Contacts of the helix formed by residues 269 - 279 (chain A) in PDB entry 5H8Q
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A VAL 3.4 10.7 + - - -
267A GLY 3.3 4.6 + - - -
268A ASP* 1.3 77.2 - - - +
270A GLU* 1.3 62.4 + - - +
271A MET 3.3 3.1 - - - -
272A GLU* 3.2 14.8 + - - +
273A GLU* 3.1 22.7 + - - +
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Residues in contact with GLU 270 (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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68A LYS* 2.8 41.5 + - - +
71A ARG* 3.7 14.5 + - - -
264A GLN* 3.9 3.8 - - - +
265A PHE* 3.0 28.9 + - + +
268A ASP* 2.8 37.4 + - - +
269A GLY* 1.3 76.1 - - - +
271A MET* 1.3 61.3 + - - +
273A GLU* 3.4 13.6 + - - +
274A LEU* 3.2 26.8 + - - +
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Residues in contact with MET 271 (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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61A PHE* 3.2 28.7 - - + -
65A ILE* 3.8 28.7 - - - -
130A PHE* 3.2 33.4 - - + +
262A LEU* 4.8 3.4 - - + +
265A PHE* 3.1 21.8 + - + +
266A VAL* 3.8 37.2 - - + +
270A GLU* 1.3 74.1 - - - +
272A GLU* 1.4 64.2 + - - +
274A LEU* 3.2 10.0 + - - +
275A GLU* 3.0 38.4 + - + +
302B 5YE 6.0 0.9 - - + -
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Residues in contact with GLU 272 (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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266A VAL 5.6 0.8 + - - +
269A GLY* 3.2 16.0 + - - +
271A MET* 1.4 76.7 - - - +
273A GLU* 1.3 61.0 + - - +
275A GLU* 3.3 16.0 + - + +
276A THR* 3.0 32.9 + - - +
246B PHE 4.4 14.8 - - - +
247B PHE* 5.5 1.7 - - - -
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Residues in contact with GLU 273 (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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68A LYS* 5.0 9.9 + - - -
269A GLY 3.1 11.9 + - - +
270A GLU* 3.5 15.2 - - - +
272A GLU* 1.3 75.4 - - - +
274A LEU* 1.4 59.8 + - + +
276A THR* 3.3 8.5 + - - -
277A LEU* 3.0 30.3 + - + +
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Residues in contact with LEU 274 (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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61A PHE* 3.6 16.8 - - + +
64A ASP* 3.6 37.9 - - + +
65A ILE* 3.7 31.6 - - + +
68A LYS* 3.9 28.7 - - + -
270A GLU 3.2 14.1 + - - +
271A MET* 3.2 13.2 + - - +
273A GLU* 1.4 76.2 - - + +
275A GLU* 1.3 58.9 + - - +
277A LEU* 3.3 11.7 + - + -
278A TRP* 2.9 36.3 + - - +
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Residues in contact with GLU 275 (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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61A PHE* 3.7 19.1 - - + -
130A PHE 5.2 1.1 - - - +
131A VAL* 5.1 5.2 - - - +
271A MET* 3.0 34.6 + - - +
272A GLU* 3.3 15.6 + - + +
274A LEU* 1.3 74.4 - - - +
276A THR* 1.3 57.9 + - - +
279A LEU* 2.7 49.0 + - + +
280A THR* 3.4 7.6 + - - +
248B ARG* 2.7 31.5 + - - -
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Residues in contact with THR 276 (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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272A GLU* 3.0 18.8 + - - +
273A GLU* 3.6 11.2 - - - -
274A LEU 3.3 0.2 - - - -
275A GLU* 1.3 75.4 - - - +
277A LEU* 1.3 61.9 + - - +
280A THR* 3.0 35.2 + - + +
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Residues in contact with LEU 277 (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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34A ASN* 5.8 1.6 - - - +
64A ASP* 3.5 11.4 - - - +
224A ARG* 5.3 2.9 + - - -
273A GLU* 3.0 18.0 + - + +
274A LEU* 3.3 11.9 + - + +
276A THR* 1.3 79.4 - - - +
278A TRP* 1.4 90.6 + - + +
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Residues in contact with TRP 278 (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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17A PRO* 3.8 17.6 - - + +
20A ILE* 3.8 18.6 - - + -
34A ASN* 3.6 28.5 - - - -
59A LYS* 4.1 11.4 - - + -
60A GLY* 3.5 36.0 + - - -
61A PHE* 3.6 33.4 - + + -
64A ASP* 2.8 31.6 + - - -
220A TYR* 3.4 19.2 + - - -
224A ARG* 3.7 7.3 + - - +
274A LEU* 2.9 28.0 + - + +
277A LEU* 1.4 99.8 - - + +
279A LEU* 1.3 65.0 + - + +
280A THR 3.7 1.6 - - - -
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Residues in contact with LEU 279 (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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17A PRO* 3.5 28.5 - - + -
18A PHE* 3.8 28.0 - - + -
61A PHE* 3.7 34.8 - - + -
131A VAL* 4.3 8.1 - - + -
220A TYR* 4.0 22.0 - - + -
275A GLU* 2.7 36.9 + - + +
278A TRP* 1.3 78.9 - - + +
280A THR* 1.3 64.0 + - - +
281A GLY 3.8 0.9 + - - -
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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