Contacts of the helix formed by residues 250 - 261 (chain C) in PDB entry 1DS5
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 GLY 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C ALA 2.4 28.3 + - - -
248C VAL 3.2 2.6 + - - -
249C LEU* 1.3 80.2 - - - +
251C THR* 1.3 64.5 + - - -
252C ASP 3.4 2.9 - - - -
253C GLY 3.3 8.0 + - - -
276C HIS 3.4 12.1 - - - -
277C SER 3.5 16.4 - - - -
278C ARG* 3.6 1.6 - - - -
307C TYR* 3.1 11.8 + - - -
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Residues in contact with THR 251 (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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246C ALA* 4.1 7.6 - - + -
250C GLY* 1.3 65.6 - - - -
252C ASP* 1.3 59.2 + - - -
253C GLY 2.8 11.8 + - - -
254C LEU* 2.9 19.5 + - + -
255C ASN* 3.0 26.3 + - - -
273C VAL* 3.8 19.7 - - + -
274C GLY 2.9 26.2 - - - +
275C ARG* 3.7 9.9 - - - +
276C HIS* 2.9 37.6 + - + +
307C TYR* 4.4 0.2 - - - -
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Residues in contact with ASP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C GLY 3.4 2.2 + - - -
251C THR* 1.3 80.4 + - - +
253C GLY* 1.3 58.5 + - - +
255C ASN* 4.1 6.0 - - - +
256C VAL* 3.0 25.7 + - - +
275C ARG* 4.9 14.8 + - - -
276C HIS 4.3 6.1 + - - +
277C SER* 5.6 2.5 - - - -
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Residues in contact with GLY 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU 4.8 2.1 + - - -
250C GLY 3.3 5.2 + - - -
251C THR 2.9 0.8 - - - -
252C ASP* 1.3 80.3 - - - +
254C LEU* 1.3 63.5 + - - +
255C ASN 2.8 6.3 + - - -
256C VAL* 3.1 7.0 + - - +
257C TYR* 3.0 23.9 + - - +
307C TYR* 3.6 16.3 - - - -
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Residues in contact with LEU 254 (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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200C PRO* 5.7 0.2 - - + -
204C VAL* 4.5 7.6 - - + -
242C LEU* 4.2 28.0 - - + -
246C ALA* 4.7 3.4 - - + -
251C THR* 2.9 13.4 + - + +
253C GLY* 1.3 75.9 - - - +
255C ASN* 1.3 62.4 + - - +
257C TYR* 3.4 9.9 - - + +
258C LEU* 3.0 50.4 + - + +
265C LEU* 4.5 7.6 - - + -
273C VAL* 3.7 30.1 - - + -
307C TYR* 3.2 46.8 - - + +
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Residues in contact with ASN 255 (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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251C THR* 3.0 30.8 + - - +
252C ASP* 4.5 6.1 - - - +
253C GLY 2.8 1.8 + - - -
254C LEU* 1.3 84.8 - - - +
256C VAL* 1.3 68.8 + - + +
257C TYR 3.0 1.6 - - - -
258C LEU* 3.0 13.5 + - - +
259C ASN* 2.9 36.0 + - - +
265C LEU* 6.4 0.2 - - - +
275C ARG* 5.8 4.2 + - - -
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Residues in contact with VAL 256 (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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252C ASP 3.0 22.0 - - - +
253C GLY* 3.6 7.4 - - - +
255C ASN* 1.3 77.5 - - + +
257C TYR* 1.3 62.6 + - - +
259C ASN* 3.4 5.3 + - - +
260C LYS* 3.0 25.7 + - + +
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Residues in contact with TYR 257 (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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200C PRO* 4.6 7.6 - - + -
201C GLU* 3.4 29.3 + - - +
204C VAL* 3.8 24.0 - - + -
206C LEU* 3.5 18.4 - - + +
253C GLY 3.0 16.1 + - - +
254C LEU* 3.4 13.2 - - + +
256C VAL* 1.3 77.2 - - - +
258C LEU* 1.3 74.0 + - + +
260C LYS* 3.2 7.5 + - - +
261C TYR* 3.2 45.7 + + - +
263C ILE* 5.7 1.1 - - + -
307C TYR* 3.1 47.3 + - + -
308C ASP* 3.6 15.7 - - + -
309C HIS* 3.8 4.4 + - - -
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Residues in contact with LEU 258 (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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204C VAL* 4.1 7.9 - - + -
254C LEU* 3.0 29.0 + - + +
255C ASN* 3.0 15.4 + - - +
257C TYR* 1.3 93.7 - - + +
259C ASN* 1.3 65.7 + - - +
261C TYR 3.5 0.3 + - - -
262C ARG* 3.1 2.6 + - - -
263C ILE* 2.8 71.3 + - + +
265C LEU* 3.4 42.2 - - + +
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Residues in contact with ASN 259 (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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255C ASN* 2.9 28.3 + - - +
256C VAL* 4.0 4.7 - - - +
258C LEU* 1.3 78.5 + - - +
260C LYS* 1.3 67.3 + - - +
262C ARG* 2.7 19.7 + - - +
263C ILE 5.5 1.8 + - - -
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Residues in contact with LYS 260 (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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6C MET* 3.9 25.7 - - + +
256C VAL* 3.0 17.0 + - + +
257C TYR* 3.5 10.5 - - - +
259C ASN* 1.3 75.6 - - - +
261C TYR* 1.3 95.2 + - + +
262C ARG* 3.5 4.2 + - - +
308C ASP* 3.2 23.0 + - - +
310C GLN* 4.5 8.5 - - - +
311C GLU* 4.4 7.6 - - - +
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Residues in contact with TYR 261 (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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6C MET* 3.4 53.1 + - + +
206C LEU* 3.8 9.9 - - + -
257C TYR* 3.2 32.5 + + + +
259C ASN 3.1 1.0 - - - -
260C LYS* 1.3 101.4 + - + +
262C ARG* 1.3 83.6 + - - +
263C ILE* 2.9 28.5 + - + +
308C ASP* 2.9 35.7 + - - -
309C HIS* 3.7 19.3 + + - -
310C GLN* 3.4 19.7 + - - +
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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