Contacts of the helix formed by residues 498 - 512 (chain H) in PDB entry 5A31
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 THR 498 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F GLU* 4.3 9.4 - - + +
30F ARG* 2.9 32.7 + - - +
33F ALA* 3.4 33.2 - - + -
494H HIS 3.8 5.7 + - - +
495H HIS* 2.5 23.0 + - - +
496H TYR 3.5 3.6 - - - +
497H ASN* 1.3 79.4 - - - +
499H GLY* 1.3 65.6 - - - +
500H TRP 4.3 0.2 - - - -
501H VAL* 3.2 12.8 + - - +
502H LEU* 3.2 10.6 + - - +
528H ILE* 5.2 1.3 - - - -
529H GLU* 4.9 2.5 - - - +
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Residues in contact with GLY 499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497H ASN 3.6 3.0 + - - -
498H THR* 1.3 70.9 - - - +
500H TRP* 1.3 66.0 + - - +
502H LEU* 3.9 7.5 - - - +
503H CYS* 2.9 28.2 + - - +
525H VAL* 4.3 7.9 - - - +
528H ILE* 5.4 1.3 - - - -
529H GLU* 3.5 33.0 + - - +
532H ARG* 4.0 10.8 + - - -
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Residues in contact with TRP 500 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F PHE* 4.0 18.0 - + - -
29F GLU* 3.3 12.4 + - - +
30F ARG* 3.2 23.6 - - - +
149H TRP* 3.8 17.2 - + - -
153H GLU* 3.9 10.7 + - - -
469H MET* 3.5 37.7 - - + -
473H TYR* 3.5 28.3 - + + -
488H LEU* 4.7 5.6 - - + -
498H THR 3.2 0.6 - - - -
499H GLY* 1.3 77.0 - - - +
501H VAL* 1.3 80.2 + - + +
503H CYS* 4.0 1.2 - - - +
504H GLN* 3.1 68.2 + - + +
532H ARG* 3.7 24.3 - - - +
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Residues in contact with VAL 501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ARG* 4.2 6.7 - - - +
469H MET* 4.4 1.6 - - + -
488H LEU* 4.2 11.0 - - + -
491H LEU* 3.6 30.5 - - + -
495H HIS 3.3 23.8 - - - +
496H TYR* 4.0 17.5 - - + +
498H THR* 3.2 8.1 + - - +
500H TRP* 1.3 97.3 - - + +
502H LEU* 1.3 68.1 + - - +
504H GLN* 3.0 14.3 + - - +
505H ILE* 3.0 26.9 + - + +
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Residues in contact with LEU 502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496H TYR* 3.4 44.6 - - + +
497H ASN* 4.0 6.7 - - - +
498H THR 3.2 4.6 + - - +
499H GLY* 3.9 4.5 - - - +
501H VAL* 1.3 79.1 - - - +
503H CYS* 1.3 59.1 + - - +
505H ILE* 2.9 24.5 + - + +
506H GLY 3.0 10.9 + - - -
521H ILE* 3.6 22.0 - - + +
524H GLU* 4.1 17.5 - - + +
525H VAL* 3.3 30.5 - - + +
528H ILE* 3.3 33.9 - - + -
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Residues in contact with CYS 503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499H GLY 2.9 18.1 + - - +
500H TRP* 4.0 3.8 - - - +
502H LEU* 1.3 78.2 - - - +
504H GLN* 1.3 66.4 + - - +
506H GLY 3.5 0.9 + - - -
507H ARG* 3.2 23.2 + - - +
522H PHE* 3.8 22.1 - - - -
525H VAL* 3.8 9.4 - - + +
532H ARG* 4.0 18.6 - - - +
534H GLU* 4.8 1.1 - - - -
535H GLY* 3.4 36.1 - - - -
536H MET* 5.4 2.0 - - - -
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Residues in contact with GLN 504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H GLU* 4.9 0.8 + - - -
473H TYR* 3.9 18.3 - - + -
476H LEU* 3.5 29.5 - - + +
488H LEU* 4.3 13.0 - - + -
500H TRP* 3.1 75.4 + - + +
501H VAL* 3.0 9.0 + - - +
503H CYS* 1.3 79.3 - - - +
505H ILE* 1.3 64.5 + - - +
507H ARG* 3.1 27.7 + - - +
508H ALA* 3.0 17.2 + - - +
532H ARG* 5.4 1.8 - - - +
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Residues in contact with ILE 505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485H ILE* 3.6 15.9 - - + +
488H LEU* 4.3 21.3 - - + -
489H SER* 5.4 1.3 - - - +
496H TYR* 3.1 45.1 - - + +
501H VAL* 3.0 18.9 + - + +
502H LEU* 2.9 16.9 + - + +
504H GLN* 1.3 76.9 - - - +
506H GLY* 1.3 57.0 + - - +
508H ALA* 3.0 10.1 + - - +
509H TYR* 2.8 37.6 + - + +
521H ILE* 3.3 26.0 - - + -
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Residues in contact with GLY 506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502H LEU 3.0 10.5 + - - -
503H CYS 3.5 0.2 + - - -
504H GLN 3.3 0.2 - - - -
505H ILE* 1.3 76.0 - - - +
507H ARG* 1.3 58.2 + - - +
509H TYR* 3.2 8.5 + - - +
510H PHE* 2.8 30.3 + - - +
518H ALA* 4.0 4.8 - - - +
521H ILE* 3.8 13.8 - - - +
522H PHE* 3.5 27.3 - - - -
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Residues in contact with ARG 507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ARG* 6.2 0.4 - - - +
157H GLU* 5.4 0.6 + - - -
473H TYR* 4.0 22.0 + - - -
476H LEU* 4.5 16.6 - - + +
477H CYS* 5.9 5.9 - - - +
503H CYS* 3.2 15.2 + - - +
504H GLN* 3.1 37.2 + - - +
506H GLY* 1.3 74.2 - - - +
508H ALA* 1.3 56.9 + - - +
510H PHE* 3.3 6.3 + - - +
511H GLU* 3.0 50.8 + - + +
522H PHE* 3.8 1.4 - - - -
535H GLY* 6.6 0.4 - - - -
538H ILE* 4.1 35.5 - - + +
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Residues in contact with ALA 508 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476H LEU* 4.1 22.1 - - + +
481H CYS* 3.2 19.7 - - - +
484H SER* 4.3 7.0 - - - -
485H ILE* 3.2 24.7 - - + -
488H LEU* 6.0 0.7 - - + -
504H GLN 3.0 11.1 + - - +
505H ILE* 3.0 11.6 + - - +
507H ARG* 1.3 75.4 - - - +
509H TYR* 1.3 63.5 + - - +
511H GLU* 3.3 3.1 + - - -
512H LEU* 3.0 19.2 + - - +
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Residues in contact with TYR 509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485H ILE* 3.6 35.9 - - + +
505H ILE* 2.8 29.3 + - + +
506H GLY* 3.2 2.0 + - - +
508H ALA* 1.3 73.9 - - - +
510H PHE* 1.3 63.1 + - - +
512H LEU* 3.1 11.7 + - + +
513H SER 3.0 16.6 + - - -
514H GLU* 3.1 38.4 + - - +
517H GLN* 3.5 33.4 + - + -
518H ALA* 3.7 25.8 - - + +
521H ILE* 3.5 28.5 - - + +
108X LYS* 5.9 1.2 + - - -
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Residues in contact with PHE 510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506H GLY 2.8 21.4 + - - +
507H ARG* 3.6 7.6 - - - +
509H TYR* 1.3 73.4 - - - +
511H GLU* 1.3 69.0 + - + +
513H SER* 3.1 17.3 + - - +
514H GLU 5.0 0.9 - - - +
515H TYR* 3.5 36.4 + + - -
518H ALA* 4.1 5.6 - - + +
538H ILE* 3.9 33.2 - - + -
541H THR* 3.5 33.7 - - + -
542H THR* 3.1 29.2 - - - +
545H HIS* 4.4 4.0 - + - -
602H TYR* 4.4 5.2 - + - -
635H TYR* 5.4 5.6 - - - -
636H ASN* 5.2 6.7 - - - -
183L ILE* 6.0 3.4 - - + -
184L ARG 4.6 7.9 - - - -
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Residues in contact with GLU 511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476H LEU* 3.2 32.4 - - - +
479H TYR* 3.0 46.9 + - + -
481H CYS* 3.3 19.8 - - - -
507H ARG* 3.0 34.2 + - + +
508H ALA* 3.3 0.5 + - - -
510H PHE* 1.3 81.8 - - + +
512H LEU* 1.3 57.6 + - - +
513H SER* 3.1 8.9 + - - -
538H ILE* 6.4 0.4 - - + -
635H TYR* 4.8 12.6 + - + +
665H ASN* 4.3 4.7 + - - +
667H GLN* 4.1 8.0 + - - +
668H SER* 4.3 13.3 + - - -
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Residues in contact with LEU 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481H CYS* 3.0 42.5 - - + +
482H LYS* 4.0 35.7 - - + +
485H ILE* 4.7 2.2 - - + -
508H ALA 3.0 7.1 + - - +
509H TYR* 3.1 20.1 + - + +
511H GLU* 1.3 75.1 - - - +
513H SER* 1.3 67.9 + - - +
514H GLU* 3.2 35.6 + - - +
667H GLN* 3.7 15.0 - - + +
699H ASP* 3.6 21.1 - - - +
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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