Contacts of the helix formed by residues 200 - 205 (chain C) in PDB entry 5NXR
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 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157C LYS* 5.7 0.4 - - + -
159C GLY* 3.9 17.3 - - - -
160C ASP* 2.9 22.4 + - - +
168C MET* 5.6 0.2 - - - -
171C ASP* 4.2 3.5 - - + +
172C ASN 3.4 39.0 - - - +
173C GLY* 3.7 2.5 - - - +
199C ARG* 1.3 75.3 - - - +
201C PRO* 1.3 73.2 - - - +
202C ASN* 4.2 0.3 - - - +
203C GLN* 2.9 30.5 + - - +
204C LYS* 3.0 21.8 + - - -
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Residues in contact with PRO 201 (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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28B LYS* 3.5 40.8 - - + +
159C GLY 5.8 0.7 - - - +
160C ASP* 3.7 18.6 - - + +
199C ARG 4.5 1.6 - - - +
200C THR* 1.3 85.2 - - - +
202C ASN* 1.3 57.8 + - - +
204C LYS* 3.3 16.3 + - - +
205C ALA* 2.9 29.6 + - - +
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Residues in contact with ASN 202 (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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160C ASP* 3.0 37.1 + - - +
161C ASN* 6.0 1.0 - - - +
168C MET* 3.7 29.2 - - + +
200C THR* 3.2 0.6 - - - +
201C PRO* 1.3 77.4 - - - +
203C GLN* 1.3 68.0 + - - +
205C ALA* 3.4 17.7 + - - +
206C GLY 4.0 2.3 + - - -
207C VAL 4.8 5.2 + - - +
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Residues in contact with GLN 203 (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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124C ASN* 6.0 0.2 - - - +
125C PHE* 3.6 20.4 - - - -
168C MET* 3.3 38.8 + - + +
169C ALA* 5.2 1.8 - - - +
171C ASP 2.8 33.7 + - - +
172C ASN* 3.8 0.9 - - - -
199C ARG* 3.2 42.8 + - + +
200C THR* 2.9 38.7 + - - +
202C ASN* 1.3 78.8 - - - +
204C LYS* 1.3 61.1 + - - +
205C ALA 3.2 1.8 + - - -
206C GLY* 3.2 9.4 + - - -
217C SER* 5.5 1.2 + - - -
218C ALA 3.6 3.6 - - - +
258C ILE* 5.8 4.2 - - + +
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Residues in contact with LYS 204 (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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28B LYS* 6.4 0.2 - - - +
198C SER* 5.9 1.4 - - - -
199C ARG* 3.4 41.0 + - + +
200C THR 3.0 16.8 + - - +
201C PRO* 3.6 11.4 - - + +
203C GLN* 1.3 72.1 - - - +
205C ALA* 1.3 59.9 + - - +
206C GLY* 3.0 7.8 + - - -
218C ALA 5.1 0.4 - - - -
219C THR* 4.3 15.8 - - + +
220C GLY 3.4 22.2 - - - +
221C LYS* 3.9 33.6 + - + +
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Residues in contact with ALA 205 (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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201C PRO 2.9 15.9 + - - +
202C ASN* 3.6 14.1 - - - +
203C GLN 3.2 1.2 - - - -
204C LYS* 1.3 77.7 - - - +
206C GLY* 1.3 63.1 + - - +
207C VAL* 3.4 19.4 + - + +
219C THR* 5.2 1.0 + - - -
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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