Contacts of the helix formed by residues 485 - 506 (chain D) in PDB entry 5X22
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 485 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D HIS* 3.1 36.8 + - - +
484D PRO* 1.3 77.5 - - - +
486D ARG* 1.3 64.4 + - - +
487D ALA* 3.7 5.7 + - - +
488D ARG* 3.5 27.0 + - - +
489D ARG* 3.4 16.2 + - - +
2G C 3.8 27.0 + - - +
3G T 4.0 7.0 + - - -
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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
----------------------------------------------------------
484D PRO 3.6 3.0 + - - +
485D SER* 1.3 72.7 + - - +
487D ALA* 1.3 61.8 + - - +
489D ARG* 3.2 25.4 + - - +
490D ALA* 2.9 28.9 + - + +
3G T 3.5 54.2 + - - +
4G G 3.7 23.0 + - - -
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Residues in contact with ALA 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D SER* 3.5 6.6 + - - +
486D ARG* 1.3 79.8 - - - +
488D ARG* 1.3 59.6 + - + +
490D ALA* 3.2 7.8 + - - +
491D LYS* 2.9 49.6 + - - +
2G C 6.0 0.4 - - + -
3G T 3.9 18.6 + - + +
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Residues in contact with ARG 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480D GLU* 2.8 45.6 + - - +
483D HIS* 3.1 50.1 + - + +
485D SER* 3.5 19.4 + - - +
486D ARG 3.3 0.4 - - - -
487D ALA* 1.3 77.2 - - + +
489D ARG* 1.3 57.4 + - - +
491D LYS* 3.5 5.1 + - - +
492D ALA* 2.9 31.4 + - - +
2G C 4.4 14.1 + - - +
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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
----------------------------------------------------------
480D GLU 4.2 2.7 - - - +
481D MET* 3.2 40.6 - - + +
482D LYS 4.9 1.1 - - - -
483D HIS 3.2 25.2 + - - +
484D PRO* 4.5 9.7 + - - +
485D SER 3.4 9.8 + - - +
486D ARG* 3.2 28.8 + - - +
488D ARG* 1.3 75.0 - - - +
490D ALA* 1.3 60.1 + - - +
492D ALA* 4.3 4.9 - - - -
493D ARG* 2.9 31.9 + - - +
1391D GLU* 2.9 40.1 + - - +
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Residues in contact with ALA 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D ARG* 2.9 16.3 + - + +
487D ALA* 3.3 12.3 - - - +
489D ARG* 1.3 77.4 - - - +
491D LYS* 1.3 66.2 + - - +
493D ARG* 3.2 24.6 + - - +
494D LYS* 2.9 42.1 + - - +
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Residues in contact with LYS 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D ALA* 2.9 35.6 + - + +
488D ARG* 4.1 4.7 - - - +
490D ALA* 1.3 76.2 - - - +
492D ALA* 1.3 60.3 + - - +
494D LYS* 3.2 33.9 + - + +
495D ARG* 2.9 38.9 + - + +
22H T 4.9 18.9 + - - +
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Residues in contact with ALA 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D LEU* 3.9 24.0 - - + +
480D GLU* 3.6 30.5 - - + -
481D MET* 4.0 9.2 - - - -
488D ARG 2.9 19.3 + - - +
489D ARG* 3.8 5.6 - - - +
491D LYS* 1.3 75.5 - - - +
493D ARG* 1.3 56.7 + - - +
495D ARG* 3.5 2.6 + - - +
496D LEU* 2.9 31.5 + - - +
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Residues in contact with ARG 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D MET* 3.8 9.4 - - - -
489D ARG 2.9 19.6 + - - +
490D ALA* 3.3 33.3 - - - +
492D ALA* 1.3 76.0 - - - +
494D LYS* 1.3 85.3 + - - +
496D LEU* 3.1 5.9 + - - +
497D GLU* 2.9 52.8 + - - +
1390D LEU* 3.9 20.2 - - + -
1391D GLU 3.3 25.2 + - - +
1392D GLY* 3.7 18.4 + - - -
1393D GLN* 3.6 16.2 - - + +
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Residues in contact with LYS 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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109D PRO* 6.1 4.9 - - + -
114D THR* 4.3 3.2 - - + +
490D ALA* 2.9 24.3 + - - +
491D LYS* 3.2 38.7 + - + +
493D ARG* 1.3 97.7 - - - +
495D ARG* 1.3 61.6 + - + +
497D GLU* 3.7 18.0 + - - +
498D VAL* 3.5 19.8 + - - +
21H A 3.8 33.3 + - - +
22H T 6.1 1.6 - - - +
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Residues in contact with ARG 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D THR* 3.2 35.2 + - + +
115D LEU* 3.3 22.6 + - - +
116D LEU 5.0 0.2 - - - -
117D ASP* 3.7 34.5 + - - +
473D LEU* 3.4 33.9 - - - +
477D LEU* 3.7 27.3 - - + +
491D LYS* 2.9 23.0 + - + +
492D ALA 3.8 1.8 - - - +
494D LYS* 1.3 75.5 - - + +
496D LEU* 1.3 58.9 + - - +
497D GLU 3.1 0.2 - - - -
498D VAL* 3.0 7.3 + - - +
499D VAL* 2.9 30.2 + - + +
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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
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474D GLU* 3.6 40.6 - - + -
477D LEU* 3.7 20.6 - - + -
478D LEU* 3.7 30.3 - - + -
481D MET* 4.5 8.1 - - + -
492D ALA 2.9 18.0 + - - +
493D ARG 3.1 4.0 + - - +
495D ARG* 1.3 77.0 - - - +
497D GLU* 1.3 56.6 + - - +
499D VAL* 3.8 4.3 - - + -
500D ARG* 2.9 49.1 + - + +
1390D LEU* 3.7 27.6 - - + -
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Residues in contact with GLU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D ARG* 2.9 45.6 + - + +
494D LYS* 3.7 13.9 - - - +
495D ARG 3.1 0.2 - - - -
496D LEU* 1.3 76.2 - - - +
498D VAL* 1.3 61.4 + - + +
500D ARG* 3.9 3.3 - - - +
501D ALA* 2.9 29.5 + - - +
1390D LEU* 4.8 7.0 - - + -
1393D GLN* 4.4 20.3 - - + +
1394D VAL 5.3 0.7 + - - -
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Residues in contact with VAL 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LYS* 4.4 34.1 - - + +
114D THR* 3.8 20.0 - - + +
115D LEU* 4.0 16.4 - - + -
494D LYS 3.5 16.6 - - - +
495D ARG 3.0 5.5 + - - +
497D GLU* 1.3 74.8 - - + +
499D VAL* 1.3 65.5 + - - +
501D ALA* 3.1 8.1 + - - +
502D PHE* 2.9 52.3 + - + -
1452D ILE* 4.9 2.7 - - + -
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Residues in contact with VAL 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D LEU* 3.8 24.7 - - + -
470D LEU* 3.6 35.4 - - + +
473D LEU* 3.8 13.2 - - + -
474D GLU* 4.3 12.8 - - + +
477D LEU* 3.8 17.9 - - + -
495D ARG* 2.9 21.3 + - + +
496D LEU* 3.9 8.3 - - + +
498D VAL* 1.3 76.7 - - - +
500D ARG* 1.3 58.2 + - - +
502D PHE* 3.3 4.6 + - - +
503D LEU* 2.9 36.4 + - + +
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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
----------------------------------------------------------
474D GLU* 3.0 31.0 + - - +
478D LEU* 3.7 31.3 - - - +
496D LEU* 2.9 36.4 + - + +
497D GLU* 4.1 3.4 - - - +
499D VAL* 1.3 73.1 - - - +
501D ALA* 1.3 60.6 + - - +
503D LEU* 3.9 7.6 - - + -
504D ASP* 2.9 44.3 + - - +
1388D ARG* 2.5 63.2 + - - +
1389D LEU* 4.7 0.4 - - - +
1390D LEU* 3.4 23.0 - - - +
1393D GLN* 5.4 0.8 + - - -
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Residues in contact with ALA 501 (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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497D GLU 2.9 20.5 + - - +
498D VAL* 3.2 8.5 - - - +
500D ARG* 1.3 77.1 - - - +
502D PHE* 1.3 51.7 + - - +
504D ASP* 3.9 3.0 - - - +
505D SER* 2.7 40.4 + - - -
1452D ILE* 3.7 21.3 - - + +
1453D ALA* 4.3 17.1 - - + +
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Residues in contact with PHE 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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12D LEU* 3.7 21.3 - - + -
111D LYS* 5.2 0.2 - - + -
115D LEU* 3.6 21.8 - - + -
470D LEU* 4.0 16.9 - - + +
498D VAL* 2.9 36.7 + - + -
499D VAL 3.6 7.0 - - - +
501D ALA* 1.3 76.5 - - - +
503D LEU* 1.3 63.8 + - - +
505D SER* 3.3 11.3 + - - -
506D GLY* 3.3 8.3 + - - -
507D ASN* 3.2 35.6 + - + +
508D ARG 4.3 0.2 - - - -
509D PRO* 3.6 24.2 - - + -
512D MET* 3.4 30.3 - - + -
1452D ILE* 3.6 29.1 + - + -
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Residues in contact with LEU 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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470D LEU* 3.6 31.9 - - + +
471D GLU* 4.2 21.3 - - + +
474D GLU* 3.3 33.9 - - - +
499D VAL* 2.9 28.4 + - + +
500D ARG* 3.4 13.5 - - + +
501D ALA 3.2 0.2 - - - -
502D PHE* 1.3 80.7 - - - +
504D ASP* 1.3 68.8 + - - +
506D GLY* 3.5 8.1 + - - -
1388D ARG* 5.6 1.3 - - - +
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Residues in contact with ASP 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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500D ARG* 2.9 23.2 + - - +
501D ALA* 4.2 2.9 - - - +
503D LEU* 1.3 78.7 - - - +
505D SER* 1.3 64.6 + - - +
506D GLY* 3.3 1.0 + - - -
1388D ARG* 3.5 28.5 + - - -
1453D ALA 5.7 1.6 - - - +
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Residues in contact with SER 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D ALA 2.7 19.6 + - - -
502D PHE* 3.3 7.3 + - - -
504D ASP* 1.3 77.9 - - - +
506D GLY* 1.3 63.0 + - - +
507D ASN* 3.2 24.6 + - - +
1452D ILE 2.9 25.8 + - - -
1453D ALA 3.3 19.7 + - - -
1454D GLY* 3.8 5.5 - - - -
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Residues in contact with GLY 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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502D PHE 3.3 7.2 + - - -
503D LEU 3.5 6.0 + - - -
504D ASP 3.2 5.2 - - - -
505D SER* 1.3 79.7 + - - +
507D ASN* 1.3 61.7 + - - +
508D ARG* 3.8 5.8 + - - +
511D TRP* 3.9 13.0 - - - -
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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