Contacts of the helix formed by residues 376 - 389 (chain D) in PDB entry 7ATU
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 GLU 376 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374D ASP* 2.4 12.4 + - + +
375D GLU* 1.3 71.5 - - - +
377D THR* 1.3 64.0 + - - +
379D ARG* 3.5 18.3 - - - +
380D THR* 3.9 8.7 + - - +
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Residues in contact with THR 377 (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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373D PHE* 4.8 12.8 - - - -
374D ASP* 2.3 43.2 + - - +
376D GLU* 1.3 63.1 - - - +
378D GLN* 1.3 53.3 + - - -
379D ARG 2.7 14.9 + - - -
380D THR* 2.9 25.5 + - - -
381D PHE* 3.3 6.4 + - - +
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Residues in contact with GLN 378 (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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373D PHE* 4.8 18.9 - - + +
374D ASP 3.8 1.4 + - - -
375D GLU* 3.5 14.8 + - - +
377D THR* 1.3 76.5 - - - +
379D ARG* 1.3 59.1 + - - +
381D PHE* 3.9 14.2 - - + +
382D LEU* 3.7 16.1 + - - +
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Residues in contact with ARG 379 (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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375D GLU 3.3 11.6 + - - +
376D GLU* 3.5 16.8 - - + +
377D THR 2.7 5.9 + - - -
378D GLN* 1.3 73.2 - - - +
380D THR* 1.3 63.8 + - + +
381D PHE 3.3 0.9 + - - -
382D LEU* 3.4 7.0 + - - +
383D LYS* 3.3 16.5 + - - +
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Residues in contact with THR 380 (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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376D GLU 3.9 6.9 + - - +
377D THR* 2.9 15.8 + - - -
379D ARG* 1.3 75.0 - - + +
381D PHE* 1.3 62.7 + - - +
383D LYS* 3.6 13.3 + - + +
384D GLU* 3.5 17.8 + - - +
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Residues in contact with PHE 381 (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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377D THR 3.3 6.2 + - - +
378D GLN* 4.1 18.8 - - + +
379D ARG 3.2 1.2 - - - -
380D THR* 1.3 75.2 + - - +
382D LEU* 1.3 57.1 + - - +
384D GLU* 2.7 28.2 + - - +
385D VAL* 3.1 11.9 + - - +
388D MET* 4.1 4.9 - - + +
411D PHE* 4.4 19.7 - - + -
481D LEU* 6.0 4.3 - - + -
483D ARG* 5.5 4.9 - - - +
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Residues in contact with LEU 382 (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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378D GLN 3.7 9.4 + - - +
379D ARG* 3.4 8.7 + - - +
381D PHE* 1.3 74.9 - - - +
383D LYS* 1.3 64.4 + - - +
384D GLU 3.4 0.3 + - - -
385D VAL* 3.4 27.4 + - + +
386D LYS 4.8 0.9 + - - -
402D VAL* 6.4 0.7 - - + -
411D PHE* 5.4 2.6 - - + -
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Residues in contact with LYS 383 (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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379D ARG 3.3 8.4 + - - +
380D THR* 3.6 22.2 - - + +
381D PHE 3.1 0.6 - - - -
382D LEU* 1.3 77.7 - - - +
384D GLU* 1.3 58.9 + - - +
385D VAL 3.7 0.2 + - - -
386D LYS* 4.3 9.7 + - - +
387D VAL* 5.2 1.2 + - - +
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Residues in contact with GLU 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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380D THR 3.5 9.3 + - - +
381D PHE* 2.7 13.3 + - - +
383D LYS* 1.3 76.9 - - - +
385D VAL* 1.3 61.9 + - - -
386D LYS 3.2 3.1 - - - -
387D VAL* 2.9 20.9 + - - +
388D MET* 2.9 13.6 + - - +
483D ARG* 3.9 23.3 - - - +
485D MET* 4.1 15.5 - - + -
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Residues in contact with VAL 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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381D PHE 3.1 1.8 + - - +
382D LEU* 3.5 29.6 - - + +
383D LYS 3.4 1.0 - - - -
384D GLU* 1.3 76.9 - - - +
386D LYS* 1.3 57.8 + - - +
388D MET* 3.1 24.4 + - + +
389D ARG* 2.8 56.4 + - - +
399D PHE* 4.1 9.9 - - + -
401D GLY* 6.0 0.4 - - - -
402D VAL* 4.3 27.6 - - + -
411D PHE* 4.6 4.5 - - + -
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Residues in contact with LYS 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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613C GLY* 4.4 15.8 - - - +
615C LEU* 3.8 6.7 - - + +
382D LEU 4.8 0.6 + - - -
383D LYS 4.3 9.0 + - - +
384D GLU 3.2 0.8 - - - -
385D VAL* 1.3 80.2 - - - +
387D VAL* 1.3 61.2 + - + +
389D ARG* 3.8 19.0 + - - +
390D CYS* 3.1 27.4 - - - -
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Residues in contact with VAL 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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615C LEU* 3.5 31.1 - - + +
383D LYS 5.2 0.6 + - - +
384D GLU* 2.9 13.1 + - - +
386D LYS* 1.3 76.5 - - + +
388D MET* 1.3 66.9 + - - +
390D CYS* 3.3 11.3 + - - +
391D LEU* 3.6 19.7 + - + +
454D MET* 6.3 0.4 - - + -
456D ILE* 4.7 12.3 - - + -
485D MET* 3.7 30.7 - - + -
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Residues in contact with MET 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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381D PHE* 4.1 4.5 - - + +
384D GLU 2.9 9.3 + - - +
385D VAL* 3.1 37.9 + - + +
387D VAL* 1.3 79.2 - - - +
389D ARG* 1.3 62.9 + - - +
390D CYS 3.0 1.7 + - - -
391D LEU* 3.3 12.6 + - - +
399D PHE* 3.6 30.3 + - + +
411D PHE* 3.9 20.6 - - + -
481D LEU* 4.9 0.9 - - - -
483D ARG* 2.9 34.3 - - - +
485D MET* 4.2 7.6 - - + -
701D RXN 3.1 48.0 + - - +
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Residues in contact with ARG 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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612C ALA 5.6 2.0 + - - -
613C GLY* 5.5 8.1 - - - -
385D VAL* 2.8 39.2 + - - +
386D LYS* 3.8 16.7 + - - +
387D VAL 3.4 0.4 - - - -
388D MET* 1.3 71.6 - - - +
390D CYS* 1.3 61.0 + - - +
391D LEU 3.6 0.2 - - - -
392D GLU* 5.7 2.4 - - - +
399D PHE* 3.8 27.1 - - + +
400D ILE 3.5 24.9 - - - +
401D GLY* 4.8 4.3 - - - -
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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