Contacts of the helix formed by residues 498 - 512 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494F HIS 3.8 6.0 + - - +
495F HIS* 2.5 23.8 + - - +
496F TYR 3.5 2.9 - - - +
497F ASN* 1.3 80.4 - - - +
499F GLY* 1.3 65.3 + - - +
501F VAL* 3.2 13.5 + - - +
502F LEU* 3.2 10.8 + - - +
528F ILE* 5.2 1.1 - - - -
529F GLU* 4.9 4.0 - - - +
29H GLU* 4.8 6.3 - - + +
30H ARG* 2.7 40.7 + - - +
33H ALA* 3.5 27.4 - - + -
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Residues in contact with GLY 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497F ASN 3.5 2.7 + - - -
498F THR* 1.3 71.1 - - - +
500F TRP* 1.3 64.7 + - - +
502F LEU* 3.9 7.5 - - - +
503F CYS* 2.9 28.8 + - - +
525F VAL* 4.3 7.8 - - - +
528F ILE* 5.4 1.3 - - - -
529F GLU* 3.6 33.9 + - - +
532F ARG* 4.1 11.3 + - - -
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Residues in contact with TRP 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F TRP* 3.9 19.9 - + - +
153F GLU* 3.9 10.3 + - - -
469F MET* 3.5 37.7 - - + -
473F TYR* 3.5 28.0 - + + -
488F LEU* 4.7 6.3 - - + -
498F THR* 3.3 2.0 - - - -
499F GLY* 1.3 75.6 - - - +
501F VAL* 1.3 79.9 + - + +
503F CYS* 3.9 1.0 - - - +
504F GLN* 3.1 70.1 + - + +
532F ARG* 3.7 31.1 - - - +
26H PHE* 4.1 18.3 - + + -
29H GLU* 4.7 7.2 + - - +
30H ARG* 3.4 22.4 - - - +
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Residues in contact with VAL 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469F MET* 4.4 2.7 - - + -
488F LEU* 4.2 10.8 - - + -
491F LEU* 3.6 30.1 - - + -
495F HIS 3.3 24.0 - - - +
496F TYR* 4.0 17.9 - - + -
498F THR* 3.2 7.9 + - - +
500F TRP* 1.3 99.1 - - + +
502F LEU* 1.3 66.3 + - - +
504F GLN* 3.0 14.4 + - - +
505F ILE* 3.0 27.1 + - + +
30H ARG* 4.3 5.8 - - - +
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Residues in contact with LEU 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496F TYR* 3.4 42.0 - - + +
497F ASN* 4.0 5.6 - - - +
498F THR 3.2 5.7 + - - +
499F GLY* 3.9 2.9 - - - +
501F VAL* 1.3 77.9 - - - +
503F CYS* 1.3 57.8 + - - +
505F ILE* 2.9 27.3 + - + +
506F GLY 3.0 11.1 + - - -
521F ILE* 3.5 22.4 - - + +
524F GLU* 4.1 17.5 - - + +
525F VAL* 3.3 29.8 - - + +
528F ILE* 3.3 34.8 - - + -
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Residues in contact with CYS 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499F GLY 2.9 18.9 + - - +
500F TRP* 4.0 3.4 - - - +
502F LEU* 1.3 77.9 - - - +
504F GLN* 1.3 66.1 + - - +
506F GLY 3.5 0.5 + - - -
507F ARG* 3.2 22.5 + - - +
522F PHE* 3.8 22.3 - - - -
525F VAL* 3.7 10.2 - - + +
532F ARG* 4.1 18.4 - - - +
534F GLU* 4.8 0.4 - - - -
535F GLY* 3.4 37.7 - - - -
536F MET* 5.4 1.8 - - - -
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Residues in contact with GLN 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F GLU* 4.9 0.6 + - - -
473F TYR* 3.8 17.8 - - + -
476F LEU* 3.4 27.9 - - + +
488F LEU* 4.3 12.6 - - + -
500F TRP* 3.1 74.7 + - + +
501F VAL* 3.0 9.4 + - - +
503F CYS* 1.3 77.1 - - - +
505F ILE* 1.3 66.8 + - - +
507F ARG* 3.1 17.6 + - - +
508F ALA* 3.0 17.5 + - - +
532F ARG* 5.5 1.4 - - - +
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Residues in contact with ILE 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485F ILE* 3.6 16.2 - - + +
488F LEU* 4.3 21.8 - - + -
489F SER 5.6 0.4 - - - +
496F TYR* 3.4 42.4 - - + +
501F VAL* 3.0 20.7 + - + +
502F LEU* 2.9 17.6 + - + +
504F GLN* 1.3 76.2 - - - +
506F GLY* 1.3 56.8 + - - +
508F ALA* 3.0 9.4 + - - +
509F TYR* 2.9 37.6 + - + +
521F ILE* 3.2 26.0 - - + -
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Residues in contact with GLY 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502F LEU 3.0 11.1 + - - -
503F CYS 3.5 0.2 + - - -
504F GLN 3.3 0.2 - - - -
505F ILE* 1.3 76.1 - - - +
507F ARG* 1.3 56.1 + - - +
509F TYR* 3.2 7.9 + - - +
510F PHE* 2.8 31.2 + - - +
518F ALA* 4.0 5.1 - - - +
521F ILE* 3.8 13.6 - - - +
522F PHE* 3.5 27.1 - - - -
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Residues in contact with ARG 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F GLU* 5.6 2.2 + - - +
473F TYR* 3.7 27.5 + - - -
476F LEU* 3.9 29.2 + - + +
477F CYS* 5.0 10.7 - - - +
479F TYR* 4.3 23.8 + - - -
503F CYS* 3.2 14.3 + - - +
504F GLN* 3.1 22.7 + - - +
506F GLY* 1.3 74.6 - - - +
508F ALA* 1.3 57.7 + - - +
510F PHE* 3.3 6.8 + - - +
511F GLU* 3.0 41.5 + - - +
522F PHE* 3.8 1.2 - - - -
538F ILE* 3.6 39.7 - - + -
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Residues in contact with ALA 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476F LEU* 4.1 23.5 - - + +
481F CYS* 3.6 13.2 - - - +
484F SER* 4.2 10.8 - - - -
485F ILE* 3.2 23.3 - - + -
488F LEU* 6.0 0.7 - - + -
504F GLN 3.0 10.2 + - - +
505F ILE* 3.0 11.8 + - - +
507F ARG* 1.3 76.2 - - - +
509F TYR* 1.3 62.6 + - - +
511F GLU 3.3 1.7 + - - -
512F LEU* 3.0 23.6 + - - +
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Residues in contact with TYR 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485F ILE* 3.5 35.9 - - + +
505F ILE* 2.9 23.0 + - + +
506F GLY* 3.2 2.0 + - - +
508F ALA* 1.3 76.1 - - - +
510F PHE* 1.3 62.5 + - - +
512F LEU* 3.1 11.1 + - + +
513F SER 3.0 17.3 + - - -
514F GLU* 3.1 39.9 + - - +
517F GLN* 3.5 33.3 + - + -
518F ALA* 3.7 25.6 - - + +
521F ILE* 3.5 30.4 - - + +
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Residues in contact with PHE 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F GLY 2.8 21.0 + - - +
507F ARG* 3.6 6.7 - - - +
509F TYR* 1.3 73.8 - - - +
511F GLU* 1.3 73.2 + - + +
513F SER* 3.1 15.5 + - - +
515F TYR* 3.6 33.3 + + - -
518F ALA* 4.0 5.8 - - + +
538F ILE* 4.1 31.2 - - + -
541F THR* 3.4 34.1 - - + -
542F THR* 3.1 31.4 - - - +
545F HIS* 4.0 9.0 - + - -
602F TYR* 4.5 7.0 - + - -
635F TYR* 6.1 0.4 - - - -
636F ASN* 5.6 3.6 - - - -
492R ILE 5.4 4.7 - - - -
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Residues in contact with GLU 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476F LEU* 5.0 2.5 - - + -
479F TYR* 3.0 29.4 + - + -
481F CYS* 3.5 23.1 - - - -
507F ARG* 3.0 34.2 + - - +
510F PHE* 1.3 88.9 - - + +
512F LEU* 1.3 58.2 + - - +
513F SER* 3.1 8.8 + - - -
538F ILE* 5.6 1.9 - - - +
635F TYR* 3.2 21.6 + - - -
636F ASN* 5.2 0.9 + - - -
665F ASN* 3.0 31.2 + - - -
667F GLN* 4.8 6.5 - - - +
668F SER* 5.5 1.7 + - - -
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Residues in contact with LEU 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F CYS* 4.0 23.1 - - + -
482F LYS* 4.0 39.9 - - + +
485F ILE* 4.7 6.7 - - + -
508F ALA 3.0 15.0 + - - +
509F TYR* 3.1 19.9 + - + +
511F GLU* 1.3 74.8 - - - +
513F SER* 1.3 66.4 + - - +
514F GLU* 3.2 35.6 + - - +
667F GLN* 4.8 12.3 - - - +
699F ASP* 5.3 12.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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