Contacts of the helix formed by residues 468 - 490 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B LEU 3.6 4.9 - - - +
467B PRO* 1.3 87.3 - - + +
469B LYS* 1.3 53.0 - - - +
470B GLY* 2.8 18.4 + - - +
471B LYS* 2.8 46.6 + - + +
472B LEU 4.2 0.7 + - - -
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLU* 5.6 0.3 - - - +
427B ASN* 4.2 32.1 + - - +
429B HIS* 4.9 11.7 + - - +
443B GLN* 5.8 4.6 + - - +
467B PRO 3.7 2.9 + - - +
468B PRO* 1.3 70.0 - - - +
470B GLY* 1.3 61.5 + - - +
471B LYS 3.2 0.8 + - - -
472B LEU* 3.5 13.4 + - + +
473B ARG* 3.2 25.7 + - - +
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Residues in contact with GLY 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PRO* 2.8 11.6 + - - +
469B LYS* 1.3 72.8 - - - +
471B LYS* 1.3 58.3 + - - -
473B ARG* 4.0 18.7 + - - +
474B SER* 3.0 31.0 + - - -
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Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PHE* 4.0 21.8 - - + -
467B PRO* 4.4 5.8 - - + -
468B PRO* 2.8 48.4 + - + +
470B GLY* 1.3 70.2 - - - +
472B LEU* 1.3 64.1 + - - +
474B SER* 3.3 6.1 + - - -
475B LEU* 3.1 30.9 + - + +
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLU* 3.6 58.3 - - + +
362B LEU* 4.2 13.2 - - + -
363B VAL* 4.2 6.5 - - + -
403B PHE* 3.6 32.7 - - + -
420B TYR* 4.6 7.0 - - - +
424B VAL* 4.2 20.6 - - + -
468B PRO 4.2 0.8 + - - +
469B LYS* 3.5 13.7 + - + +
471B LYS* 1.3 77.9 - - - +
473B ARG* 1.3 58.2 + - - +
475B LEU* 3.3 8.7 + - + +
476B CYS* 3.0 33.4 + - - -
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLU* 4.5 11.8 + - - +
430B ARG* 5.9 4.7 - - - +
469B LYS 3.2 16.5 + - - +
470B GLY* 4.1 15.5 + - - +
472B LEU* 1.3 79.1 - - - +
474B SER* 1.3 57.5 + - - +
476B CYS* 3.7 4.5 + - - +
477B SER* 2.9 39.8 + - - +
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Residues in contact with SER 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLY 3.0 20.1 + - - -
471B LYS* 3.6 5.2 - - - -
472B LEU 3.3 0.2 - - - -
473B ARG* 1.3 76.3 - - - +
475B LEU* 1.3 55.8 + - - +
477B SER* 3.3 6.4 + - - -
478B GLN* 2.8 53.1 + - - +
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Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B MET* 5.7 0.5 - - - +
362B LEU* 4.0 26.2 - - + -
396B LEU* 3.5 14.7 - - + +
399B SER* 3.6 36.8 - - - +
400B ILE* 4.0 16.0 - - + +
403B PHE* 3.8 38.4 - - + -
471B LYS* 3.1 20.2 + - + +
472B LEU* 3.5 9.4 - - - +
474B SER* 1.3 77.3 - - - +
476B CYS* 1.3 57.1 + - - +
478B GLN* 4.1 9.0 - - - +
479B HIS* 3.1 24.9 + - - +
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Residues in contact with CYS 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ALA 5.0 4.5 - - - -
358B MET* 3.8 30.7 - - + -
359B GLU* 3.7 27.1 - - - +
362B LEU* 4.4 4.7 - - - -
472B LEU 3.0 19.3 + - - +
473B ARG* 4.0 6.5 - - + +
474B SER 3.3 0.2 - - - -
475B LEU* 1.3 74.3 - - - +
477B SER* 1.3 65.0 + - - +
479B HIS* 3.2 9.6 + - - +
480B VAL* 3.0 27.9 + - + +
506B PHE* 5.9 1.7 - - + -
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Residues in contact with SER 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ARG* 2.9 30.6 + - - +
474B SER* 3.3 6.7 + - - -
476B CYS* 1.3 76.4 - - - +
478B GLN* 1.3 58.4 + - - +
480B VAL* 3.4 7.7 + - - +
481B GLU* 2.9 42.4 + - - +
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Residues in contact with GLN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU* 4.1 15.3 - - - +
396B LEU* 3.5 43.8 + - + +
399B SER* 3.9 11.8 + - - -
474B SER* 2.8 44.6 + - - +
475B LEU* 4.1 13.7 - - - +
477B SER* 1.3 72.9 - - - +
479B HIS* 1.3 58.1 + - - +
481B GLU* 3.3 13.8 + - - +
482B ARG* 2.8 39.3 + - + +
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Residues in contact with HIS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 4.8 2.7 - + - -
324B LEU* 3.8 12.0 - - + +
358B MET* 3.7 18.0 - - + +
396B LEU* 3.8 14.3 - - + +
475B LEU 3.1 15.8 + - - +
476B CYS* 3.2 11.3 + - - +
478B GLN* 1.3 77.1 - - - +
480B VAL* 1.3 60.5 + - - +
482B ARG* 3.4 1.0 + - - +
483B LEU* 3.1 21.5 + - - +
502B TYR* 2.8 35.1 + + - -
506B PHE* 3.7 43.2 - + + -
601B C3S 3.8 30.5 - - + +
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B CYS 3.0 15.9 + - - +
477B SER* 3.4 9.4 + - - +
479B HIS* 1.3 74.4 - - - +
481B GLU* 1.3 62.3 + - + +
483B LEU* 3.5 5.2 + - - +
484B GLN* 3.2 34.3 + - + +
505B LEU 5.1 1.6 - - - +
506B PHE* 3.9 44.6 - - + +
507B SER 5.9 0.9 - - - +
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Residues in contact with GLU 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B SER* 2.9 29.1 + - - +
478B GLN* 3.5 15.5 + - - +
479B HIS 3.3 0.2 - - - -
480B VAL* 1.3 77.4 - - + +
482B ARG* 1.3 63.8 + - - +
484B GLN* 3.0 33.3 + - - +
485B ILE* 3.2 17.9 + - + +
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Residues in contact with ARG 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 3.6 20.5 - - + -
392B GLY 2.7 25.2 + - - -
393B CYS* 3.5 31.5 - - + +
395B GLU* 5.1 13.9 + - - +
396B LEU* 4.1 14.8 - - + +
478B GLN* 2.8 29.6 + - + +
479B HIS 4.0 3.4 - - - +
481B GLU* 1.3 76.6 - - - +
483B LEU* 1.3 56.7 + - - +
485B ILE* 3.5 41.6 + - - +
486B PHE* 3.0 21.5 + - - +
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B TRP* 3.6 28.6 - - + -
479B HIS 3.1 17.5 + - - +
480B VAL 3.7 5.2 - - - +
481B GLU 3.1 0.2 - - - -
482B ARG* 1.3 76.0 - - - +
484B GLN* 1.3 55.4 + - - +
486B PHE* 3.3 11.4 + - + -
487B GLN* 2.8 41.2 + - - +
494B VAL* 4.5 9.4 - - + -
498B PHE* 4.4 4.9 - - + -
502B TYR* 3.8 23.1 - - + +
506B PHE* 3.5 44.9 - - + +
507B SER* 3.8 11.7 - - - +
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Residues in contact with GLN 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL* 3.2 24.9 + - + +
481B GLU* 3.0 20.6 + - - +
483B LEU* 1.3 77.1 - - + +
485B ILE* 1.3 62.6 - - + +
487B GLN* 3.5 7.0 + - - +
488B HIS* 3.1 23.2 + - - +
506B PHE 6.1 0.7 - - - +
507B SER 6.0 6.3 - - - -
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Residues in contact with ILE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B GLU* 3.2 14.2 + - + +
482B ARG* 3.5 51.8 - - - +
484B GLN* 1.3 78.2 - - + +
486B PHE* 1.3 63.9 + - - +
488B HIS* 3.2 9.7 + - - +
489B LEU* 3.1 36.5 + - + +
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Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B MET* 3.7 12.1 - - - -
314B TRP* 3.7 28.5 - - + -
317B TRP* 3.4 55.4 - + + +
482B ARG 3.0 17.2 + - - +
483B LEU* 3.3 7.2 + - + +
485B ILE* 1.3 78.0 - - - +
487B GLN* 1.3 54.2 + - - +
489B LEU* 3.2 7.2 + - - +
490B HIS* 2.8 62.9 + - + -
493B VAL* 4.4 4.0 - - + -
494B VAL* 3.9 18.2 - - + -
498B PHE* 3.6 23.3 - + - -
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Residues in contact with GLN 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 2.8 29.1 + - - +
484B GLN* 3.8 8.0 - - - +
485B ILE 3.3 0.2 - - - -
486B PHE* 1.3 73.9 - - - +
488B HIS* 1.3 59.7 + - - +
490B HIS 4.0 4.9 - - - -
491B PRO* 3.1 42.0 + - + +
494B VAL* 4.4 23.8 - - + +
503B LYS* 5.8 3.4 - - - +
507B SER* 2.7 34.3 + - - -
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Residues in contact with HIS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B GLN 3.1 14.5 + - - +
485B ILE* 3.4 11.2 + - - +
487B GLN* 1.3 77.7 - - - +
489B LEU* 1.3 76.1 + - + +
491B PRO* 4.2 10.1 - - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B MET* 3.7 34.3 - - + -
485B ILE* 3.1 31.7 + - + +
486B PHE* 3.2 5.6 + - - +
488B HIS* 1.3 91.1 - - + +
490B HIS* 1.3 83.1 + - + +
491B PRO* 3.9 4.1 - - - +
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Residues in contact with HIS 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B MET* 4.0 26.9 - - + -
314B TRP* 4.4 21.8 - + + +
486B PHE* 2.8 41.4 + + + +
487B GLN* 3.4 8.6 - - - +
489B LEU* 1.3 103.7 + - + +
491B PRO* 1.4 66.9 - - - +
492B ILE 3.3 3.1 + - - -
493B VAL* 3.8 26.6 + - + +
494B VAL* 4.3 8.0 + - - +
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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