Contacts of the helix formed by residues 383 - 394 (chain D) in PDB entry 2YPT
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 383 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D TRP* 3.5 41.3 - - + +
119D GLU* 3.6 12.1 - - + +
373D PHE* 3.3 13.6 - - + -
378D PHE* 4.1 11.4 - - + -
381D SER* 3.4 19.7 - - - +
382D GLN* 1.4 83.7 - - - +
384D THR* 1.3 59.8 + - - +
386D ILE* 3.8 27.6 - - + +
387D GLY* 3.0 22.9 + - - -
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Residues in contact with THR 384 (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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119D GLU* 3.1 22.1 + - - -
186D LEU* 3.7 21.3 - - + +
189D ILE* 3.7 40.2 - - + -
190D LYS* 3.6 18.3 - - + +
363D PHE* 4.5 2.2 - - + -
367D ILE* 4.9 10.8 - - + +
382D GLN 3.8 2.1 + - - -
383D PRO* 1.3 68.5 - - - +
385D LEU* 1.3 65.9 + - - +
387D GLY* 3.1 3.9 + - - -
388D LEU* 3.0 23.5 + - + +
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Residues in contact with LEU 385 (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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102D TRP* 4.2 4.7 - - + -
119D GLU* 4.3 1.6 + - - -
123D SER* 3.4 43.7 - - - +
126D PHE* 3.4 30.1 - - + -
127D LEU* 3.7 28.5 - - + -
182D SER* 5.2 3.6 - - - +
186D LEU* 3.5 29.1 - - + +
383D PRO 3.6 0.4 - - - -
384D THR* 1.3 76.5 - - - +
386D ILE* 1.3 56.3 + - - +
388D LEU* 3.3 17.3 + - + +
389D LEU* 3.1 33.7 + - + +
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Residues in contact with ILE 386 (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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98D ILE* 3.9 6.7 - - + -
102D TRP* 3.8 17.7 - - + -
126D PHE* 3.8 33.9 - - + -
373D PHE* 4.1 8.1 - - + -
378D PHE* 3.6 56.1 - - + -
383D PRO* 3.5 23.5 + - + +
384D THR 3.3 0.6 - - - -
385D LEU* 1.3 71.1 - - - +
387D GLY* 1.3 59.9 + - - +
389D LEU* 3.2 8.9 + - + +
390D ILE* 2.9 44.0 + - + +
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Residues in contact with GLY 387 (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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363D PHE* 3.5 12.3 - - - -
367D ILE* 5.4 1.3 - - - -
373D PHE* 3.7 24.5 - - - -
383D PRO 3.0 10.8 + - - -
384D THR* 3.1 5.6 + - - -
386D ILE* 1.3 77.0 - - - +
388D LEU* 1.4 53.8 + - - +
390D ILE* 4.6 2.9 - - - -
391D ILE* 3.1 39.5 + - - +
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Residues in contact with LEU 388 (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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185D LEU* 4.2 18.2 - - + -
186D LEU* 4.3 9.6 - - + -
189D ILE* 4.1 25.8 - - + -
360D PHE* 4.5 8.7 - - + -
363D PHE* 3.7 19.5 - - + -
384D THR* 3.0 20.2 + - + +
385D LEU* 3.3 23.3 + - + +
387D GLY* 1.4 76.2 - - - +
389D LEU* 1.4 56.4 + - + +
392D PHE* 3.0 60.1 + - + +
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Residues in contact with LEU 389 (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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98D ILE* 4.9 6.5 - - + -
126D PHE* 3.8 30.5 - - + -
127D LEU* 5.9 6.1 - - + -
385D LEU* 3.1 25.3 + - + +
386D ILE* 3.2 17.9 + - + +
388D LEU* 1.4 75.5 - - + +
390D ILE* 1.4 61.9 + - + +
393D GLN* 2.9 41.0 + - + +
394D PHE* 3.7 9.4 + - + -
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Residues in contact with ILE 390 (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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372D LEU* 3.8 28.9 - - + +
373D PHE* 4.1 17.0 - - + -
376D PHE* 3.6 51.8 - - + -
378D PHE* 4.3 3.8 - - + -
386D ILE* 2.9 43.0 + - + +
387D GLY* 4.3 3.4 - - - +
389D LEU* 1.4 72.3 - - + +
391D ILE* 1.3 61.9 + - + +
394D PHE* 3.0 22.9 + - + +
395D ILE* 3.0 25.1 + - + -
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Residues in contact with ILE 391 (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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363D PHE* 3.7 31.0 - - + -
366D LEU* 3.8 23.3 - - + +
367D ILE* 3.8 30.1 - - + +
372D LEU* 5.4 7.0 - - + -
373D PHE* 5.4 4.3 - - + -
387D GLY* 3.1 22.9 + - - +
390D ILE* 1.3 80.5 - - + +
392D PHE* 1.3 60.3 + - - +
395D ILE* 3.4 9.9 + - + -
396D PHE* 2.9 63.8 + - + -
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Residues in contact with PHE 392 (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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356D SER* 5.9 0.9 - - - -
359D CYS* 3.6 31.2 - - + -
360D PHE* 4.1 31.9 - + - -
363D PHE* 3.5 40.6 - + + -
388D LEU* 3.0 43.8 + - + +
391D ILE* 1.3 76.7 - - - +
393D GLN* 1.3 59.2 + - + +
396D PHE* 3.6 17.8 - + - +
400D ASN* 2.9 26.9 + - - -
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Residues in contact with GLN 393 (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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389D LEU* 2.9 29.9 + - + +
392D PHE* 1.3 75.0 - - + +
394D PHE* 1.4 77.6 + - + +
397D SER* 3.0 14.2 + - - -
400D ASN* 4.9 2.1 + - - +
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Residues in contact with PHE 394 (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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23D VAL* 3.7 39.3 - - + +
27D SER* 5.3 4.7 - - - -
93D LEU* 3.8 33.9 - - + -
98D ILE* 4.8 10.8 - - + -
376D PHE* 3.8 25.4 - + + -
389D LEU* 3.7 21.5 - - + -
390D ILE* 3.0 22.0 + - + +
392D PHE 3.6 0.4 - - - -
393D GLN* 1.4 91.3 - - + +
395D ILE* 1.4 65.6 + - - +
397D SER* 2.9 23.1 + - - -
398D PRO* 4.4 1.6 - - - +
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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