Contacts of the helix formed by residues 376 - 394 (chain D) in PDB entry 4TNR
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 HIS 376 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LYS* 5.4 7.7 + - - -
156D VAL* 3.5 28.5 - - + +
157D PHE* 4.5 7.4 - + + -
370D HIS 4.2 0.4 + - - -
371D ARG 4.5 5.1 + - - -
372D ARG 3.8 20.4 - - - +
373D ALA* 3.0 19.4 + - - +
374D TYR 3.4 0.6 - - - -
375D GLN* 1.3 77.2 - - - +
377D LYS* 1.3 81.3 + - + +
378D VAL* 3.2 39.5 + - + -
379D GLY* 3.1 13.9 + - - +
380D ASN* 2.9 21.8 + - - +
551D ARG* 4.9 0.2 - - - +
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Residues in contact with LYS 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ARG* 5.4 4.7 - - - +
354B LYS* 3.8 28.3 - - - +
375D GLN 3.2 2.4 + - - -
376D HIS* 1.3 85.4 + - + +
378D VAL* 1.3 76.6 + - + +
381D ILE 3.3 9.9 + - - -
456D TYR* 3.7 53.4 - - + -
551D ARG* 3.8 14.7 - - - +
553D TYR* 2.7 40.3 + - - +
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Residues in contact with VAL 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D VAL* 4.0 5.8 - - + -
376D HIS* 3.2 20.9 + - + -
377D LYS* 1.3 95.4 - - + +
379D GLY* 1.3 65.9 + - - +
380D ASN 3.1 1.3 - - - -
381D ILE* 3.2 8.2 + - + +
382D ILE* 2.9 24.0 + - + +
451D ARG* 3.9 16.6 - - - +
453D LEU* 3.8 28.7 - - + -
456D TYR* 5.7 4.3 - - + -
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Residues in contact with GLY 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLY* 4.2 15.7 - - - -
153D GLY* 4.8 4.0 - - - -
156D VAL* 3.5 17.3 - - - +
373D ALA 5.8 0.9 - - - -
374D TYR 6.0 0.2 - - - -
376D HIS* 3.1 16.6 + - - -
378D VAL* 1.3 77.2 - - - +
380D ASN* 1.3 58.9 + - - +
382D ILE* 3.3 4.1 + - - +
383D ASP* 3.0 30.1 + - - +
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Residues in contact with ASN 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ARG* 3.5 17.8 + - - +
374D TYR 3.4 20.3 - - - +
375D GLN* 3.0 25.2 + - - +
376D HIS 2.9 15.6 + - - +
377D LYS 3.9 5.4 - - - +
379D GLY* 1.3 75.0 - - - +
381D ILE* 1.3 59.6 + - - +
383D ASP* 3.4 11.5 + - - +
384D THR* 2.8 31.6 + - - -
501D ASP* 3.4 19.8 + - - +
503D ILE* 3.5 14.6 - - - +
551D ARG* 3.5 6.7 - - - +
553D TYR* 4.0 5.6 - - - +
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Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D LYS 3.3 3.4 + - - +
378D VAL* 3.2 28.2 + - + +
380D ASN* 1.3 80.4 - - - +
382D ILE* 1.3 66.6 + - + +
384D THR* 3.3 10.1 + - + +
385D MET* 2.9 29.0 + - + +
453D LEU* 4.6 8.5 - - + -
454D PHE* 3.7 49.4 - - + +
499D ILE* 4.0 9.9 - - + -
553D TYR* 3.5 48.5 - - + -
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Residues in contact with ILE 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLY* 4.2 10.3 - - - +
155D TYR* 3.4 39.9 - - + +
156D VAL* 4.7 1.1 - - + -
378D VAL* 2.9 22.6 + - + +
379D GLY 3.6 4.5 - - - +
381D ILE* 1.3 74.3 - - + +
383D ASP* 1.3 58.8 + - - +
385D MET* 3.2 7.5 + - - +
386D ILE* 2.9 47.5 + - + +
448D ILE* 4.5 12.3 - - + -
451D ARG* 4.1 23.8 - - - +
453D LEU* 4.2 26.5 - - + -
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Residues in contact with ASP 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D LEU 5.0 3.1 - - - +
151D GLY* 4.4 1.3 - - - -
152D GLY* 2.9 30.7 + - - -
153D GLY 5.4 0.3 + - - -
213D PHE* 4.8 0.7 - - - +
216D MET* 3.6 33.2 + - + +
220D ARG* 3.7 19.5 + - - +
374D TYR 5.7 0.5 - - - +
379D GLY 3.0 16.0 + - - +
380D ASN* 3.5 15.8 - - - +
381D ILE 3.4 0.2 - - - -
382D ILE* 1.3 74.6 - - - +
384D THR* 1.3 56.7 + - - +
386D ILE* 3.4 3.3 + - - +
387D THR* 2.9 33.6 + - - -
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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
----------------------------------------------------------
220D ARG* 3.6 22.6 + - - +
380D ASN 2.8 19.4 + - - -
381D ILE* 3.4 17.2 - - + +
383D ASP* 1.3 77.0 - - - +
385D MET* 1.3 57.7 + - - +
387D THR* 3.4 7.9 + - + +
388D ASP* 3.0 35.4 + - - +
454D PHE* 4.9 0.7 - - + -
499D ILE* 4.2 33.1 - - + +
501D ASP* 5.1 3.3 + - - -
553D TYR* 6.0 0.3 - - - -
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Residues in contact with MET 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D ILE* 2.9 23.4 + - - +
382D ILE* 3.2 4.9 + - - +
384D THR* 1.3 71.9 - - - +
386D ILE* 1.3 66.2 + - - +
388D ASP* 3.3 6.6 + - - +
389D ALA 3.0 18.0 + - - -
444D ILE* 3.4 24.0 - - + +
447D GLN* 4.1 18.8 - - + +
448D ILE* 3.7 28.3 - - + -
452D ASN 3.8 20.9 - - - +
453D LEU* 3.9 18.8 - - + -
454D PHE* 3.6 50.0 - - + +
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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
----------------------------------------------------------
152D GLY* 5.0 1.1 - - - -
155D TYR* 4.9 4.7 - - + -
213D PHE* 4.1 28.0 - - + -
216D MET* 3.5 17.9 - - - -
382D ILE* 2.9 36.0 + - + +
383D ASP* 3.8 8.5 - - - +
385D MET* 1.3 76.7 - - - +
387D THR* 1.3 57.8 + - - +
389D ALA* 3.2 2.0 + - - +
390D PHE* 2.9 53.1 + - + -
427D PHE* 4.1 23.6 - - + -
445D LEU* 4.5 6.3 - - + -
448D ILE* 3.8 15.5 - - + -
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Residues in contact with THR 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D MET* 3.3 22.8 - - - +
220D ARG* 3.5 19.2 - - + +
221D PHE* 3.9 27.1 + - - +
224D LEU* 4.5 7.4 - - + -
383D ASP 2.9 22.9 + - - -
384D THR* 3.5 9.2 - - + +
385D MET 3.3 0.2 - - - -
386D ILE* 1.3 76.9 - - - +
388D ASP* 1.3 59.6 + - - +
390D PHE* 3.1 8.5 + - - +
391D LEU* 2.9 46.8 + - + +
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Residues in contact with ASP 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LEU* 5.6 2.3 - - - +
384D THR* 3.0 23.4 + - - +
385D MET* 3.5 9.4 - - - +
386D ILE 3.2 0.2 - - - -
387D THR* 1.3 78.2 - - - +
389D ALA* 1.3 62.4 + - - +
391D LEU* 3.3 20.2 + - - +
392D LYS* 3.1 39.0 + - - +
444D ILE* 4.1 16.6 - - + -
454D PHE* 3.9 22.6 - - + -
499D ILE* 5.1 0.9 - - - +
555D LYS* 4.5 12.1 + - - -
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D MET 3.0 10.8 + - - +
386D ILE 3.2 5.1 + - - +
388D ASP* 1.3 75.0 - - - +
390D PHE* 1.3 61.2 + - + +
392D LYS 3.2 1.7 + - - -
393D ALA* 3.0 24.7 + - - +
430D ILE* 4.6 1.6 - - + -
441D ALA* 3.3 30.5 - - + +
444D ILE* 4.0 12.4 - - + +
445D LEU* 3.4 34.5 - - + -
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Residues in contact with PHE 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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212D PRO* 4.0 18.2 - - + -
213D PHE* 4.2 14.8 - + - -
216D MET* 3.9 26.0 - - + -
217D PHE* 5.2 1.6 - + - -
221D PHE* 3.8 20.9 - + + -
386D ILE* 2.9 34.9 + - + +
387D THR* 3.5 9.0 - - - +
389D ALA* 1.3 77.2 - - + +
391D LEU* 1.3 58.3 + - - +
393D ALA* 3.1 5.5 + - - +
394D ASP* 2.9 31.2 + - - +
409D ILE* 4.1 21.6 - - + +
426D ILE* 3.5 32.3 - - + -
427D PHE* 4.2 11.2 - + - -
430D ILE* 3.9 15.5 - - + -
445D LEU* 5.6 1.1 - - + -
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Residues in contact with LEU 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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221D PHE* 3.8 14.1 - - + +
224D LEU* 4.4 18.4 - - + +
225D ALA* 3.8 38.6 - - + +
387D THR* 2.9 28.7 + - + +
388D ASP* 3.5 24.5 - - - +
390D PHE* 1.3 76.7 - - - +
392D LYS* 1.3 64.2 + - + +
393D ALA 3.3 0.9 + - - -
394D ASP* 3.4 17.4 + - + +
395D ASP* 4.7 4.0 + - - -
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Residues in contact with LYS 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ASP* 3.1 31.9 + - - +
389D ALA 3.2 4.5 + - - +
391D LEU* 1.3 78.8 - - + +
393D ALA* 1.3 58.1 + - - +
395D ASP* 5.1 0.9 - - - -
396D TYR* 3.4 24.1 - - - -
437D LYS 4.8 1.4 - - - +
438D LEU* 4.7 0.3 - - - +
440D ASP* 4.6 16.8 - - + +
441D ALA* 4.0 18.7 + - + +
444D ILE* 3.6 28.2 - - + +
555D LYS* 5.7 3.8 - - - +
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Residues in contact with ALA 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D ALA 3.0 16.1 + - - +
390D PHE* 3.1 4.4 + - - +
392D LYS* 1.3 77.4 - - - +
394D ASP* 1.3 59.5 + - - +
395D ASP 3.3 2.5 - - - -
396D TYR* 2.9 21.4 + - - +
397D ILE* 3.2 19.1 + - + +
409D ILE* 4.5 1.8 - - + -
430D ILE* 3.4 27.4 - - + -
438D LEU* 3.8 21.3 - - + -
441D ALA* 3.9 4.0 - - + -
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Residues in contact with ASP 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D PHE* 4.4 4.8 - - - -
225D ALA* 4.5 5.4 - - - +
390D PHE 2.9 15.4 + - - +
391D LEU* 3.4 15.4 + - + +
393D ALA* 1.3 78.4 - - - +
395D ASP* 1.3 66.3 + - - +
396D TYR 3.4 0.7 + - - -
397D ILE 3.9 5.8 - - - +
408D ARG* 3.4 23.4 + - - +
409D ILE* 3.3 17.9 + - + +
410D SER* 2.6 49.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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