Contacts of the helix formed by residues 244 - 256 (chain A) in PDB entry 5E3H
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 ARG 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A LYS 3.3 2.7 + - - +
243A PRO* 1.3 75.1 - - - +
245A ASN* 1.3 67.4 + - - +
246A TYR* 3.2 43.5 + - + -
247A GLN* 2.7 31.8 + - - +
248A LEU* 3.4 7.0 + - - +
267A GLY 4.6 2.0 + - - -
268A CYS 3.6 11.7 + - - -
448A GLU* 3.5 17.0 - - + +
452A VAL* 3.8 31.1 - - + +
1006A ADP 3.2 60.4 + - - +
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Residues in contact with ASN 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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243A PRO 3.7 2.5 + - - +
244A ARG* 1.3 71.4 - - - +
246A TYR* 1.3 56.9 + - - +
248A LEU* 3.4 21.3 + - - +
249A GLU* 3.1 19.6 + - - +
445A ASN* 3.1 31.0 + - - +
448A GLU* 3.0 20.0 + - - +
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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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244A ARG* 3.4 37.7 + - + -
245A ASN* 1.3 74.3 - - - +
247A GLN* 1.3 70.0 + - + +
248A LEU 3.3 0.2 - - - -
249A GLU* 3.5 4.2 - - - +
250A LEU* 3.0 38.0 + - + +
268A CYS* 2.6 42.2 + - + +
442A VAL* 3.8 24.6 - - + +
445A ASN* 3.6 23.1 - - + +
448A GLU* 3.1 31.8 + - + -
449A LEU* 3.4 42.1 - - + +
452A VAL* 4.0 8.7 - - + +
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Residues in contact with GLN 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 PRO* 3.4 5.7 - - - +
244A ARG* 2.7 41.0 + - + +
246A TYR* 1.3 94.4 - - + +
248A LEU* 1.3 63.6 + - - +
250A LEU* 3.6 3.2 + - - +
251A ALA* 3.1 23.4 + - - +
268A CYS 3.7 7.0 + - - +
269A GLY 3.2 17.2 + - - -
272A PHE* 3.5 12.1 - - - +
273A VAL* 3.9 23.4 - - + +
276A LEU* 4.6 11.9 - - + +
1006A ADP 3.2 39.4 + - - -
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Residues in contact with LEU 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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243A PRO* 4.4 20.0 - - + +
244A ARG 3.4 12.1 + - - +
245A ASN* 3.4 21.3 + - - +
246A TYR 3.3 0.2 - - - -
247A GLN* 1.3 75.9 - - - +
249A GLU* 1.3 59.1 + - - +
251A ALA* 3.0 7.6 + - + +
252A LEU* 2.9 30.9 + - - +
255A MET* 5.1 8.4 - - + +
276A LEU* 4.0 23.8 - - + -
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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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245A ASN 3.1 5.4 + - - +
246A TYR* 3.5 7.8 - - - +
248A LEU* 1.3 77.9 - - - +
250A LEU* 1.3 60.9 + - - +
251A ALA 3.3 0.7 + - - -
252A LEU* 3.3 17.0 + - + +
253A PRO* 3.5 10.2 - - - +
440A ALA* 5.2 0.5 - - - +
441A THR 3.7 11.3 - - - +
442A VAL* 3.9 6.1 - - - +
443A LYS* 2.9 32.9 + - - +
444A HIS* 3.2 22.7 + - + -
445A ASN* 2.7 49.8 + - - +
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Residues in contact with LEU 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 TYR* 3.0 30.4 + - + +
247A GLN 4.0 4.0 - - - +
249A GLU* 1.3 75.5 - - - +
251A ALA* 1.3 60.1 + - - +
253A PRO* 3.4 10.1 - - - +
254A ALA 4.9 1.2 + - - -
260A THR* 4.9 0.7 - - - +
262A ILE* 3.6 38.2 - - + +
263A CYS 4.5 3.6 - - - +
264A ALA* 3.7 24.2 - - + -
268A CYS* 4.8 2.5 - - - -
270A LYS* 5.1 0.7 - - + -
273A VAL* 4.3 16.6 - - + -
440A ALA* 3.9 13.6 - - - +
441A THR* 3.5 43.1 - - - +
442A VAL* 3.7 12.8 - - + +
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Residues in contact with ALA 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 GLN 3.1 18.6 + - - +
248A LEU* 3.0 9.0 + - - +
250A LEU* 1.3 78.9 - - - +
252A LEU* 1.3 64.6 + - - +
253A PRO 3.4 0.2 - - - -
254A ALA* 3.1 5.9 + - - +
255A MET* 3.0 41.2 + - - +
273A VAL* 4.2 9.6 - - + +
276A LEU* 4.8 7.6 - - + -
277A ILE* 4.1 20.4 - - + -
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Residues in contact with LEU 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 LEU 2.9 12.0 + - - +
249A GLU* 3.3 13.0 + - + +
251A ALA* 1.3 76.2 - - - +
253A PRO* 1.3 70.1 - - + +
255A MET* 3.2 12.8 + - + +
256A LYS* 3.2 55.2 + - + +
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Residues in contact with PRO 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 GLU 3.5 7.2 - - - +
250A LEU 3.4 10.5 - - - +
251A ALA 3.4 4.3 - - - -
252A LEU* 1.3 96.9 - - + +
254A ALA* 1.3 59.7 + - - +
256A LYS* 3.2 11.5 + - + +
257A GLY 3.4 0.2 + - - -
258A LYS* 3.2 36.9 + - + +
260A THR* 3.4 17.5 - - + +
438A VAL* 3.9 19.5 - - + -
440A ALA* 4.0 19.7 - - + -
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Residues in contact with ALA 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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250A LEU 5.2 0.4 - - - +
251A ALA* 3.1 9.5 + - - +
253A PRO* 1.3 80.5 - - - +
255A MET* 1.3 59.3 + - - +
257A GLY* 3.1 8.3 + - - -
258A LYS 3.7 4.3 - - - -
260A THR* 3.6 5.5 + - - +
262A ILE* 5.1 1.8 - - + -
277A ILE* 3.6 29.6 - - + +
280A HIS* 5.4 0.3 - - - -
404A GLN* 2.7 29.5 + - - +
406A ILE* 3.3 27.4 - - + -
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Residues in contact with MET 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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248A LEU* 5.1 9.0 - - + +
251A ALA* 3.0 40.7 + - + +
252A LEU* 3.2 12.5 + - + +
254A ALA* 1.3 77.5 - - - +
256A LYS* 1.3 59.8 - - + +
257A GLY 3.3 1.2 + - - -
276A LEU* 4.8 9.9 - - + +
277A ILE* 4.4 11.9 - - - -
280A HIS* 2.8 70.6 + - + +
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Residues in contact with LYS 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 LEU* 3.2 47.3 + - + +
253A PRO* 3.7 6.7 - - + +
254A ALA 3.1 1.0 - - - -
255A MET* 1.3 77.6 - - + +
257A GLY* 1.3 58.4 + - - +
258A LYS* 3.5 25.5 + - - +
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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