Contacts of the helix formed by residues 487 - 506 (chain D) in PDB entry 6E7P
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 SER 487 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A ASP* 3.6 24.6 + - - -
450D TYR* 3.8 17.4 + - - -
483D GLN* 4.0 2.8 - - - +
485D GLY 3.1 5.1 + - - -
486D ARG* 1.3 76.7 - - - +
488D SER* 1.3 57.9 + - - +
489D LEU* 3.0 12.2 + - - -
490D VAL* 3.1 19.4 + - - +
491D TRP 3.6 5.4 + - - -
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Residues in contact with SER 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D GLN 4.3 8.7 - - - -
484D GLN 3.9 17.1 + - - -
485D GLY 4.1 5.2 + - - -
486D ARG 3.6 0.8 - - - -
487D SER* 1.3 72.5 - - - +
489D LEU* 1.3 58.3 + - - +
491D TRP* 4.1 13.8 - - - +
492D LEU* 3.7 19.1 + - - +
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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
----------------------------------------------------------
384A ASP* 5.2 6.7 - - + +
385A VAL* 4.8 19.1 - - + -
388A ILE* 3.8 25.6 - - + -
487D SER 3.0 2.2 + - - -
488D SER* 1.3 75.3 - - - +
490D VAL* 1.3 64.9 + - + +
491D TRP 3.2 0.2 - - - -
492D LEU* 3.1 15.8 + - + -
493D PHE* 2.9 26.2 + - + +
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Residues in contact with VAL 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 3.5 41.3 - - + +
388A ILE* 5.0 7.4 - - + -
446D VAL* 4.1 19.1 - - + +
447D LEU* 4.2 13.3 - - + +
450D TYR* 3.9 28.7 - - + -
451D HIS* 5.7 1.8 - - - +
483D GLN* 5.9 5.4 - - + +
487D SER* 3.1 12.9 + - - +
489D LEU* 1.3 74.1 - - + +
491D TRP* 1.3 60.0 + - - +
493D PHE* 3.5 6.7 + - - +
494D SER* 3.0 27.0 + - - -
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Residues in contact with TRP 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A SER* 4.3 19.7 - - - -
480D MET 3.8 23.5 - - - -
481D GLN* 3.8 18.8 - - + +
483D GLN* 3.6 24.0 + - + +
484D GLN* 4.2 39.0 - - + +
487D SER 3.6 3.6 + - - -
488D SER* 4.2 15.9 - - - +
489D LEU 3.2 0.4 - - - -
490D VAL* 1.3 79.4 - - - +
492D LEU* 1.3 84.3 + - + +
494D SER* 2.4 32.0 + - - -
495D GLN* 3.0 42.3 + - + +
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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
----------------------------------------------------------
488D SER* 3.7 12.0 + - - +
489D LEU* 3.1 18.9 + - + +
491D TRP* 1.3 97.8 - - + +
493D PHE* 1.3 62.4 + - - +
495D GLN* 3.8 5.0 + - + +
496D LEU* 3.5 26.7 + - + +
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Residues in contact with PHE 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 3.9 24.2 - - + -
392A THR* 3.8 26.5 - - + -
395A LEU* 5.6 3.1 - - + -
442D CYS* 4.0 15.3 - - - -
443D GLY* 6.0 0.2 - - - -
446D VAL* 3.5 38.4 - - + -
447D LEU* 5.3 2.9 - - + -
489D LEU* 2.9 16.6 + - + +
490D VAL* 3.8 8.1 - - - +
492D LEU* 1.3 80.0 - - - +
494D SER* 1.3 54.1 + - - +
496D LEU* 3.1 15.1 + - + +
497D TYR* 2.6 61.1 + + + +
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Residues in contact with SER 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D LEU* 3.8 24.9 - - - -
480D MET* 4.0 24.0 - - - +
490D VAL 3.0 12.8 + - - -
491D TRP* 2.4 33.7 + - - -
493D PHE* 1.3 72.8 - - - +
495D GLN* 1.3 65.7 + - - +
497D TYR* 4.2 6.3 - - - -
498D LEU* 3.2 31.1 + - - +
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Residues in contact with GLN 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A SER* 4.8 3.6 + - - +
462A GLU* 3.2 30.8 + - - +
477D PHE* 4.1 9.8 - - - -
480D MET* 4.7 6.8 - - - +
491D TRP* 3.0 54.9 + - + +
492D LEU* 4.1 6.1 - - + +
493D PHE 3.3 0.4 - - - -
494D SER* 1.3 81.6 + - - +
496D LEU* 1.3 57.1 + - - +
498D LEU* 5.2 1.1 - - - -
499D TYR* 3.3 61.1 + - + +
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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* 3.5 22.5 + - + +
493D PHE* 3.1 15.5 + - + +
495D GLN* 1.3 77.1 - - - +
497D TYR* 1.3 56.1 + - - +
499D TYR* 5.0 2.7 - - + -
500D SER* 2.7 41.0 + - - +
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Residues in contact with TYR 497 (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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395A LEU* 5.1 2.0 - - + -
439D TYR* 2.3 64.4 + + + +
442D CYS* 4.2 8.3 - - - -
443D GLY* 3.4 26.3 + - - -
447D LEU* 4.0 15.3 - - + -
454D PHE* 5.2 3.6 - + - -
464D LEU* 3.9 19.6 - - + +
493D PHE* 2.6 48.1 + + + +
494D SER* 4.0 7.2 - - - +
495D GLN 3.4 0.2 - - - -
496D LEU* 1.3 74.1 - - - +
498D LEU* 1.3 83.8 + - + +
500D SER* 3.2 14.0 + - - -
501D PHE* 3.5 15.5 + - + +
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Residues in contact with LEU 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D LEU* 5.3 1.6 - - + -
454D PHE* 4.7 15.0 - - + -
464D LEU* 5.1 4.5 - - + -
467D LEU* 4.7 23.5 - - + +
476D THR* 4.6 11.7 - - - +
477D PHE* 3.7 36.6 - - + -
480D MET* 4.3 25.1 - - + -
494D SER* 3.2 19.7 + - - +
497D TYR* 1.3 95.0 - - + +
499D TYR* 1.3 64.0 + - - +
501D PHE* 3.1 5.7 + - + +
502D ILE* 3.1 29.7 + - + +
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Residues in contact with TYR 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A SER 5.2 0.2 + - - -
461A SER* 2.8 42.7 + - - -
462A GLU* 3.7 10.5 - - + +
465A PHE* 3.8 30.0 - + + -
477D PHE* 3.5 31.2 - + - -
495D GLN* 3.3 35.9 + - + +
496D LEU* 4.9 3.6 - - + +
498D LEU* 1.3 78.4 - - - +
500D SER* 1.3 61.2 + - - +
502D ILE* 4.1 3.0 - - - +
503D SER* 3.2 28.9 + - - -
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Residues in contact with SER 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D TYR* 4.1 19.5 + - - -
496D LEU* 2.7 31.9 + - - -
497D TYR* 3.2 8.5 + - - -
499D TYR* 1.3 78.9 - - - +
501D PHE* 1.3 57.1 + - - +
503D SER* 4.6 1.5 - - - -
504D LEU* 3.3 21.9 + - - +
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Residues in contact with PHE 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D TYR* 4.3 8.5 - + - -
439D TYR* 3.7 45.3 - + + -
464D LEU* 3.7 45.1 - - + -
467D LEU* 4.6 9.9 - - + -
468D ILE* 3.7 22.7 - - + -
497D TYR* 3.5 17.9 + + + +
498D LEU* 3.1 7.3 + - + +
500D SER* 1.3 79.0 + - - +
502D ILE* 1.3 70.1 + - - +
503D SER 3.2 1.3 - - - -
504D LEU* 3.1 13.0 + - + +
505D PHE* 3.3 49.1 + + - +
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Residues in contact with ILE 502 (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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465A PHE* 3.5 25.6 - - + -
469A ASN* 4.0 10.1 - - - +
467D LEU* 3.2 42.6 - - + +
468D ILE* 3.7 12.8 - - + -
473D MET* 3.7 20.2 - - + -
477D PHE* 5.1 4.9 - - + -
498D LEU 3.1 21.2 + - - +
499D TYR* 4.1 4.0 - - + +
501D PHE* 1.3 79.8 - - - +
503D SER* 1.3 62.2 + - - +
504D LEU 3.2 1.1 + - - -
505D PHE* 4.7 0.2 - - - -
506D ILE* 3.6 40.8 + - + +
507D TYR* 5.2 0.3 - - - -
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Residues in contact with SER 503 (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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429A CYS* 5.8 3.5 - - - -
465A PHE* 4.3 13.0 - - - -
499D TYR 3.2 18.6 + - - -
500D SER* 4.6 2.0 - - - -
501D PHE 3.2 0.8 - - - -
502D ILE* 1.3 78.7 - - - +
504D LEU* 1.3 58.6 + - - +
507D TYR* 3.3 43.4 - - - +
508D MET* 5.0 6.1 - - - +
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Residues in contact with LEU 504 (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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435D ILE* 4.8 11.4 - - + -
439D TYR* 4.3 24.9 - - + +
500D SER 3.3 17.9 + - - +
501D PHE* 3.1 7.6 + - + +
503D SER* 1.3 79.8 - - - +
505D PHE* 1.3 84.2 + - + +
506D ILE 3.4 0.7 - - - -
507D TYR 4.1 0.2 - - - -
508D MET* 3.2 48.4 + - + +
509D VAL* 3.5 10.5 + - + +
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Residues in contact with PHE 505 (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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432D VAL* 3.7 31.2 - - + -
435D ILE* 4.9 11.9 - - + -
436D TYR* 3.9 28.7 - + + -
439D TYR* 5.5 0.2 - + - -
468D ILE* 3.6 49.1 - - + +
501D PHE* 3.3 34.5 + + - +
502D ILE 5.1 0.4 - - - +
504D LEU* 1.3 94.7 - - + +
506D ILE* 1.3 61.2 + - - +
509D VAL* 3.5 26.2 - - + +
510D LEU* 2.8 28.5 + - - +
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Residues in contact with ILE 506 (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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469A ASN* 3.5 29.8 - - + +
510A LEU* 4.4 13.3 - - + +
513A PHE* 5.8 0.2 - - - +
468D ILE* 3.6 22.9 - - - +
469D ASN 5.8 0.4 - - - -
470D GLY 5.6 0.9 - - - +
473D MET* 5.3 0.2 - - + -
502D ILE* 3.6 37.7 + - + +
504D LEU 3.4 0.6 - - - -
505D PHE* 1.3 78.6 - - - +
507D TYR* 1.3 85.5 + - + +
508D MET 3.6 0.4 + - - -
510D LEU* 3.4 34.9 + - + +
511D SER* 4.0 6.4 + - - -
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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