Contacts of the helix formed by residues 375 - 385 (chain D) in PDB entry 2DB3
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 375 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D VAL* 4.7 0.4 - - - -
325D SER 3.5 6.1 - - - +
327D THR 3.6 33.7 - - - +
328D ARG* 3.7 16.4 - - + +
331D ALA* 4.1 4.3 - - + -
352D VAL 3.4 3.2 + - - -
353D TYR* 3.6 16.2 - - + +
374D ALA* 1.3 76.2 - - - +
376D PRO* 1.3 75.1 - - - +
377D GLY 3.2 0.3 + - - -
378D ARG* 3.5 0.9 + - - +
379D LEU* 3.3 17.0 + - - +
5H U 3.2 13.9 + - - -
6H U 2.4 27.4 + - - -
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Residues in contact with PRO 376 (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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324D VAL* 3.8 6.1 - - + -
325D SER 3.4 15.5 - - - +
374D ALA 4.1 0.2 - - - -
375D THR* 1.3 85.0 - - - +
377D GLY* 1.3 65.9 + - - +
379D LEU* 3.2 2.3 + - + +
380D LEU* 3.1 29.0 + - - +
404D MET* 3.4 23.8 - - + -
409D PHE* 3.5 26.5 - - + -
412D ASP* 4.1 18.4 - - + +
413D MET* 3.6 10.3 - - + -
416D ILE* 4.4 11.4 - - + -
5H U 3.8 7.0 - - - +
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Residues in contact with GLY 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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375D THR 3.2 1.4 + - - -
376D PRO* 1.3 78.4 - - - +
378D ARG* 1.3 60.8 + - - +
380D LEU* 3.5 4.8 + - - +
381D ASP 3.3 11.8 + - - -
412D ASP* 4.5 6.9 + - - -
5H U 2.9 15.0 + - - -
6H U 2.9 42.0 - - - +
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Residues in contact with ARG 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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352D VAL* 3.0 31.6 - - + -
353D TYR* 3.5 14.4 - - - -
354D GLY* 3.6 5.0 - - - +
356D THR* 2.4 47.5 + - - -
358D PHE* 3.3 34.9 - - - +
361D GLN* 2.9 11.6 + - - +
375D THR 3.5 1.1 + - - +
376D PRO 3.5 0.2 - - - -
377D GLY* 1.3 70.9 - - - +
379D LEU* 1.3 66.0 + - - +
381D ASP* 3.2 0.9 + - - +
382D PHE* 3.0 32.3 + - + -
6H U 2.8 48.6 + - - +
7H U 2.7 38.6 + - - -
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Residues in contact with LEU 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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322D VAL* 4.0 25.1 - - + -
324D VAL* 4.4 5.8 - - + -
352D VAL* 4.3 7.5 - - + +
372D VAL* 4.7 5.8 - - + -
374D ALA* 4.0 22.0 - - + -
375D THR 3.3 11.0 + - - +
376D PRO* 3.2 8.6 + - + +
378D ARG* 1.3 76.5 - - - +
380D LEU* 1.3 59.5 + - + +
382D PHE* 3.1 7.9 + - - +
383D VAL* 2.8 36.5 + - + +
388D ILE* 4.1 33.4 - - + -
390D PHE* 4.3 6.3 - - + -
416D ILE* 4.0 29.4 - - + -
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Residues in contact with LEU 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 PRO 3.1 12.5 + - - +
377D GLY* 3.7 4.5 - - - +
379D LEU* 1.3 79.0 - - + +
381D ASP* 1.3 57.4 + - - +
383D VAL* 4.0 13.5 - - + -
384D ASP* 2.6 40.7 + - - +
390D PHE* 6.0 0.2 - - + -
412D ASP* 3.2 53.6 - - + +
415D ARG* 3.6 32.3 - - + +
416D ILE* 3.1 35.2 - - + +
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Residues in contact with ASP 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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358D PHE* 3.2 26.3 - - + -
377D GLY 3.3 4.6 + - - +
378D ARG 3.2 10.7 + - - +
379D LEU 3.2 0.6 - - - -
380D LEU* 1.3 77.7 - - - +
382D PHE* 1.3 58.3 + - - +
384D ASP* 3.1 6.0 + - - +
385D ARG* 2.9 62.4 + - - +
6H U 3.0 46.8 + - - +
7H U 4.7 4.9 - - - +
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Residues in contact with PHE 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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352D VAL* 3.3 23.8 - - + -
358D PHE* 3.1 43.7 - + - -
361D GLN* 3.8 24.2 - - + -
362D ASN* 3.8 27.1 - - - -
365D ILE* 4.7 6.3 - - + -
378D ARG* 3.0 29.8 + - + -
379D LEU 3.3 7.9 - - - +
381D ASP* 1.3 78.1 - - - +
383D VAL* 1.3 55.0 + - - +
385D ARG* 3.4 4.8 + - - -
386D THR 3.1 4.9 + - - -
387D PHE* 2.7 46.7 + - + +
388D ILE* 3.3 32.5 + - + -
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Residues in contact with VAL 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 LEU* 2.8 24.0 + - + +
380D LEU* 3.7 13.9 - - + +
382D PHE* 1.3 75.5 - - - +
384D ASP* 1.3 66.8 + - - +
385D ARG 3.1 0.2 - - - -
386D THR* 3.0 19.6 + - - -
388D ILE* 3.5 29.4 - - + +
390D PHE* 4.0 28.9 - - + -
415D ARG* 5.3 0.7 - - - +
419D HIS* 3.4 39.8 + - + +
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Residues in contact with ASP 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 LEU 2.6 24.4 + - - +
381D ASP* 3.8 5.8 - - - +
383D VAL* 1.3 77.0 - - - +
385D ARG* 1.3 61.9 + - - +
386D THR* 3.1 6.7 + - - -
415D ARG* 2.6 39.9 + - - -
419D HIS* 5.3 1.4 - - - -
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Residues in contact with ARG 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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358D PHE* 3.5 33.0 - - + -
381D ASP* 2.9 47.2 + - - +
382D PHE 3.6 1.3 - - - +
384D ASP* 1.3 77.5 - - - +
386D THR* 1.3 68.6 + - - +
387D PHE* 3.1 54.6 - - + -
7H U 5.4 11.5 + - - -
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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