Contacts of the helix formed by residues 473 - 497 (chain D) in PDB entry 6W4E
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 LYS 473 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A LYS 5.2 0.2 - - - +
301A LEU* 3.5 41.2 + - + -
304A GLU* 2.6 31.2 + - - +
305A MET* 3.2 37.8 - - - -
469D LEU* 2.8 34.2 + - - +
470D TYR* 3.2 3.3 + - + -
471D ARG 3.3 0.4 - - - -
472D GLN* 1.3 85.5 - - + +
474D VAL* 1.3 60.9 + - + +
475D GLU 3.2 1.1 - - - -
476D PRO* 3.2 3.1 - - - +
477D LEU* 2.7 50.6 + - + +
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Residues in contact with VAL 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D TYR* 2.7 46.5 + - + +
473D LYS* 1.3 79.2 - - + +
475D GLU* 1.3 56.6 + - + +
477D LEU* 3.7 6.9 - - - +
478D ARG* 2.8 46.4 + - + +
481D LEU* 6.0 0.2 - - - +
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Residues in contact with GLU 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D TYR 2.9 7.3 + - - +
471D ARG* 3.2 47.7 + - + +
474D VAL* 1.3 78.3 - - + +
476D PRO* 1.3 68.7 - - + +
478D ARG* 3.0 30.4 + - - +
479D ALA* 3.6 3.5 + - - +
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Residues in contact with PRO 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS* 5.1 6.5 - - - +
301A LEU* 6.0 1.8 - - + -
471D ARG 3.2 19.7 - - - +
472D GLN* 3.4 20.4 - - - +
473D LYS* 3.2 17.0 - - - +
475D GLU* 1.3 90.7 - - + +
477D LEU* 1.3 56.1 + - + +
479D ALA* 3.0 23.0 + - + +
480D GLU* 3.2 24.5 + - - +
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Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU 5.6 0.4 - - - +
294A LEU* 4.2 21.5 - - + -
297A LYS* 3.9 33.9 - - + +
301A LEU* 5.1 1.8 - - + -
473D LYS* 2.7 45.2 + - + +
474D VAL* 3.9 5.6 - - + +
476D PRO* 1.3 69.8 - - + +
478D ARG* 1.3 56.1 + - - +
479D ALA 3.1 0.2 - - - -
480D GLU* 3.6 20.8 - - + +
481D LEU* 2.7 49.7 + - + +
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Residues in contact with ARG 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D VAL* 2.8 30.6 + - + +
475D GLU* 3.0 25.0 + - - +
477D LEU* 1.3 77.8 - - - +
479D ALA* 1.3 55.0 + - - +
481D LEU* 3.8 8.0 - - + +
482D GLN* 2.8 36.1 + - - +
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Residues in contact with ALA 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D GLU 3.6 3.2 + - - +
476D PRO* 3.0 13.9 + - + +
478D ARG* 1.3 77.6 - - - +
480D GLU* 1.3 59.9 + - - +
482D GLN* 3.6 9.6 - - - +
483D GLU* 2.7 37.6 + - - +
486D ARG* 5.0 1.5 + - - +
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Residues in contact with GLU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 3.7 33.5 - - + +
294A LEU* 5.8 2.7 - - + -
297A LYS* 2.7 41.2 + - - +
476D PRO* 3.2 23.3 + - - +
477D LEU* 3.6 22.5 - - + +
479D ALA* 1.3 82.4 - - - +
481D LEU* 1.3 57.8 + - + +
483D GLU* 3.5 5.1 + - - +
484D GLY* 3.0 23.7 + - - -
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Residues in contact with LEU 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 4.3 24.5 - - + -
474D VAL 6.0 0.2 - - - +
477D LEU* 2.7 39.9 + - + +
478D ARG* 4.0 7.6 - - + +
480D GLU* 1.3 71.3 - - - +
482D GLN* 1.3 54.5 + - - +
484D GLY* 3.3 2.2 + - - -
485D ALA* 2.7 34.7 + - - +
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Residues in contact with GLN 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D ARG* 2.8 25.8 + - - +
479D ALA* 3.2 8.2 + - - +
481D LEU* 1.3 75.1 - - - +
483D GLU* 1.3 55.1 + - - +
485D ALA* 3.2 8.3 + - + +
486D ARG* 2.7 74.1 + - + +
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Residues in contact with GLU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D ALA 2.7 20.5 + - - +
480D GLU* 3.8 6.7 - - - +
482D GLN* 1.3 69.7 - - - +
484D GLY* 1.3 60.7 + - - +
486D ARG* 2.7 43.6 + - - +
487D GLN* 2.9 34.8 + - + +
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Residues in contact with GLY 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LYS* 3.7 25.8 - - - -
480D GLU 3.0 15.8 + - - -
481D LEU* 3.7 3.6 - - - -
482D GLN 3.3 0.2 - - - -
483D GLU* 1.3 75.4 - - - +
485D ALA* 1.3 57.4 + - - +
487D GLN* 3.4 4.6 + - - -
488D LYS* 2.8 29.6 + - - +
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Residues in contact with ALA 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 LEU 2.7 17.9 + - - +
482D GLN* 3.2 10.5 + - + +
484D GLY* 1.3 75.8 - - - +
486D ARG* 1.3 54.3 + - - +
488D LYS* 3.2 11.2 + - + +
489D LEU* 2.7 46.7 + - + +
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Residues in contact with ARG 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D ALA* 5.0 1.6 + - - +
482D GLN* 2.7 60.7 + - + +
483D GLU* 2.7 52.7 + - - +
485D ALA* 1.3 74.9 - - + +
487D GLN* 1.3 57.4 + - + +
489D LEU* 3.2 12.8 + - + +
490D HIS* 2.8 29.5 + - - +
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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
----------------------------------------------------------
289A GLN* 5.6 6.0 + - - +
290A LYS* 4.6 5.8 - - - -
483D GLU* 2.9 22.8 + - + +
484D GLY* 3.7 7.4 - - - +
486D ARG* 1.3 76.9 - - - +
488D LYS* 1.3 51.9 + - - +
490D HIS* 3.2 22.3 + - - +
491D GLU* 2.8 51.9 + - - +
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Residues in contact with LYS 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LYS* 4.1 12.1 - - + +
484D GLY 2.8 20.2 + - - +
485D ALA* 3.4 10.5 - - + +
487D GLN* 1.3 77.2 - - - +
489D LEU* 1.3 58.3 + - + +
491D GLU* 3.3 14.1 + - + +
492D LEU* 2.8 53.7 + - + +
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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
----------------------------------------------------------
485D ALA* 2.7 34.7 + - + +
486D ARG* 3.2 12.3 + - + +
488D LYS* 1.3 72.5 - - + +
490D HIS* 1.3 54.1 + - - +
492D LEU* 3.1 20.6 + - + +
493D GLN* 2.7 44.7 + - + +
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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
----------------------------------------------------------
486D ARG 2.8 16.5 + - - +
487D GLN* 3.5 23.6 + - - +
489D LEU* 1.3 75.0 - - - +
491D GLU* 1.3 68.2 + - - +
493D GLN* 3.0 23.8 + - + +
494D GLU* 2.9 57.8 + - + +
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Residues in contact with GLU 491 (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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282A GLU* 3.3 39.1 - - + +
283A LEU* 4.4 8.6 + - + +
286A GLY* 4.5 3.5 - - - -
290A LYS* 2.7 32.3 + - - -
487D GLN* 2.8 37.8 + - + +
488D LYS* 3.5 8.0 - - - +
490D HIS* 1.3 75.8 - - + +
492D LEU* 1.3 63.0 + - + +
494D GLU* 3.3 7.2 + - - +
495D LYS* 2.9 47.7 + - - +
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Residues in contact with LEU 492 (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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283A LEU* 6.5 1.3 - - + -
488D LYS* 2.8 50.4 + - + +
489D LEU* 3.1 21.5 + - + +
491D GLU* 1.3 75.6 - - + +
493D GLN* 1.3 54.3 + - + +
495D LYS* 2.9 16.5 + - + +
496D LEU* 2.6 57.2 + - + +
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Residues in contact with GLN 493 (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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489D LEU* 2.7 26.3 + - + +
490D HIS* 3.3 28.9 - - + +
492D LEU* 1.3 68.9 - - + +
494D GLU* 1.3 58.3 + - + +
495D LYS 2.9 9.4 + - - -
496D LEU* 4.5 6.7 - - + +
497D SER* 2.7 34.2 + - - +
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Residues in contact with GLU 494 (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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279A LEU* 5.5 1.6 - - - +
282A GLU* 5.1 10.5 - - - +
490D HIS* 2.9 50.0 + - + +
491D GLU* 3.7 8.5 - - - +
492D LEU 3.2 0.4 - - - -
493D GLN* 1.3 75.7 - - + +
495D LYS* 1.3 62.8 + - + +
497D SER* 5.2 0.4 - - - -
498D PRO* 3.1 22.5 - - - +
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Residues in contact with LYS 495 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 3.6 42.2 - - + +
282A GLU* 2.6 34.2 + - - +
283A LEU* 4.9 13.2 - - - -
491D GLU* 2.9 41.7 + - - +
492D LEU* 2.9 18.1 + - + +
493D GLN 2.9 0.2 - - - -
494D GLU* 1.3 83.1 - - - +
496D LEU* 1.3 60.5 + - + +
497D SER 3.1 4.0 - - - -
498D PRO* 4.0 2.0 - - - -
499D LEU* 2.9 48.1 + - + +
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Residues in contact with LEU 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D LEU* 2.6 42.6 + - + +
493D GLN* 4.5 6.1 - - + +
495D LYS* 1.3 75.3 - - + +
497D SER* 1.3 58.1 + - - +
499D LEU* 5.0 1.1 - - + -
500D GLY* 3.1 23.6 - - - +
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Residues in contact with SER 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D GLN* 2.7 22.4 + - - +
494D GLU* 5.2 0.7 - - - -
495D LYS 3.1 1.0 - - - -
496D LEU* 1.3 77.9 - - - +
498D PRO* 1.4 69.0 - - - +
501D GLU* 2.9 35.5 + - - +
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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