Contacts of the helix formed by residues 247 - 260 (chain A) in PDB entry 3R5J
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 THR 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLN* 1.3 74.8 - - - +
248A ALA* 1.3 58.2 + - - +
249A GLN* 3.6 7.5 + - - +
250A GLU* 2.9 40.7 + - - +
251A MET* 2.8 27.7 + - - +
285A GLY* 3.9 0.4 - - - -
286A VAL* 3.9 15.7 - - + +
287A ASP* 3.7 28.0 - - + -
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Residues in contact with ALA 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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247A THR* 1.3 72.0 - - - +
249A GLN* 1.3 62.5 + - - +
251A MET* 3.5 18.5 + - + +
252A GLN* 3.1 23.4 + - - +
285A GLY* 3.6 2.4 - - - -
287A ASP* 3.2 7.9 + - - +
289A LYS* 3.5 42.6 - - + +
290A LEU 4.1 14.8 - - - +
291A LEU* 4.3 5.9 - - + +
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Residues in contact with GLN 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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247A THR* 3.2 7.9 + - - +
248A ALA* 1.3 80.3 - - - +
250A GLU* 1.3 56.7 + - + +
252A GLN* 3.4 6.9 + - + +
253A GLU* 3.0 60.5 + - + +
287A ASP* 4.9 2.5 + - - +
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Residues in contact with GLU 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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245A ASP 4.4 2.3 - - - +
246A GLN* 3.3 30.4 + - - +
247A THR* 2.9 45.3 + - - +
249A GLN* 1.3 73.2 - - + +
251A MET* 1.3 62.3 + - - +
253A GLU* 4.2 12.1 - - - +
254A LYS* 2.8 50.4 + - - +
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Residues in contact with MET 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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205A LEU* 4.0 25.8 - - + -
207A ASN* 3.4 25.6 - - - -
246A GLN* 3.7 16.8 - - + +
247A THR 2.8 14.6 + - - +
248A ALA* 3.5 24.2 - - - +
250A GLU* 1.3 75.4 - - - +
252A GLN* 1.3 57.1 + - - +
254A LYS* 4.2 1.3 - - - +
255A LEU* 2.8 39.0 + - + +
283A ILE* 4.2 15.5 - - + +
284A TYR 3.9 3.6 - - - +
285A GLY* 3.6 18.2 - - - +
291A LEU* 3.8 29.4 - - + -
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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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248A ALA 3.1 14.6 + - - +
249A GLN* 3.6 10.1 - - + +
251A MET* 1.3 76.7 - - - +
253A GLU* 1.3 71.2 + - - +
255A LEU* 3.9 4.0 - - - +
256A GLN* 3.0 39.8 + - - +
291A LEU* 4.1 23.7 - - + +
295A GLU* 5.7 5.5 - - + +
299A LEU* 4.0 27.4 - - + +
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Residues in contact with GLU 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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249A GLN* 3.0 49.6 + - + +
250A GLU* 3.8 14.7 - - - +
252A GLN* 1.3 87.7 - - - +
254A LYS* 1.3 63.1 + - + +
256A GLN* 3.4 7.5 + - - +
257A ASN* 3.0 36.8 + - - +
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Residues in contact with LYS 254 (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 LEU* 3.6 40.1 - - + +
246A GLN* 2.7 36.7 + - - +
250A GLU* 2.8 36.8 + - - +
251A MET* 4.2 1.3 - - - +
253A GLU* 1.3 76.5 - - + +
255A LEU* 1.3 60.2 + - - +
257A ASN* 3.6 13.5 - - - +
258A PHE* 2.9 29.3 + - - +
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Residues in contact with LEU 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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203A LEU* 3.6 26.5 - - + -
205A LEU* 4.6 5.6 - - + -
251A MET* 2.8 26.3 + - + +
252A GLN* 3.9 1.6 - - - +
254A LYS* 1.3 73.1 - - - +
256A GLN* 1.3 60.3 + - - +
258A PHE* 3.3 4.9 + - - +
259A ALA* 2.8 30.3 + - - +
272A VAL* 4.1 20.4 - - + -
274A LEU* 4.3 12.8 - - + -
283A ILE* 6.0 0.2 - - + -
291A LEU* 3.9 24.7 - - + -
296A VAL* 4.0 17.9 - - + -
299A LEU* 3.8 17.0 - - + -
300A PHE* 4.1 18.5 - - + -
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Residues in contact with GLN 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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252A GLN* 3.0 33.4 + - - +
253A GLU* 3.7 7.3 - - - +
254A LYS 3.3 0.2 - - - -
255A LEU* 1.3 77.2 - - - +
257A ASN* 1.3 66.5 + - - +
259A ALA* 3.2 4.9 + - + +
260A GLN* 3.1 42.2 + - + +
299A LEU* 3.7 31.0 - - + +
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Residues in contact with ASN 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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253A GLU* 3.0 25.0 + - - +
254A LYS* 3.6 16.6 - - - +
255A LEU 3.3 0.2 - - - -
256A GLN* 1.3 78.4 + - - +
258A PHE* 1.3 63.1 + - - +
260A GLN* 3.2 15.7 + - - +
261A LEU* 3.3 18.4 + - + +
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Residues in contact with PHE 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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201A LEU* 3.6 37.9 - - + -
202A ALA 3.8 7.9 - - - -
203A LEU* 3.8 43.3 - - + -
241A HIS* 4.0 17.0 - + + -
254A LYS 2.9 18.1 + - - +
255A LEU* 3.5 5.8 - - - +
257A ASN* 1.3 78.4 - - - +
259A ALA* 1.3 61.7 + - - +
260A GLN 3.1 0.9 + - - -
261A LEU* 3.2 27.7 + - + +
264A HIS* 2.9 24.8 + + - -
270A CYS* 3.8 23.3 - - - -
272A VAL* 4.0 11.2 - - + -
300A PHE* 3.8 15.0 - + - -
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Residues in contact with ALA 259 (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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255A LEU 2.8 20.3 + - - +
256A GLN* 3.2 5.1 + - + +
258A PHE* 1.3 73.8 - - - +
260A GLN* 1.3 63.5 + - - +
261A LEU 3.4 0.7 - - - +
264A HIS* 3.3 17.1 - - - +
299A LEU* 3.6 30.1 - - + +
300A PHE* 3.6 27.6 - - + -
305A CYS* 3.5 16.9 - - - -
307A SER* 5.8 0.9 - - - -
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Residues in contact with GLN 260 (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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256A GLN* 3.1 29.9 + - + +
257A ASN* 3.2 8.9 + - - +
258A PHE 3.1 0.6 - - - -
259A ALA* 1.3 87.6 + - - +
261A LEU* 1.3 66.4 + - - +
262A PRO* 3.5 5.5 - - - +
299A LEU 4.5 1.8 + - - -
304A ASN* 2.9 29.5 + - - +
305A CYS* 4.5 2.6 - - - +
306A PRO* 5.6 2.1 - - - +
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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