Contacts of the helix formed by residues 244 - 252 (chain A) in PDB entry 1A8H
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 GLU 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.7 11.8 + - - +
242A GLU 3.6 3.8 + - - -
243A GLY* 1.3 72.3 - - - -
245A ALA* 1.3 61.2 + - - +
247A ARG* 3.2 22.2 + - - +
248A THR* 2.9 46.2 + - - -
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Residues in contact with ALA 245 (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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44A PHE* 5.9 4.0 - - + -
237A ALA 5.2 1.1 - - - +
238A LEU* 3.8 32.2 - - + +
239A ASP* 4.9 5.4 - - - +
244A GLU* 1.3 81.5 - - - +
246A TYR* 1.3 55.6 + - - +
248A THR* 4.5 0.9 - - - -
249A PHE* 2.9 52.0 + - + +
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Residues in contact with TYR 246 (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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235A VAL* 4.2 13.5 - - + -
238A LEU* 3.2 27.5 + - + +
240A TYR* 2.8 60.4 - + + +
241A PRO 4.1 5.8 - - - -
243A GLY 3.4 6.5 + - - +
244A GLU 3.2 0.4 - - - -
245A ALA* 1.3 78.4 - - - +
247A ARG* 1.3 69.2 + - + +
250A TRP* 3.1 54.5 + + + +
251A PRO* 3.7 0.7 - - - +
277A GLY 5.4 0.2 + - - -
278A ILE* 3.5 6.6 - - + +
279A PRO* 3.3 30.1 - - - +
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Residues in contact with ARG 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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243A GLY 3.5 8.3 + - - +
244A GLU* 3.2 25.4 + - - +
246A TYR* 1.3 88.3 - - + +
248A THR* 1.3 63.1 + - - +
251A PRO* 3.3 19.1 - - - +
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Residues in contact with THR 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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1A MET* 5.4 2.0 - - - +
4A VAL* 3.6 17.3 - - + +
42A ARG* 3.4 42.2 + - - +
244A GLU* 2.9 31.8 + - - -
245A ALA* 3.9 2.4 - - - -
247A ARG* 1.3 79.3 - - - +
249A PHE* 1.3 70.8 + - + +
251A PRO* 3.5 3.6 - - - +
252A HIS* 3.3 26.0 + - - -
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Residues in contact with PHE 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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4A VAL* 3.6 18.2 - - + -
5A PHE 3.7 6.5 - - - -
6A TYR* 3.6 24.4 - - + +
42A ARG* 3.5 50.3 - - + -
43A THR 3.7 5.6 - - - -
44A PHE* 3.6 43.1 - + + -
238A LEU* 4.1 7.0 - - + -
245A ALA* 2.9 44.3 + - + +
248A THR* 1.3 79.2 - - + +
250A TRP* 1.3 65.4 + - - +
251A PRO* 3.2 3.8 - - - -
252A HIS* 2.9 13.9 + - - +
253A ALA 3.5 6.4 + - - -
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Residues in contact with TRP 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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6A TYR* 3.9 14.4 - + - -
234A TYR* 4.2 10.1 - - + -
235A VAL* 4.2 12.1 - - + -
238A LEU* 3.9 7.9 - - + +
246A TYR* 3.1 55.0 + + + +
249A PHE* 1.3 75.0 - - - +
251A PRO* 1.3 63.8 - - + +
252A HIS 2.9 6.1 + - - -
253A ALA* 3.0 32.1 + - + +
255A HIS* 3.7 30.3 - + - -
269A TRP* 4.1 12.6 - + - -
273A LEU* 4.0 19.1 - - + -
278A ILE* 3.4 8.6 - - + +
279A PRO* 2.8 42.8 + - + -
280A MET 4.4 5.6 + - - +
281A TYR* 4.2 9.1 - - + -
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Residues in contact with PRO 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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246A TYR 3.7 0.9 - - - +
247A ARG* 3.3 26.2 - - - +
248A THR 3.5 4.5 - - - +
249A PHE 3.2 4.9 - - - -
250A TRP* 1.3 99.6 - - + +
252A HIS* 1.3 70.2 + - + +
253A ALA 3.6 0.4 - - - -
279A PRO* 6.1 2.5 - - + -
280A MET 5.5 3.7 - - - +
282A ARG* 3.0 30.4 + - - +
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Residues in contact with HIS 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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2A GLU 4.7 6.2 + - - -
4A VAL* 3.2 59.3 - - + +
5A PHE* 4.9 0.8 - - - -
6A TYR* 3.6 12.0 + - - +
248A THR 3.3 15.9 + - - -
249A PHE 2.9 7.7 + - - +
251A PRO* 1.3 88.1 - - + +
253A ALA* 1.3 65.5 + - - +
254A TRP* 3.2 18.6 + - + +
282A ARG* 3.1 39.5 + - - +
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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