Contacts of the helix formed by residues 393 - 409 (chain D) in PDB entry 5NTN
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 CYS 393 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317D TRP* 4.2 17.5 - - + -
388D PHE 5.4 0.6 + - - -
391D LEU* 3.7 25.3 - - - +
392D GLY* 1.3 79.5 - - - +
394D SER* 1.3 65.9 + - - +
395D GLU* 3.2 4.5 - - - -
396D LEU* 3.0 25.0 + - + +
397D ILE* 3.1 27.4 + - - +
482D ARG* 3.5 34.1 - - + +
601D 98H 4.9 1.6 - - - -
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Residues in contact with SER 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D MET* 5.4 0.3 - - - +
388D PHE 5.9 1.8 + - - -
389D ARG* 5.9 9.9 - - - +
392D GLY* 3.9 0.8 - - - -
393D CYS* 1.3 76.6 - - - +
395D GLU* 1.3 59.7 + - - +
397D ILE* 3.7 10.5 - - - +
398D SER* 2.8 32.4 + - - -
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Residues in contact with GLU 395 (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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393D CYS 3.2 1.3 - - - -
394D SER* 1.3 81.3 + - - +
396D LEU* 1.3 61.6 + - - +
398D SER* 2.9 17.6 + - - -
399D SER* 3.1 21.4 + - - +
478D GLN* 4.1 15.2 - - - +
482D ARG* 5.8 2.2 + - - -
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Residues in contact with LEU 396 (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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393D CYS* 3.0 25.1 + - + +
395D GLU* 1.3 79.1 - - - +
397D ILE* 1.3 66.7 + - + +
399D SER* 3.4 3.8 + - - -
400D ILE* 3.1 50.7 + - + +
475D LEU* 3.6 27.1 - - + +
478D GLN* 3.7 25.7 + - + +
479D HIS* 3.7 33.7 - - + -
482D ARG* 3.8 21.8 - - + -
601D 98H 5.4 3.1 - - + -
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Residues in contact with ILE 397 (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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385D MET* 3.8 33.4 - - + +
388D PHE* 4.1 21.3 - - + +
391D LEU* 3.9 23.3 - - + -
393D CYS* 3.1 27.0 + - - +
394D SER* 3.7 10.1 - - - +
396D LEU* 1.3 78.7 - - + +
398D SER* 1.3 57.0 + - - +
400D ILE* 3.2 8.1 + - + +
401D PHE* 3.0 46.0 + - + -
601D 98H 3.9 27.8 - - + -
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Residues in contact with SER 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D MET* 3.7 29.7 - - - +
394D SER 2.8 21.4 + - - -
395D GLU* 2.9 18.4 + - - -
397D ILE* 1.3 73.2 - - - +
399D SER* 1.3 55.6 + - - +
401D PHE* 3.3 2.9 + - - +
402D ASP* 2.8 38.8 + - - +
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Residues in contact with SER 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D GLU* 3.1 19.1 + - - +
396D LEU* 3.6 6.7 - - - -
398D SER* 1.3 76.2 + - - +
400D ILE* 1.3 60.9 + - - +
402D ASP* 3.3 14.5 + - - +
403D PHE* 2.9 27.0 + - - +
475D LEU* 3.7 20.9 - - - +
478D GLN* 4.6 9.1 + - - -
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Residues in contact with ILE 400 (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 MET* 5.1 6.1 - - + -
362D LEU* 3.7 28.7 - - + +
365D MET* 3.6 29.6 - - + -
396D LEU* 3.1 45.5 + - + +
397D ILE* 3.2 8.9 + - - +
399D SER* 1.3 73.6 - - - +
401D PHE* 1.3 66.0 + - + +
403D PHE* 3.2 9.0 + - - +
404D SER* 3.2 21.8 + - - -
475D LEU* 4.3 10.5 - - + -
601D 98H 3.8 32.5 - - + -
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Residues in contact with PHE 401 (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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365D MET* 4.3 17.9 - - + -
369D TYR* 3.7 27.0 + + + +
374D ARG* 3.5 22.9 - - + -
376D VAL* 3.8 29.8 - - + -
383D GLY 4.1 4.0 - - - -
384D GLY 3.8 4.7 - - - -
385D MET* 3.5 47.3 - - + -
388D PHE* 4.1 9.6 - + - -
397D ILE* 3.0 41.0 + - + +
398D SER 3.5 8.1 - - - +
400D ILE* 1.3 75.7 - - + +
402D ASP* 1.3 59.0 + - - +
404D SER* 3.4 2.6 + - - -
405D HIS* 3.0 29.0 + - - +
601D 98H 5.6 3.8 - - + -
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Residues in contact with ASP 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D MET* 5.2 4.9 - - - +
398D SER* 2.8 26.2 + - - +
399D SER* 3.3 17.6 + - - +
401D PHE* 1.3 78.2 - - - +
403D PHE* 1.3 56.7 + - - +
405D HIS* 3.3 8.8 + - - +
406D SER* 3.0 32.1 + - - -
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Residues in contact with PHE 403 (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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362D LEU* 3.8 27.6 - - + -
363D VAL* 3.9 7.6 - - + -
399D SER 2.9 14.0 + - - +
400D ILE* 3.2 9.2 + - + +
402D ASP* 1.3 76.1 - - - +
404D SER* 1.3 62.0 + - - +
406D SER* 3.1 10.5 + - - -
407D LEU* 3.0 45.5 + - + +
420D TYR* 4.0 16.8 - - - -
467D PRO* 3.8 30.7 - - + -
471D LYS* 4.7 11.4 - - + -
472D LEU* 3.6 35.0 - - + -
475D LEU* 3.9 19.5 - - + -
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Residues in contact with SER 404 (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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362D LEU 4.2 3.8 + - - -
365D MET* 3.4 31.7 - - - +
366D CYS* 3.5 21.9 + - - +
369D TYR* 3.6 28.9 - - - -
400D ILE 3.2 9.7 + - - -
401D PHE 3.8 5.2 - - - -
403D PHE* 1.3 80.6 - - - +
405D HIS* 1.3 57.0 + - - +
407D LEU* 3.3 3.8 + - - +
408D SER* 2.9 28.8 + - - -
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Residues in contact with HIS 405 (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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369D TYR* 2.7 26.7 + - - +
371D ALA* 3.4 35.1 - - + +
374D ARG* 3.7 30.0 + - - +
401D PHE 3.0 14.5 + - - +
402D ASP* 3.4 11.9 - - - +
403D PHE 3.2 0.2 - - - -
404D SER* 1.3 72.9 - - - +
406D SER* 1.3 66.4 + - - +
408D SER* 2.5 23.6 + - - -
409D ALA* 3.5 6.5 + - + +
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Residues in contact with SER 406 (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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402D ASP 3.0 16.9 + - - -
403D PHE* 3.2 13.7 - - - -
405D HIS* 1.3 77.3 - - - +
407D LEU* 1.3 62.3 + - - +
409D ALA* 3.6 13.2 + - - +
410D LEU* 3.7 14.7 - - - +
467D PRO* 4.5 17.5 - - - -
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Residues in contact with LEU 407 (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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362D LEU 4.6 0.2 - - - +
363D VAL* 3.9 36.1 - - + +
366D CYS* 3.9 18.8 - - + -
403D PHE* 3.0 39.0 + - + +
404D SER* 3.8 7.0 - - - +
405D HIS 3.2 0.4 - - - -
406D SER* 1.3 75.5 - - - +
408D SER* 1.3 64.9 + - - +
410D LEU* 3.1 25.1 + - + +
411D HIS 3.8 3.1 + - - -
412D PHE* 4.1 17.4 + - + -
420D TYR* 3.8 22.0 - - + +
467D PRO* 3.9 28.5 - - + -
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Residues in contact with SER 408 (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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366D CYS* 4.8 6.7 - - - +
369D TYR* 4.4 9.2 - - - -
371D ALA* 3.5 30.6 - - - +
404D SER 2.9 13.7 + - - -
405D HIS* 2.5 26.3 + - - -
407D LEU* 1.3 76.8 - - - +
409D ALA* 1.3 60.6 + - - +
411D HIS* 3.3 25.7 + - - +
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Residues in contact with ALA 409 (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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405D HIS* 3.5 5.5 + - + +
406D SER* 3.7 11.9 - - - +
407D LEU 3.2 0.6 - - - -
408D SER* 1.3 80.6 + - - +
410D LEU* 1.3 62.8 + - + +
411D HIS* 3.1 24.6 + - - -
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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