Contacts of the helix formed by residues 468 - 490 (chain D) in PDB entry 5NTI
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 468 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D LEU 3.6 4.6 - - - +
467D PRO* 1.3 87.1 - - + +
469D LYS* 1.3 58.3 + - - +
470D GLY* 2.8 13.5 + - - +
471D LYS* 2.8 41.2 + - + +
472D LEU* 4.1 1.7 + - - +
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Residues in contact with LYS 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D GLU* 5.0 0.9 - - - +
423D LEU* 5.5 7.2 - - - -
427D ASN* 3.6 25.8 + - - +
429D HIS* 3.2 35.7 + - + +
443D GLN* 3.3 25.7 + - - +
447D GLU* 5.6 2.6 + - - -
467D PRO 3.5 3.1 + - - +
468D PRO* 1.3 70.7 - - - +
470D GLY* 1.3 60.3 + - - +
471D LYS 3.3 0.6 + - - -
472D LEU* 3.5 15.9 + - + +
473D ARG* 3.3 35.2 + - - +
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Residues in contact with GLY 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D PRO* 2.8 6.2 + - - +
469D LYS* 1.3 78.0 - - - +
471D LYS* 1.3 58.3 + - - +
472D LEU 3.4 0.2 - - - -
473D ARG* 3.7 23.6 - - - +
474D SER* 2.9 29.8 + - - -
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Residues in contact with LYS 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D PHE* 4.3 23.3 - - + -
467D PRO* 4.5 4.9 - - + -
468D PRO* 2.8 36.4 + - + +
470D GLY* 1.3 77.0 - - - +
472D LEU* 1.3 60.3 + - - +
474D SER* 3.4 9.0 + - - -
475D LEU* 3.3 34.2 + - + +
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Residues in contact with LEU 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D GLU* 3.7 52.7 - - + +
362D LEU* 4.1 14.1 - - + -
363D VAL* 4.2 4.0 - - + -
403D PHE* 3.6 39.5 - - + -
420D TYR* 4.5 4.9 - - + +
424D VAL* 4.0 26.2 - - + -
468D PRO 4.1 0.8 + - - +
469D LYS* 3.5 14.1 + - + +
470D GLY 3.4 0.2 - - - -
471D LYS* 1.3 74.1 - - - +
473D ARG* 1.3 65.1 + - - +
475D LEU* 3.5 5.7 + - + +
476D CYS* 3.2 28.4 + - - -
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Residues in contact with ARG 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D GLU* 3.9 13.9 + - - +
427D ASN* 5.3 5.3 - - - +
429D HIS* 5.5 8.5 - - - +
430D ARG* 4.5 10.2 - - - +
469D LYS* 3.3 32.7 + - - +
470D GLY* 3.7 21.7 - - - +
471D LYS 3.4 0.2 - - - -
472D LEU* 1.3 75.0 - - - +
474D SER* 1.3 59.7 + - - +
476D CYS* 3.3 4.6 + - - +
477D SER* 2.8 37.0 + - - +
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Residues in contact with SER 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D GLY 2.9 18.1 + - - -
471D LYS* 3.5 11.7 - - - -
473D ARG* 1.3 75.8 - - - +
475D LEU* 1.3 58.3 + - - +
477D SER* 3.3 6.6 + - - -
478D GLN* 2.9 54.2 + - - +
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Residues in contact with LEU 475 (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* 5.9 0.7 - - - +
362D LEU* 3.8 31.0 - - + -
396D LEU* 3.4 18.9 - - + +
399D SER* 3.5 35.9 - - - +
400D ILE* 4.2 13.7 - - + +
403D PHE* 4.0 34.3 - - + -
471D LYS* 3.3 20.3 + - + +
472D LEU* 3.9 6.1 - - + +
473D ARG 3.4 0.2 - - - -
474D SER* 1.3 76.7 - - - +
476D CYS* 1.3 58.0 + - - +
478D GLN* 4.4 7.9 - - - +
479D HIS* 3.0 26.9 + - - +
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Residues in contact with CYS 476 (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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355D ALA 4.7 6.1 - - - +
358D MET* 3.8 31.2 - - + -
359D GLU* 3.5 28.0 - - + +
362D LEU* 4.5 3.8 - - - -
472D LEU 3.2 21.7 + - - +
473D ARG* 3.7 6.5 - - - +
475D LEU* 1.3 75.2 - - - +
477D SER* 1.3 62.6 + - - +
479D HIS* 3.6 7.9 + - - +
480D VAL* 3.1 29.3 + - + +
506D PHE* 5.8 0.8 - - + -
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Residues in contact with SER 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D ARG* 2.8 23.9 + - - +
474D SER* 3.6 7.0 - - - -
476D CYS* 1.3 70.7 - - - +
478D GLN* 1.3 60.5 + - - +
480D VAL* 3.5 7.5 + - - +
481D GLU* 3.0 28.2 + - - +
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Residues in contact with GLN 478 (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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395D GLU* 4.4 6.2 - - - +
396D LEU* 3.6 41.6 + - + +
399D SER* 4.7 6.4 + - - -
474D SER* 2.9 42.3 + - - +
475D LEU* 4.2 9.9 - - - +
477D SER* 1.3 74.4 - - - +
479D HIS* 1.3 60.4 + - - +
481D GLU* 3.2 13.7 + - - +
482D ARG* 2.8 39.1 + - + +
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Residues in contact with HIS 479 (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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317D TRP* 5.0 2.0 - + - -
324D LEU* 4.0 6.0 - - + +
358D MET* 4.4 17.2 - - + +
396D LEU* 3.7 15.6 - - + +
475D LEU 3.0 17.7 + - - +
476D CYS* 3.6 9.0 + - - +
477D SER 3.4 0.2 - - - -
478D GLN* 1.3 77.5 - - - +
480D VAL* 1.3 62.2 + - - +
482D ARG* 3.3 1.4 + - - +
483D LEU* 3.0 23.8 + - + +
502D TYR* 2.9 29.6 + + - -
506D PHE* 3.4 55.3 - + + -
601D C3S 3.8 30.7 - - + +
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Residues in contact with VAL 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D CYS* 3.1 17.9 + - + +
477D SER* 3.8 7.0 - - - +
479D HIS* 1.3 78.9 - - - +
481D GLU* 1.3 64.3 + - - +
483D LEU* 3.5 4.7 + - - +
484D GLN* 3.2 27.4 + - - +
505D LEU 5.2 1.8 - - - +
506D PHE* 3.8 45.5 - - + +
507D SER 5.8 2.0 - - - -
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Residues in contact with GLU 481 (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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477D SER 3.0 14.6 + - - +
478D GLN* 3.2 15.4 + - - +
480D VAL* 1.3 76.2 - - - +
482D ARG* 1.3 81.3 + - - +
484D GLN* 3.1 21.6 + - - +
485D ILE* 3.2 22.5 + - + +
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Residues in contact with ARG 482 (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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317D TRP* 3.7 20.1 - - + -
392D GLY 2.8 25.2 + - - -
393D CYS* 3.4 24.6 - - + +
396D LEU* 4.1 16.2 - - + -
478D GLN* 2.8 25.9 + - - +
479D HIS 3.9 3.6 - - - +
481D GLU* 1.3 85.4 + - - +
483D LEU* 1.3 57.6 + - - +
485D ILE* 3.2 38.2 + - - +
486D PHE* 2.9 28.2 + - - +
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Residues in contact with LEU 483 (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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317D TRP* 3.5 21.0 - - + -
479D HIS* 3.0 17.3 + - - +
480D VAL 3.7 3.8 - - - +
482D ARG* 1.3 76.8 - - - +
484D GLN* 1.3 53.9 + - - +
486D PHE* 4.3 6.3 - - + -
487D GLN* 2.7 49.8 + - + +
494D VAL* 5.2 2.5 - - + -
498D PHE* 4.1 12.3 - - + -
502D TYR* 3.5 34.1 - - + +
506D PHE* 3.5 45.8 - - + +
507D SER* 3.9 13.7 - - - +
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Residues in contact with GLN 484 (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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480D VAL* 3.2 18.6 + - + +
481D GLU* 3.1 18.2 + - - +
483D LEU* 1.3 77.3 - - - +
485D ILE* 1.3 62.1 + - + +
487D GLN* 4.1 5.6 - - - +
488D HIS* 3.1 23.6 + - - +
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Residues in contact with ILE 485 (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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481D GLU* 3.2 22.3 + - + +
482D ARG* 3.4 45.1 - - - +
484D GLN* 1.3 75.7 - - + +
486D PHE* 1.3 67.8 + - - +
488D HIS* 3.1 7.1 + - - +
489D LEU* 3.1 41.2 + - + +
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Residues in contact with PHE 486 (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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313D MET* 3.5 36.6 - - + -
314D TRP* 3.6 17.9 - - + -
317D TRP* 3.4 44.9 - + + +
482D ARG 2.9 19.0 + - - +
483D LEU* 3.8 5.4 - - + +
485D ILE* 1.3 74.3 - - - +
487D GLN* 1.3 59.9 + - - +
489D LEU* 3.1 8.8 + - - +
490D HIS* 2.8 50.6 + - + +
493D VAL* 4.2 3.1 - - + -
494D VAL* 3.6 19.5 - - + -
498D PHE* 3.4 29.6 - + - -
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Residues in contact with GLN 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D LEU* 2.7 27.3 + - + +
484D GLN* 4.1 6.0 - - - +
486D PHE* 1.3 74.1 - - - +
488D HIS* 1.3 61.7 + - - +
491D PRO* 3.1 33.9 + - + +
494D VAL* 3.7 40.4 - - + +
503D LYS* 5.2 5.1 - - - +
507D SER* 2.7 34.6 + - - -
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Residues in contact with HIS 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D GLN 3.1 20.3 + - - +
485D ILE* 3.1 5.8 + - - +
487D GLN* 1.3 76.4 - - - +
489D LEU* 1.3 69.2 + - + +
491D PRO* 3.6 11.1 - - - +
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Residues in contact with LEU 489 (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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313D MET* 4.7 20.4 - - + -
485D ILE* 3.1 36.6 + - + +
486D PHE* 3.7 8.3 - - - +
488D HIS* 1.3 85.8 - - - +
490D HIS* 1.3 79.8 + - + +
491D PRO* 3.6 5.5 - - - +
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Residues in contact with HIS 490 (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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313D MET* 4.2 26.5 - - + -
314D TRP* 4.4 22.0 - + + +
486D PHE* 2.8 37.2 + + + +
487D GLN 3.4 3.4 - - - -
489D LEU* 1.3 94.6 + - + +
491D PRO* 1.4 64.8 - - - +
492D ILE* 3.2 4.4 + - - -
493D VAL* 3.4 19.9 + - + -
494D VAL* 3.4 22.5 + - - +
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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
------------------------------------------------------------
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