Contacts of the helix formed by residues 246 - 258 (chain A) in PDB entry 5DTQ
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ALA 3.6 3.1 + - - -
245A PHE* 1.3 77.9 - - - +
247A PRO* 1.4 74.5 - - - +
248A GLU 3.4 2.5 - - - -
249A VAL* 4.1 13.2 - - - +
250A ASP* 3.2 20.6 + - - +
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Residues in contact with PRO 247 (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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246A GLY* 1.4 83.5 - - - +
248A GLU* 1.3 65.3 + - + +
250A ASP* 3.5 8.3 + - + +
251A HIS* 2.9 29.9 + - - +
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Residues in contact with GLU 248 (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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246A GLY 3.4 0.2 - - - -
247A PRO* 1.3 82.2 - - + +
249A VAL* 1.3 60.8 + - + +
251A HIS* 3.4 16.8 + - - +
252A GLN* 2.9 68.2 + - + +
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Residues in contact with VAL 249 (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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223A PHE* 4.5 9.9 - - + -
224A LEU* 4.4 24.6 - - + +
245A PHE* 3.6 35.9 - - + -
246A GLY* 3.8 19.4 + - - +
248A GLU* 1.3 77.4 - - + +
250A ASP* 1.3 56.6 + - - +
252A GLN* 3.5 1.6 + - - +
253A LEU* 2.9 29.5 + - - +
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Residues in contact with ASP 250 (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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242A ASN* 4.7 4.2 + - - -
245A PHE* 4.9 7.6 - - + +
246A GLY 3.2 19.4 + - - +
247A PRO* 3.5 8.9 - - + +
249A VAL* 1.3 76.5 - - - +
251A HIS* 1.4 58.6 + - - +
253A LEU* 3.4 8.1 + - - +
254A LYS* 2.8 61.3 + - - +
271A PRO 5.2 1.6 - - - +
272A PHE* 3.5 29.0 - - - -
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Residues in contact with HIS 251 (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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247A PRO 2.9 17.7 + - - +
248A GLU* 3.6 18.4 - - - +
250A ASP* 1.4 72.6 - - - +
252A GLN* 1.3 92.6 + - - +
254A LYS* 3.4 15.9 + - - +
255A GLU* 3.2 30.9 + - + +
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Residues in contact with GLN 252 (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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224A LEU* 3.7 29.2 - - + -
229A ARG* 4.2 2.8 + - - -
248A GLU* 2.9 45.4 + - + +
249A VAL 3.8 2.0 - - - +
251A HIS* 1.3 87.6 + - - +
253A LEU* 1.3 65.3 + - - +
255A GLU* 3.2 17.4 + - - +
256A ARG* 3.0 54.1 + - - +
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Residues in contact with LEU 253 (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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162A LEU* 3.8 18.6 - - + -
223A PHE* 3.7 27.8 - - + -
224A LEU* 4.2 5.6 - - + +
232A ILE* 4.8 1.8 - - + -
240A VAL* 4.2 6.3 - - + -
245A PHE* 3.5 38.1 - - + -
249A VAL 2.9 18.7 + - - +
250A ASP* 3.6 4.9 - - - +
252A GLN* 1.3 73.7 - - - +
254A LYS* 1.3 57.6 + - - +
256A ARG* 3.1 13.5 + - + +
257A PHE* 2.9 51.8 + - + -
272A PHE* 4.0 21.5 - - + -
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Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A ASP* 2.8 48.7 + - - +
251A HIS* 3.6 14.1 - - - +
252A GLN 3.3 0.2 - - - -
253A LEU* 1.3 74.5 - - - +
255A GLU* 1.3 55.5 + - - +
257A PHE* 3.3 5.0 + - - -
258A ALA* 3.0 24.3 + - - +
272A PHE* 3.0 40.6 + - + +
287A ILE* 3.1 40.8 - - + +
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Residues in contact with GLU 255 (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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229A ARG* 2.8 33.8 + - - +
251A HIS* 3.2 26.9 + - + +
252A GLN* 3.2 23.7 + - - +
254A LYS* 1.3 73.9 - - - +
256A ARG* 1.4 66.5 + - - +
258A ALA* 3.4 19.6 + - - +
259A ASN* 3.7 13.7 + - - +
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Residues in contact with ARG 256 (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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223A PHE 4.5 1.2 + - - -
224A LEU* 2.7 51.3 + - + +
225A SER 4.6 0.2 + - - -
229A ARG* 3.5 59.4 - - - +
232A ILE* 3.6 42.0 - - + +
233A ALA 4.7 1.7 + - - -
252A GLN* 3.0 57.4 + - - +
253A LEU* 3.1 12.8 + - + +
255A GLU* 1.4 80.3 + - - +
257A PHE* 1.3 63.5 + - + +
259A ASN* 3.3 22.3 + - - +
260A MET* 4.1 2.3 + - - +
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Residues in contact with PHE 257 (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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162A LEU* 4.2 1.6 - - + -
232A ILE* 3.8 14.4 - - + -
238A ILE* 3.9 22.9 - - + -
240A VAL* 4.3 3.6 - - + -
253A LEU* 2.9 44.3 + - + +
254A LYS* 3.7 10.1 - - + +
255A GLU 3.3 0.2 - - - -
256A ARG* 1.3 73.8 - - - +
258A ALA* 1.3 54.7 + - - +
259A ASN 3.1 5.4 - - - -
260A MET* 3.2 33.4 + - - +
266A ILE* 3.8 33.2 - - + -
272A PHE* 3.6 44.6 - + + -
287A ILE* 4.2 8.3 - - + -
291A MET* 4.4 4.9 - - + -
317A ILE* 3.3 20.5 - - - +
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Residues in contact with ALA 258 (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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254A LYS 3.0 13.1 + - - +
255A GLU* 3.5 16.4 - - - +
256A ARG 3.2 0.4 - - - -
257A PHE* 1.3 74.6 - - - +
259A ASN* 1.3 62.4 + - - +
260A MET 3.5 0.4 - - - -
287A ILE* 4.1 3.6 - - + +
290A ILE* 3.8 20.1 - - + +
319A ARG* 2.8 19.8 + - - -
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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