Contacts of the helix formed by residues 242 - 250 (chain A) in PDB entry 3RAW
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 ASN 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A 3RA 3.9 18.0 - - - -
240A GLY 3.8 1.6 + - - -
241A LYS* 1.3 77.5 - - - +
243A THR* 1.3 60.3 + - - +
244A PHE* 3.0 14.0 + - - +
245A GLU* 2.9 46.6 + - - +
246A PHE* 3.0 25.8 + - - +
287A GLU* 3.3 38.8 + - - +
289A ILE 3.2 14.8 - - - +
290A LEU* 3.9 13.0 - - + +
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Residues in contact with THR 243 (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* 1.3 73.1 - - - +
244A PHE* 1.3 59.0 + - - +
246A PHE 4.0 0.2 - - - -
247A LEU* 3.3 12.8 + - - +
255A TYR* 2.6 30.6 + - - -
263A MET* 4.6 1.6 - - - -
286A PRO* 2.7 26.8 + - - +
289A ILE* 2.8 30.7 + - + +
290A LEU 4.6 0.4 - - - +
291A PHE* 3.9 26.7 - - + -
316A ILE* 4.4 7.6 - - + -
367A TYR* 2.8 37.6 + - + +
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Residues in contact with PHE 244 (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* 3.0 10.1 + - - +
243A THR* 1.3 79.6 + - - +
245A GLU* 1.3 82.6 + - + +
247A LEU* 3.1 9.5 + - + +
248A LYS* 2.8 47.8 + - + +
252A PHE* 3.9 26.7 - + - -
286A PRO* 3.6 8.7 + - + -
287A GLU* 3.7 26.9 - - + +
366A GLU* 4.5 15.9 - - - -
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Residues in contact with GLU 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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1A 3RA 5.7 3.4 - - + -
162A LEU 6.2 0.2 - - - +
241A LYS* 4.5 13.7 - - + +
242A ASN* 2.9 38.1 + - - +
244A PHE* 1.3 92.5 - - + +
246A PHE* 1.3 66.3 + - - +
248A LYS* 3.2 18.3 + - - +
249A GLU* 2.9 44.3 + - - +
287A GLU* 6.0 0.2 - - + -
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Residues in contact with PHE 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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241A LYS* 4.4 13.6 - - + +
242A ASN 3.0 14.0 + - - +
245A GLU* 1.3 75.6 - - - +
247A LEU* 1.3 64.3 + - - +
249A GLU* 3.3 5.7 + - + +
250A ASN* 3.0 24.1 + - + +
255A TYR* 3.4 36.3 - + - +
291A PHE* 3.8 13.0 - + + -
294A SER* 3.5 35.4 - - - -
296A PHE* 3.8 23.3 - + + -
309A LYS* 4.1 28.8 - - + +
310A SER* 5.1 0.2 - - - -
311A VAL* 3.7 30.5 - - + -
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Residues in contact with LEU 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 THR 3.3 13.5 + - - +
244A PHE* 3.1 14.7 + - + +
246A PHE* 1.3 82.5 - - - +
248A LYS* 1.3 53.0 + - - +
250A ASN* 3.0 14.5 + - + +
251A ASN 3.3 0.2 + - - -
252A PHE* 2.8 50.9 + - + -
253A GLN 3.1 30.3 - - - +
254A PRO* 4.3 2.9 - - + -
255A TYR* 3.7 22.8 + - + +
286A PRO* 6.0 1.6 - - + -
366A GLU* 4.1 28.7 - - + +
367A TYR* 5.3 2.9 - - + -
370A GLY* 4.0 20.6 - - - +
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Residues in contact with LYS 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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244A PHE* 2.8 41.0 + - + +
245A GLU* 3.6 21.6 + - - +
247A LEU* 1.3 73.8 - - - +
249A GLU* 1.3 65.3 + - + +
251A ASN* 3.0 19.2 + - - -
252A PHE* 3.8 31.1 - - + -
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Residues in contact with GLU 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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241A LYS* 4.3 21.1 - - + -
245A GLU* 2.9 34.1 + - - +
246A PHE* 3.7 6.7 - - + +
248A LYS* 1.3 84.7 - - - +
250A ASN* 1.3 55.6 + - - +
251A ASN* 3.2 3.3 + - - +
309A LYS* 3.4 34.0 + - + +
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Residues in contact with ASN 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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246A PHE* 3.0 20.6 + - + +
247A LEU* 3.0 13.6 + - - +
249A GLU* 1.3 74.8 - - - +
251A ASN* 1.3 69.9 + - - +
252A PHE 3.1 0.7 - - - -
253A GLN* 3.0 50.6 + - - +
254A PRO 4.7 4.0 + - - -
255A TYR* 6.1 0.8 - - - +
308A GLU* 4.0 3.9 - - - +
309A LYS* 3.0 55.1 + - + +
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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