Contacts of the helix formed by residues 469 - 492 (chain C) in PDB entry 2GZD
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 ARG 469 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ARG* 1.3 115.2 - - + +
470C LYS* 1.3 61.2 + - + +
471C ASP 3.3 0.9 - - - -
472C THR* 3.1 36.5 - - + +
473C HIS* 3.3 9.2 + - - +
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Residues in contact with LYS 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ARG* 3.3 13.0 - - + +
469C ARG* 1.3 80.5 - - + +
471C ASP* 1.3 56.0 + - - +
473C HIS* 3.3 4.4 + - - +
474C ILE* 3.1 38.1 + - + +
470D LYS* 5.1 11.9 - - + +
471D ASP* 3.2 34.9 + - - +
474D ILE* 4.3 26.1 - - + +
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Residues in contact with ASP 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ARG* 3.9 18.1 + - - +
470C LYS* 1.3 78.5 - - - +
472C THR* 1.3 59.0 + - - +
474C ILE* 3.5 13.3 - - - +
475C ARG* 3.2 43.6 + - - +
470D LYS* 2.7 33.5 + - - +
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Residues in contact with THR 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 6.1 1.1 - - - +
468C ARG 4.4 1.3 + - - -
469C ARG* 3.1 38.7 + - + +
470C LYS 3.3 0.8 - - - -
471C ASP* 1.3 77.8 - - - +
473C HIS* 1.3 63.3 + - + +
475C ARG* 3.7 27.0 + - - +
476C GLU* 3.3 36.1 + - - +
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Residues in contact with HIS 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER* 6.2 1.6 - - - -
44B ILE* 4.9 7.6 - - + +
469C ARG 3.3 9.6 + - - +
470C LYS* 3.3 7.8 + - - +
472C THR* 1.3 78.6 - - + +
474C ILE* 1.3 67.1 + - - +
476C GLU* 2.9 25.5 + - + +
477C LEU* 2.8 55.3 + - + +
474D ILE* 4.1 19.8 - - + +
478D GLU* 3.4 24.7 - - - -
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Residues in contact with ILE 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LYS 3.1 19.7 + - - +
471C ASP* 3.5 19.7 - - - +
473C HIS* 1.3 75.5 + - - +
475C ARG* 1.3 59.0 + - + +
477C LEU* 3.2 8.0 + - - +
478C GLU* 2.9 53.7 + - - +
470D LYS* 3.9 40.2 - - + +
473D HIS* 4.0 18.4 - - + +
474D ILE* 3.9 15.7 - - + -
477D LEU* 3.9 13.8 - - + +
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Residues in contact with ARG 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 5.9 2.0 - - - +
468C ARG 5.8 1.0 + - - -
471C ASP* 3.2 26.0 + - - +
472C THR* 4.0 30.3 + - - +
473C HIS 3.3 0.2 - - - -
474C ILE* 1.3 73.1 - - + +
476C GLU* 1.3 60.1 + - - +
477C LEU 3.3 0.2 - - - -
478C GLU* 3.3 19.1 - - - +
479C ASP* 2.8 44.0 + - - +
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Residues in contact with GLU 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.5 33.0 + - - -
44B ILE* 3.9 20.6 - - + +
472C THR* 3.3 27.4 + - - +
473C HIS* 2.9 27.2 + - + +
475C ARG* 1.3 78.5 - - - +
477C LEU* 1.3 57.8 + - - +
479C ASP* 3.4 7.1 + - - +
480C TYR* 2.9 27.4 + - - +
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Residues in contact with LEU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.8 28.3 - - + -
473C HIS* 2.8 53.0 + - + +
474C ILE 3.4 7.0 - - - +
476C GLU* 1.3 74.7 - - - +
478C GLU* 1.3 59.2 + - - +
480C TYR* 3.0 7.8 + - - +
481C ILE* 2.9 34.5 + - - +
474D ILE* 3.8 31.2 - - + +
477D LEU* 4.1 15.9 - - + -
478D GLU* 3.8 13.2 - - + +
481D ILE* 4.1 14.4 - - + +
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Residues in contact with GLU 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.8 30.4 + - - +
474C ILE* 2.9 33.5 + - - +
475C ARG* 3.3 24.4 - - - +
477C LEU* 1.3 75.8 - - - +
479C ASP* 1.3 62.7 + - - +
481C ILE* 3.4 12.7 + - - +
482C ASP* 2.8 33.5 + - - +
473D HIS* 4.3 10.6 - - - -
477D LEU* 4.0 16.5 - - + +
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Residues in contact with ASP 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG* 4.6 10.6 + - - -
475C ARG* 2.8 32.5 + - - +
476C GLU* 3.7 6.4 - - - +
478C GLU* 1.3 78.1 - - - +
480C TYR* 1.3 66.3 + - - +
482C ASP* 3.8 10.1 - - - +
483C ASN* 2.8 37.5 + - - +
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Residues in contact with TYR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.3 47.8 - - + -
45B GLY* 3.7 9.9 - - - -
46B VAL 3.9 8.0 + - - -
476C GLU 2.9 15.1 + - - +
477C LEU 3.0 8.7 + - - +
479C ASP* 1.3 78.2 - - - +
481C ILE* 1.3 65.3 + - - +
483C ASN* 3.2 5.6 + - + +
484C LEU* 2.9 48.8 + - + +
487C ARG* 5.5 7.1 + - - -
481D ILE* 3.6 31.9 - - + -
485D LEU* 3.7 21.5 - - - +
496D LEU* 4.6 3.1 - - - +
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Residues in contact with ILE 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.9 2.7 - - + -
45A GLY* 4.2 9.2 - - - +
477C LEU 2.9 19.9 + - - +
478C GLU* 3.4 9.4 - - - +
480C TYR* 1.3 74.9 - - - +
482C ASP* 1.3 69.8 + - - +
484C LEU* 3.2 6.4 + - + +
485C LEU* 2.7 50.6 + - + +
477D LEU* 3.7 31.6 - - + +
480D TYR* 3.7 32.1 - - + -
481D ILE* 3.5 29.2 - - + -
484D LEU* 5.7 1.1 - - + -
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Residues in contact with ASP 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 5.6 1.0 - - - -
72A ARG* 4.7 5.4 + - - -
74A ARG* 3.7 33.4 + - - +
75A ALA* 3.7 20.6 - - + +
76A ILE* 3.3 29.9 - - + +
478C GLU* 2.8 27.0 + - - +
479C ASP* 3.5 12.0 + - - +
480C TYR 3.3 0.2 - - - -
481C ILE* 1.3 80.9 - - - +
483C ASN* 1.4 63.4 + - - +
485C LEU* 3.2 1.9 + - - +
486C VAL* 3.1 27.7 + - - +
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Residues in contact with ASN 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.6 21.0 - - - +
479C ASP* 2.8 31.4 + - - +
480C TYR* 4.1 3.8 - - - +
482C ASP* 1.4 76.3 - - - +
484C LEU* 1.3 63.9 + - - +
486C VAL* 3.7 9.2 - - - +
487C ARG* 3.7 31.7 + - - +
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Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C TYR* 2.9 48.6 + - + +
481C ILE* 3.6 4.9 - - - +
483C ASN* 1.3 76.9 - - - +
485C LEU* 1.4 57.2 + - - +
487C ARG* 3.1 25.8 + - - +
488C VAL* 3.0 31.8 + - + +
481D ILE* 5.4 1.8 - - + +
484D LEU* 3.8 28.3 - - + -
485D LEU* 4.0 15.3 - - + -
488D VAL* 4.7 2.2 - - + -
495D ILE* 3.2 36.6 - - + -
496D LEU* 4.1 7.0 - - + -
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Residues in contact with LEU 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.6 22.2 - - - -
46A VAL* 3.7 11.9 - - + +
76A ILE* 3.6 15.5 - - + -
481C ILE* 2.7 47.2 + - + +
482C ASP* 4.8 2.0 - - - +
484C LEU* 1.4 68.1 - - - +
486C VAL* 1.3 55.4 + - - +
488C VAL* 3.6 4.8 - - + +
489C MSE 2.6 47.4 + - - +
496C LEU* 3.6 28.7 - - + -
480D TYR* 3.6 8.5 - - - +
484D LEU* 3.6 26.5 - - + -
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Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.4 40.2 - - + +
76A ILE* 3.9 5.9 - - + +
79A ALA* 5.0 8.2 - - + +
482C ASP 3.1 21.8 + - - +
483C ASN* 3.7 10.8 - - - +
484C LEU 3.3 0.2 - - - -
485C LEU* 1.3 75.3 - - - +
487C ARG* 1.3 62.3 + - + +
489C MSE 3.5 7.8 + - - +
490C GLU* 3.1 53.3 + - + +
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Residues in contact with ARG 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C TYR* 5.5 7.5 + - - -
483C ASN* 3.7 19.5 + - - +
484C LEU* 3.1 30.9 + - - +
486C VAL* 1.3 77.7 - - + +
488C VAL* 1.3 65.7 + - - +
490C GLU* 3.3 4.7 + - - +
491C GLU* 3.0 31.5 + - - +
495D ILE* 3.6 31.7 + - + +
496D LEU* 5.4 3.8 - - - +
497D ARG 5.5 0.8 + - - -
500D TYR* 3.6 61.7 - - + +
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Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LEU* 3.0 30.4 + - + +
485C LEU* 3.6 10.5 - - - +
487C ARG* 1.3 74.4 - - - +
489C MSE 1.3 57.4 + - - +
491C GLU* 5.1 0.7 - - - -
492C THR* 2.9 45.1 + - - +
495C ILE* 3.4 32.1 - - + -
496C LEU* 3.7 19.1 - - + -
484D LEU* 4.8 4.0 - - + -
488D VAL* 3.8 26.7 - - + -
495D ILE* 4.5 7.9 - - + -
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Residues in contact with MSE 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 5.2 0.2 - - - +
46A VAL* 4.2 17.0 - - + -
65A TRP* 4.1 24.2 - - + -
76A ILE* 4.2 17.9 - - - +
79A ALA* 3.2 54.3 - - + +
80A TYR* 3.4 15.0 - - + +
485C LEU* 2.6 30.3 + - - +
486C VAL 3.8 4.5 - - - +
488C VAL* 1.3 72.6 - - - +
490C GLU* 1.3 62.3 + - - +
493C PRO* 3.6 25.5 - - - +
496C LEU* 3.6 19.3 - - + -
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA* 5.4 0.7 - - + -
82A ARG* 4.1 26.9 + - - +
486C VAL* 3.1 33.6 + - + +
487C ARG* 3.3 6.9 + - - +
488C VAL 3.3 0.4 - - - -
489C MSE 1.3 78.1 - - + +
491C GLU* 1.3 65.3 + - + +
493C PRO* 4.8 1.5 - - - +
500D TYR* 5.0 6.0 + - - +
502D PRO* 5.1 8.8 - - - +
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Residues in contact with GLU 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C ARG 3.0 15.1 + - - +
488C VAL* 5.1 0.7 - - - -
490C GLU* 1.3 82.5 - - + +
492C THR* 1.3 70.0 + - - +
493C PRO* 3.7 5.3 - - - +
492D THR* 4.7 12.8 - - + +
494D SER* 4.3 12.6 + - - -
495D ILE* 4.9 5.6 - - + +
500D TYR* 3.2 38.4 + - + +
501D GLU 4.4 1.9 - - - +
502D PRO 3.8 18.2 - - - +
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Residues in contact with THR 492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C VAL* 2.9 23.1 + - - +
491C GLU* 1.3 79.8 + - - +
493C PRO* 1.3 67.1 - - - +
494C SER* 3.0 17.2 + - - +
495C ILE* 3.2 31.5 + - + +
491D GLU* 4.3 8.7 - - + +
492D THR* 2.6 38.0 + - - +
495D ILE* 5.3 0.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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