Contacts of the helix formed by residues 566 - 580 (chain F) in PDB entry 5G04
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 566 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533F VAL* 3.9 21.7 - - - +
563F ASP* 2.9 21.2 + - - -
565F ASN* 1.3 78.7 - - - +
567F PRO* 1.3 76.6 - - - +
568F GLU* 3.4 4.7 + - - -
569F ALA* 3.7 21.5 + - - +
570F TRP* 3.9 17.5 - - - -
596F VAL* 3.8 6.1 - - - +
53H LYS* 4.5 12.1 - - - +
55H TYR* 5.1 0.2 - - - -
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Residues in contact with PRO 567 (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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566F SER* 1.3 87.3 - - - +
568F GLU* 1.3 71.6 + - + +
570F TRP 3.6 0.5 + - - -
571F CYS* 3.2 24.0 + - - +
593F ALA* 3.5 28.1 - - + +
596F VAL* 4.0 1.5 - - + -
597F ASP* 3.9 29.4 - - + +
600F TYR* 3.6 43.9 - - + -
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Residues in contact with GLU 568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533F VAL* 2.9 53.1 - - + +
534F GLU* 3.0 37.0 - - - +
536F MET* 5.4 1.8 - - + +
537F GLU* 4.7 13.2 + - + +
559F LEU* 4.4 2.5 - - - +
566F SER* 3.2 3.2 - - - +
567F PRO* 1.3 82.2 - - + +
569F ALA* 1.3 64.4 + - - +
571F CYS* 3.3 7.5 + - - +
572F ALA* 3.1 22.7 + - - +
600F TYR* 3.6 34.0 + - + +
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Residues in contact with ALA 569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533F VAL* 4.3 4.2 - - + +
556F SER 5.1 0.2 - - - +
559F LEU* 3.8 30.8 - - + +
560F THR* 3.9 11.4 + - - +
563F ASP* 3.5 25.4 - - - +
564F LYS* 4.8 3.6 - - - -
566F SER* 3.7 18.8 + - - +
567F PRO 3.5 0.4 - - - -
568F GLU* 1.3 78.4 - - - +
570F TRP* 1.3 62.6 + - + +
572F ALA* 3.5 5.0 + - - +
573F ALA 3.3 16.5 + - - -
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Residues in contact with TRP 570 (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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94E TRP* 3.4 29.8 - + - -
560F THR* 3.4 31.2 - - + -
564F LYS* 3.3 39.2 - - + +
565F ASN 4.0 0.8 - - - +
566F SER 3.9 14.1 + - - -
567F PRO 3.6 2.3 + - - +
568F GLU 3.3 0.6 - - - -
569F ALA* 1.3 74.6 - - - +
571F CYS* 1.3 55.0 + - - +
573F ALA* 3.6 2.2 + - + +
574F GLY* 2.8 30.7 + - - -
589F PHE* 3.5 58.0 - + + +
592F ARG* 3.3 36.3 - - + -
593F ALA* 3.8 14.1 - - - +
596F VAL* 4.0 18.2 - - + -
65M LEU* 5.0 1.3 - - + -
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Residues in contact with CYS 571 (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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537F GLU* 3.9 29.4 - - + +
540F SER* 4.9 0.7 - - - -
567F PRO 3.2 18.1 + - - +
568F GLU* 3.3 6.9 + - - +
570F TRP* 1.3 74.9 - - - +
572F ALA* 1.3 63.9 + - - +
574F GLY* 3.1 2.1 + - - -
575F ASN* 2.9 21.0 + - - +
590F PHE* 3.5 16.7 - - + -
593F ALA* 3.9 6.7 - - + +
600F TYR* 5.5 0.4 - - + -
602F TYR* 4.6 1.1 - - - -
603F ALA* 4.9 8.5 - - + -
606F LEU* 3.4 32.5 - - - -
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Residues in contact with ALA 572 (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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536F MET 4.8 4.3 - - - +
537F GLU* 5.2 0.6 - - - +
540F SER* 3.8 14.4 - - - -
552F LEU* 4.3 2.8 - - - +
555F LEU* 4.0 24.9 - - + -
556F SER* 3.0 15.6 + - - +
559F LEU* 4.1 15.5 - - + -
568F GLU 3.1 12.6 + - - +
569F ALA 3.5 9.6 - - - +
570F TRP 3.4 0.2 - - - -
571F CYS* 1.3 75.0 - - - +
573F ALA* 1.3 57.5 + - - +
575F ASN* 3.0 20.6 + - - +
576F CYS 3.3 6.1 + - - -
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Residues in contact with ALA 573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556F SER* 3.1 24.7 + - - +
560F THR* 4.0 13.5 - - - +
569F ALA 3.3 10.5 + - - +
570F TRP* 3.9 4.5 - - + +
572F ALA* 1.3 74.8 - - - +
574F GLY* 1.3 64.6 + - - +
576F CYS* 3.4 7.1 + - - +
577F PHE* 3.3 24.6 - - - -
589F PHE* 3.5 28.0 - - + -
65M LEU* 4.1 6.1 - - + -
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Residues in contact with GLY 574 (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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570F TRP 2.8 16.7 + - - -
571F CYS 3.1 6.0 + - - -
573F ALA* 1.3 77.1 - - - +
575F ASN* 1.3 60.1 + - - +
577F PHE* 3.5 2.8 + - - -
578F SER 3.2 15.9 + - - -
586F ALA* 3.6 6.1 - - - +
589F PHE* 3.8 17.2 - - - +
590F PHE* 3.3 27.7 - - - -
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Residues in contact with ASN 575 (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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540F SER* 2.5 32.4 + - - +
541F THR* 3.2 28.2 + - - +
544F TRP* 4.1 6.1 - - + -
552F LEU* 3.9 12.4 - - + +
571F CYS 2.9 6.8 + - - +
572F ALA 3.0 10.0 + - - +
574F GLY* 1.3 73.1 - - - +
576F CYS* 1.3 65.3 + - - +
578F SER* 3.1 5.1 + - - -
579F LEU* 2.8 24.3 + - - +
590F PHE* 3.5 12.8 - - - -
606F LEU* 3.7 14.1 - - - +
499R ARG* 3.6 23.3 + - - +
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Residues in contact with CYS 576 (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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549F ASP* 4.5 3.1 - - - -
552F LEU* 3.7 19.1 - - - +
553F SER* 3.2 47.3 - - - -
556F SER* 3.8 13.0 - - - +
572F ALA 3.3 3.6 + - - -
573F ALA 3.4 11.0 - - - +
575F ASN* 1.3 78.6 - - - +
577F PHE* 1.3 63.1 + - + +
579F LEU* 3.1 12.1 + - - +
580F GLN* 3.2 21.2 + - - +
60M LEU* 6.5 0.2 - - - -
62M LEU* 3.8 18.2 - - + -
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Residues in contact with PHE 577 (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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573F ALA 3.3 14.8 - - - -
574F GLY 3.5 2.5 + - - +
575F ASN 3.3 0.4 - - - -
576F CYS* 1.3 79.2 - - + +
578F SER* 1.3 63.8 + - - +
580F GLN* 3.2 14.0 + - + +
581F ARG 3.3 8.5 + - - -
582F GLU* 3.3 20.8 + - + +
585F ILE* 3.5 40.6 - - + -
586F ALA* 3.7 26.2 - - + +
589F PHE* 4.1 12.6 - + - -
62M LEU* 3.6 42.0 - - + -
65M LEU* 3.4 45.5 - - + -
66M HIS 5.6 0.7 - - - -
67M GLU 6.2 1.6 - - - -
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Residues in contact with SER 578 (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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544F TRP* 3.1 16.5 + - - -
574F GLY 3.2 13.7 + - - -
575F ASN* 3.1 11.3 + - - -
577F PHE* 1.3 76.3 - - - +
579F LEU* 1.3 58.0 + - - +
581F ARG* 3.2 22.3 + - - +
583F HIS* 4.3 6.1 + - - -
586F ALA* 3.5 7.5 - - - +
590F PHE* 4.3 1.3 - - - -
610F GLU* 3.4 19.3 + - - -
613F LEU* 5.6 3.1 - - - +
499R ARG* 2.7 33.7 + - - -
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Residues in contact with LEU 579 (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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544F TRP* 3.5 36.6 - - + +
547F GLN* 3.6 32.3 - - - +
548F LYS 4.3 0.7 - - - +
549F ASP* 3.0 40.0 - - - +
552F LEU* 3.6 23.1 - - + -
575F ASN 2.8 11.2 + - - +
576F CYS 3.1 11.2 + - - +
578F SER* 1.3 74.9 + - - +
580F GLN* 1.3 64.3 + - - +
581F ARG* 3.1 34.0 + - - +
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Residues in contact with GLN 580 (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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549F ASP* 3.6 32.1 + - - +
576F CYS* 3.2 19.4 + - - +
577F PHE* 3.2 10.8 + - + +
579F LEU* 1.3 87.9 + - - +
581F ARG* 1.3 65.0 + - - +
582F GLU* 2.9 23.3 + - + +
60M LEU* 3.6 18.9 - - + +
62M LEU* 3.7 27.4 - - + -
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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