Contacts of the helix formed by residues 481 - 500 (chain D) in PDB entry 4QGC
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 ALA 481 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D GLN* 3.3 5.2 - - - +
480D GLU* 1.3 77.4 - - - +
482D TRP* 1.3 66.9 + - - +
483D ALA* 3.3 2.7 - - + +
484D GLU* 2.9 36.5 + - + +
485D ASP 3.1 9.7 + - - -
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Residues in contact with TRP 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C TRP* 6.2 1.1 - + - -
483C ALA* 6.1 2.5 - - + -
515C TRP* 3.6 35.9 - + - -
479D GLN 4.9 1.6 - - - -
480D GLU 3.5 6.2 + - - +
481D ALA* 1.3 71.4 - - - +
483D ALA* 1.3 74.5 + - + +
485D ASP* 3.1 8.7 + - + +
486D VAL* 3.0 42.4 + - + +
489D ARG* 4.8 1.8 - - - -
513D THR* 4.6 1.6 - - - -
514D GLY* 3.3 30.7 - - - -
515D TRP* 3.0 33.9 - + - -
516D ARG* 4.0 4.2 + - - -
517D PRO* 3.5 46.0 - - + +
1002D SO4 2.8 34.4 + - - -
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Residues in contact with ALA 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C TRP* 6.3 3.4 - - + -
515C TRP* 4.5 8.7 - - + +
516C ARG* 3.1 41.4 + - - +
481D ALA* 3.3 2.8 - - + -
482D TRP* 1.3 95.1 - - + +
484D GLU* 1.3 57.0 + - - +
486D VAL* 3.9 4.8 - - - +
487D ASP* 3.1 26.7 + - - +
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Residues in contact with GLU 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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516C ARG* 3.8 15.5 + - - +
479D GLN* 4.0 20.2 + - + +
481D ALA* 2.9 27.7 + - + +
483D ALA* 1.3 79.0 - - - +
485D ASP* 1.3 59.3 + - - +
487D ASP* 3.5 8.4 + - - +
488D LEU* 3.0 28.2 + - - +
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Residues in contact with ASP 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D ARG* 2.7 40.4 + - - -
478D VAL* 3.3 12.1 - - + +
479D GLN* 3.1 36.1 + - + +
481D ALA 3.1 7.5 + - - +
482D TRP* 3.1 12.0 + - + +
484D GLU* 1.3 76.0 - - - +
486D VAL* 1.3 63.9 + - - +
488D LEU* 3.4 3.7 + - - +
489D ARG* 2.8 54.0 + - - +
1002D SO4 5.3 0.5 + - - -
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Residues in contact with VAL 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C TRP* 3.8 21.3 - - + -
431D LEU* 3.8 19.1 - - + -
482D TRP* 3.0 53.3 + - + +
483D ALA 4.0 4.0 - - - +
485D ASP* 1.3 75.7 - - - +
487D ASP* 1.3 58.7 + - - +
489D ARG* 3.1 21.0 + - - +
490D VAL* 2.9 40.2 + - + +
513D THR* 3.8 17.0 - - + -
526D ARG* 4.2 2.0 - - - +
1002D SO4 4.3 0.4 - - - +
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Residues in contact with ASP 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C TRP* 3.0 30.2 + - - -
516C ARG* 3.4 20.8 + - - +
483D ALA 3.1 18.6 + - - +
484D GLU* 3.8 11.8 - - - +
485D ASP 3.4 0.2 - - - -
486D VAL* 1.3 77.0 - - - +
488D LEU* 1.3 57.5 + - - +
490D VAL* 3.9 5.7 - - - +
491D ASN* 2.9 44.6 + - - +
526D ARG* 4.4 4.0 + - - -
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Residues in contact with LEU 488 (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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455D ARG* 4.8 6.3 - - - +
474D CYS* 5.4 3.1 - - - -
476D ASP* 3.8 39.9 - - + +
477D PRO 4.5 2.9 - - - +
479D GLN* 4.1 28.5 - - + +
484D GLU 3.0 18.8 + - - +
485D ASP 3.7 5.6 - - - +
486D VAL 3.1 0.2 - - - -
487D ASP* 1.3 77.2 - - - +
489D ARG* 1.3 56.2 + - - +
491D ASN* 3.6 7.6 + - + +
492D PHE* 3.1 28.4 + - + +
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Residues in contact with ARG 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D LEU* 3.6 33.0 - - + +
432D THR 5.4 1.6 + - - +
433D LYS* 4.6 7.7 - - - +
453D VAL* 3.9 31.2 + - + +
454D THR* 6.0 0.9 - - - +
455D ARG* 3.8 22.9 - - - +
474D CYS* 4.1 19.5 - - - -
482D TRP* 4.5 0.8 - - - +
485D ASP* 2.8 37.9 + - - +
486D VAL* 3.1 24.1 + - - +
488D LEU* 1.3 74.5 - - + +
490D VAL* 1.3 61.7 + - - +
492D PHE* 3.5 6.7 + - - +
493D ALA* 3.1 26.9 + - - +
1002D SO4 2.7 45.2 + - - -
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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
----------------------------------------------------------
429D ILE* 4.2 5.6 - - + +
431D LEU* 4.1 12.3 - - + -
486D VAL* 2.9 24.0 + - + +
487D ASP* 3.9 6.1 - - - +
489D ARG* 1.3 74.9 - - - +
491D ASN* 1.3 58.3 + - - +
493D ALA* 3.1 9.1 + - - +
494D MET* 2.8 54.7 + - + +
511D VAL* 3.8 31.4 - - + -
526D ARG* 3.8 24.2 - - - +
528D VAL* 5.3 2.9 - - + -
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Residues in contact with ASN 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D ASP* 2.9 33.7 + - - +
488D LEU* 4.0 7.8 - - + +
490D VAL* 1.3 82.4 - - - +
492D PHE* 1.3 56.8 + - - +
494D MET* 3.3 14.8 + - - +
495D ASN* 2.9 38.3 + - - +
531D PRO* 4.9 9.0 - - - +
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Residues in contact with PHE 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO* 3.4 35.9 - - + -
103D ILE* 3.8 28.7 - - + -
453D VAL* 4.7 2.9 - - + -
472D VAL* 3.4 33.7 - - + -
473D LEU 3.6 18.2 - - - -
474D CYS* 4.0 24.0 - - + -
475D LYS 5.7 0.7 - - - -
476D ASP* 5.7 5.2 - - - +
488D LEU* 3.1 20.6 + - + +
489D ARG* 3.6 5.8 - - - +
490D VAL 3.2 0.2 - - - -
491D ASN* 1.3 74.9 - - - +
493D ALA* 1.3 63.7 + - - +
495D ASN* 3.2 10.7 + - - +
496D VAL* 3.0 33.3 + - + +
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Residues in contact with ALA 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D ILE* 3.7 24.5 - - + -
451D ILE* 3.8 19.0 - - + +
453D VAL* 3.5 29.4 - - + -
472D VAL* 5.2 0.4 - - - -
489D ARG 3.1 8.2 + - - +
490D VAL 3.4 7.9 - - - +
492D PHE* 1.3 77.5 - - - +
494D MET* 1.3 57.6 + - - +
496D VAL* 3.4 6.3 + - - +
497D GLY* 2.9 26.7 + - - -
503D PHE* 4.1 0.7 - - - -
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Residues in contact with MET 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D ILE* 4.5 3.6 - - + +
490D VAL* 2.8 37.2 + - + +
491D ASN* 3.3 17.0 - - - +
493D ALA* 1.3 76.9 - - - +
495D ASN* 1.3 58.0 + - - +
497D GLY 3.4 0.9 + - - -
498D LYS* 3.1 53.8 + - - +
503D PHE* 3.5 22.1 - - - -
509D VAL* 4.0 17.7 - - + -
528D VAL* 4.1 16.8 - - + -
530D VAL* 4.0 7.6 - - + -
531D PRO* 3.7 33.7 - - + -
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Residues in contact with ASN 495 (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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103D ILE* 3.8 27.5 - - + +
491D ASN* 2.9 27.7 + - - +
492D PHE* 3.6 11.5 - - - +
494D MET* 1.3 75.4 - - - +
496D VAL* 1.3 64.4 + - - +
498D LYS* 3.4 16.7 + - - +
499D ALA* 3.0 25.0 + - - +
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Residues in contact with VAL 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ILE* 3.8 29.4 - - + +
106D ARG* 5.3 0.2 - - - +
451D ILE* 5.1 5.2 - - + -
470D PHE* 3.9 23.6 - - + -
472D VAL* 3.7 34.3 - - + -
492D PHE* 3.0 34.1 + - + +
493D ALA* 3.7 8.3 - - - +
494D MET 3.3 0.2 - - - -
495D ASN* 1.3 75.2 - - - +
497D GLY* 1.3 58.4 + - - +
499D ALA* 3.3 1.7 + - - +
500D ARG* 2.9 32.5 + - + +
502D PHE* 5.5 0.2 - - + -
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Residues in contact with GLY 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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451D ILE* 4.2 1.8 - - - +
493D ALA 2.9 11.6 + - - -
495D ASN 3.3 0.2 - - - -
496D VAL* 1.3 77.6 - - - +
498D LYS* 1.3 55.6 + - - +
500D ARG 3.4 0.7 + - - -
501D GLY 3.0 6.9 + - - -
502D PHE* 2.9 41.9 + - - -
503D PHE* 3.5 31.7 + - - -
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Residues in contact with LYS 498 (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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494D MET* 3.1 41.8 + - - +
495D ASN* 3.7 15.5 + - - +
496D VAL 3.3 0.2 - - - -
497D GLY* 1.3 74.9 - - - +
499D ALA* 1.3 64.4 + - - +
501D GLY* 3.1 13.5 + - - -
503D PHE* 3.4 24.0 - - + +
504D LYS* 4.8 1.8 - - - -
505D LYS* 4.5 13.2 - - + +
530D VAL* 3.7 13.0 - - + -
531D PRO* 3.2 28.1 + - - +
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Residues in contact with ALA 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ILE* 3.9 21.3 - - + -
104D LEU* 4.2 15.7 - - + +
495D ASN 3.0 17.1 + - - +
496D VAL 3.7 4.0 - - - +
498D LYS* 1.3 77.7 - - - +
500D ARG* 1.3 65.2 + - + +
501D GLY* 3.4 0.5 + - - -
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Residues in contact with ARG 500 (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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103D ILE 4.6 4.0 + - - +
104D LEU* 2.9 52.7 + - - +
106D ARG* 3.3 21.1 - - - +
470D PHE* 3.7 34.9 - - + -
496D VAL* 2.9 23.5 + - + +
497D GLY 4.0 1.3 - - - +
499D ALA* 1.3 79.2 + - + +
501D GLY* 1.3 60.7 + - - +
502D PHE* 3.5 28.3 + - + -
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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