Contacts of the helix formed by residues 241 - 249 (chain D) in PDB entry 3Q37
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 PRO 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.7 5.6 - - + -
28D LEU* 3.4 26.7 - - + -
239D LEU 4.7 0.4 - - - +
240D LYS* 1.3 88.0 - - + +
242D GLU* 1.3 59.8 + - - +
243D PHE 3.0 1.4 + - - -
244D VAL* 3.1 26.9 + - + +
245D GLU* 4.1 3.0 + - - +
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D THR* 3.3 8.4 - - - +
217D ALA* 2.8 29.9 + - + +
218D LYS* 2.7 30.7 + - - -
237D ALA* 4.0 19.5 - - - +
240D LYS* 2.9 24.2 + - + +
241D PRO* 1.3 78.8 - - - +
243D PHE* 1.3 62.4 + - - +
245D GLU* 3.0 27.0 + - - +
246D ILE* 3.1 14.9 + - + +
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Residues in contact with PHE 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.7 22.2 - - + -
10D ALA 3.7 17.7 - - - -
11D ALA* 3.6 27.4 - - + -
29D PHE* 3.9 23.6 - + + -
41D VAL 4.5 0.2 - - - -
61D PHE* 4.3 15.3 - + - -
234D VAL* 3.8 20.4 - - + -
237D ALA 3.6 10.6 + - - +
238D SER* 3.9 20.6 - - - +
240D LYS 3.0 13.4 + - - +
241D PRO 3.0 1.4 + - - -
242D GLU* 1.3 79.2 - - - +
244D VAL* 1.3 62.2 + - - +
246D ILE* 3.1 13.5 + - + +
247D ILE* 3.0 45.2 + - + +
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 4.1 16.8 - - + -
29D PHE* 3.9 29.8 - - + -
32D THR* 3.6 40.4 - - + +
61D PHE* 5.7 0.7 - - + -
241D PRO* 3.1 17.4 + - + +
243D PHE* 1.3 77.4 - - - +
245D GLU* 1.3 66.1 + - + +
247D ILE* 3.4 15.6 + - + +
248D GLU* 3.2 26.8 + - - +
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Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ALA* 3.4 32.4 - - + +
241D PRO 4.5 3.8 - - - +
242D GLU* 3.0 24.8 + - - +
244D VAL* 1.3 81.1 - - + +
246D ILE* 1.3 63.2 + - - +
248D GLU* 3.4 10.6 + - - +
249D ALA* 3.4 17.3 + - - +
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Residues in contact with ILE 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 5.4 2.7 - - + -
215D VAL* 3.6 36.1 - - + +
216D THR* 3.8 24.5 - - - +
217D ALA* 3.9 2.0 - - - +
220D ALA* 4.2 2.9 - - + -
232D PHE* 3.8 25.3 - - + -
234D VAL* 4.1 20.2 - - + -
237D ALA* 4.0 18.2 - - + -
242D GLU* 3.1 12.1 + - + +
243D PHE* 3.1 16.6 + - + +
245D GLU* 1.3 74.3 - - - +
247D ILE* 1.3 66.0 + - - +
249D ALA* 2.9 22.0 + - - +
250D THR* 3.7 6.4 + - - +
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Residues in contact with ILE 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.9 25.6 - - + -
32D THR* 5.8 0.9 - - + -
34D ILE* 4.2 20.4 - - + -
36D HIS* 3.5 8.3 + - + -
38D VAL* 4.3 11.7 - - + -
40D CYS* 3.9 20.2 - - - -
61D PHE* 3.9 19.7 - - + -
243D PHE* 3.0 43.0 + - + +
244D VAL* 3.5 20.0 - - + +
245D GLU 3.3 0.2 - - - -
246D ILE* 1.3 74.7 - - - +
248D GLU* 1.3 66.7 + - - +
249D ALA 3.0 0.9 + - - -
250D THR* 2.7 26.6 + - - +
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D THR* 5.1 4.7 - - + +
33D SER 3.6 20.5 - - - +
34D ILE* 4.4 6.9 - - - +
35D ASN* 4.9 1.8 + - - -
36D HIS* 4.3 19.7 + - - -
221D ARG* 4.5 12.7 + - - +
244D VAL 3.2 14.4 + - - +
245D GLU* 3.6 12.8 - - - +
246D ILE 3.2 0.2 - - - -
247D ILE* 1.3 84.4 - - - +
249D ALA* 1.3 58.6 + - - +
250D THR 3.3 4.2 + - - -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ALA 5.6 1.3 - - - +
220D ALA* 3.3 30.5 - - + -
221D ARG* 3.7 33.5 + - + +
224D TYR* 3.7 20.5 - - - +
232D PHE* 5.0 0.7 - - + -
245D GLU 3.4 9.2 + - - +
246D ILE 2.9 13.9 + - - +
248D GLU* 1.3 76.9 - - - +
250D THR* 1.3 61.0 + - - +
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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