CYS 5.4 3.1 - - - +
200A LEU* 6.2 0.7 - - + -
214A ASN* 2.6 38.8 + - - +
215A MET* 3.4 6.4 + - - +
216A LEU 3.2 0.2 - - - -
217A ASP* 1.3 76.2 - - - +
219A LEU* 1.3 60.9 + - + +
221A GLN* 3.3 2.5 + - - +
222A ALA* 2.9 31.0 + - + +
245A ILE* 4.5 19.5 - - + -
248A THR* 5.8 4.3 - - + -
249A ILE* 5.8 5.6 - - + -
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.1 26.7 - - + +
203A TYR* 3.7 21.8 - - + +
204A LYS* 3.6 57.2 - - + +
215A MET* 2.9 26.6 + - - +
216A LEU* 3.7 4.5 - - + +
218A THR* 1.3 74.8 - - + +
220A MET* 1.3 72.9 + - + +
222A ALA* 3.5 14.9 + - - +
223A LYS* 3.8 10.6 + - - +
245A ILE* 4.4 10.5 - - + -
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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