Contacts of the helix formed by residues 600 - 615 (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 TYR 600 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534F GLU 4.8 2.9 + - - -
537F GLU* 2.6 48.9 + - + +
567F PRO* 3.6 29.8 - - + -
568F GLU* 3.6 31.5 + - + +
571F CYS* 5.5 1.1 - - + -
597F ASP* 3.4 28.9 - - + +
598F PRO 3.4 2.2 - - - -
599F ASN* 1.3 77.0 - - - +
601F ALA* 1.3 66.2 + - - +
602F TYR* 4.2 2.5 - - + -
603F ALA* 3.7 22.8 - - + +
604F TYR* 3.2 17.7 - - - -
630F VAL* 3.5 2.0 - - - +
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Residues in contact with ALA 601 (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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600F TYR* 1.3 75.9 - - - +
602F TYR* 1.3 55.6 + - + +
604F TYR* 2.7 37.5 + - - +
605F THR* 3.5 6.0 + - - -
627F ALA* 4.4 4.4 - - - +
630F VAL* 3.5 17.0 - - + +
631F ASN* 3.7 33.4 - - + +
634F HIS* 4.2 15.0 - - + +
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Residues in contact with TYR 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510F PHE* 4.0 10.3 - + - -
511F GLU* 6.1 0.7 - - - -
537F GLU* 2.7 42.8 - - + +
538F ILE* 3.7 26.6 - - + +
541F THR* 3.4 30.8 + - - +
571F CYS* 4.6 0.4 - - - -
600F TYR* 3.6 3.6 - - + -
601F ALA* 1.3 75.1 - - + +
603F ALA* 1.3 64.9 + - - +
605F THR* 3.1 11.4 - - + -
606F LEU* 3.0 58.0 + - + +
634F HIS* 3.3 26.2 - + + +
636F ASN* 3.7 25.0 + - + -
498R ILE 4.6 2.3 + - - -
499R ARG* 5.0 0.2 - - - +
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Residues in contact with ALA 603 (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* 4.1 0.6 + - - -
571F CYS* 4.9 11.4 - - + -
590F PHE* 4.6 4.8 - - - +
593F ALA* 4.1 21.8 - - + -
594F ILE* 3.8 24.2 - - + +
600F TYR* 3.7 31.5 - - + +
602F TYR* 1.3 78.9 - - - +
604F TYR* 1.3 62.5 + - - +
606F LEU* 3.4 2.4 + - - +
607F LEU* 3.0 22.3 + - - +
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Residues in contact with TYR 604 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594F ILE* 3.4 45.7 - - + +
597F ASP 4.7 0.7 - - - -
598F PRO* 2.7 37.7 + - + +
600F TYR 3.2 26.5 - - - -
601F ALA* 2.7 17.0 + - - +
603F ALA* 1.3 70.4 - - - +
605F THR* 1.3 53.9 + - - +
607F LEU* 3.0 5.3 + - + +
608F GLY* 2.6 33.6 + - - -
623F CYS* 3.9 14.8 - - + +
626F ASN* 3.6 40.1 + - + -
627F ALA* 3.8 15.9 - - + -
630F VAL* 3.9 14.7 - - + +
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Residues in contact with THR 605 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F ALA 3.6 4.2 + - - -
602F TYR* 3.1 12.9 + - + -
604F TYR* 1.3 77.5 - - - +
606F LEU* 1.3 62.1 + - + +
608F GLY* 2.7 22.7 + - - -
609F HIS* 2.9 35.5 + - + +
624F PHE* 3.6 10.9 - - + -
627F ALA* 3.8 9.6 - - - +
634F HIS* 2.8 28.9 + - + -
636F ASN* 3.5 35.9 - - + +
637F ALA* 4.2 0.9 - - - +
499R ARG* 6.1 0.2 - - + -
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Residues in contact with LEU 606 (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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541F THR* 4.0 0.7 - - - +
571F CYS* 3.4 27.4 - - - -
575F ASN* 3.7 22.9 - - - +
590F PHE* 3.5 24.5 - - + -
602F TYR* 3.0 41.0 + - + +
603F ALA 3.9 2.9 - - - +
605F THR* 1.3 81.2 - - + +
607F LEU* 1.3 62.2 + - - +
609F HIS* 3.4 11.5 + - + +
610F GLU* 3.2 25.6 + - - +
499R ARG* 3.9 36.5 + - + +
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Residues in contact with LEU 607 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587F ILE* 3.9 30.5 - - + +
590F PHE* 3.8 27.0 - - + -
591F GLN* 3.8 16.6 - - + +
594F ILE* 3.7 24.2 - - + -
603F ALA 3.0 14.8 + - - +
604F TYR* 3.4 7.0 - - + +
606F LEU* 1.3 77.4 - - - +
608F GLY* 1.3 62.7 + - - +
610F GLU* 3.4 5.9 + - + +
611F PHE* 3.2 48.8 + - + -
623F CYS* 4.0 11.7 - - + -
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Residues in contact with GLY 608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604F TYR 2.6 16.9 + - - -
605F THR 2.7 9.8 + - - -
607F LEU* 1.3 69.6 - - - +
609F HIS* 1.3 55.6 + - - -
611F PHE* 3.0 22.1 + - - +
612F VAL* 3.1 14.0 + - - +
620F ALA* 3.7 2.6 - - - +
623F CYS* 3.9 17.2 - - - +
624F PHE* 3.5 21.3 - - - -
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Residues in contact with HIS 609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605F THR* 2.9 48.2 + - + +
606F LEU* 3.8 9.0 - - + +
608F GLY* 1.3 72.0 - - - +
610F GLU* 1.3 57.9 + - - +
612F VAL* 3.3 9.9 - - - +
613F LEU* 3.1 32.0 + - + +
624F PHE* 3.5 12.5 - + - -
636F ASN* 4.1 7.9 + - - -
639F TYR* 4.2 28.9 - + - -
643F MET* 4.0 13.6 - - + +
498R ILE* 4.2 6.3 - - - +
499R ARG* 2.7 55.6 + - + +
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Residues in contact with GLU 610 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578F SER* 3.4 18.7 + - - -
583F HIS* 3.0 38.1 - - - +
586F ALA* 4.1 2.4 - - + +
587F ILE* 3.8 20.4 - - + -
590F PHE* 3.7 29.4 - - + -
606F LEU 3.2 6.0 + - - +
607F LEU* 3.4 11.9 - - - +
608F GLY 3.2 0.2 - - - -
609F HIS* 1.3 77.5 - - - +
611F PHE* 1.3 53.1 + - - +
613F LEU* 3.2 8.5 + - - +
614F THR* 2.6 37.2 + - - -
499R ARG* 2.6 31.7 + - - -
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Residues in contact with PHE 611 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587F ILE* 4.0 28.3 - - + -
591F GLN* 4.3 9.4 - - - -
607F LEU* 3.2 40.8 + - + -
608F GLY 3.0 2.9 + - - +
610F GLU* 1.3 75.3 - - - +
612F VAL* 1.3 65.9 + - - +
614F THR* 3.1 2.6 + - - -
615F GLU 2.9 5.2 + - - -
616F GLU* 2.9 53.7 + - + +
619F LYS* 3.5 27.4 - - + -
620F ALA* 3.2 26.2 - - + -
623F CYS* 3.4 31.9 - - - -
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Residues in contact with VAL 612 (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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608F GLY 3.1 12.2 + - - +
609F HIS* 3.3 13.9 - - - +
611F PHE* 1.3 74.6 - - - +
613F LEU* 1.3 66.3 + - + +
615F GLU* 3.1 34.1 + - - +
616F GLU 5.2 0.2 - - - +
617F LEU* 5.3 5.1 - - - +
620F ALA* 3.7 3.0 - - + +
624F PHE* 3.8 17.0 - - + -
643F MET* 3.7 34.8 - - + -
644F ILE* 3.8 17.7 - - + -
647F LYS* 3.9 21.8 - - + +
495R HIS* 5.9 1.8 - - + -
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Residues in contact with LEU 613 (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* 5.2 3.8 - - + -
578F SER 5.6 3.4 - - - +
581F ARG* 6.0 2.0 - - + -
583F HIS* 3.8 34.5 - - + +
609F HIS* 3.1 17.2 + - + +
610F GLU* 3.2 13.4 + - - +
612F VAL* 1.3 80.8 - - + +
614F THR* 1.3 59.7 + - - +
615F GLU* 3.1 17.1 + - - +
647F LYS* 5.6 3.4 - - - +
495R HIS* 3.8 35.2 - - + +
499R ARG* 4.3 19.7 - - - +
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Residues in contact with THR 614 (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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583F HIS* 3.8 21.9 + - + +
584F ASP* 5.5 8.5 - - - +
587F ILE* 3.7 17.7 - - + +
610F GLU 2.6 25.5 + - - -
611F PHE* 3.1 5.3 + - - -
613F LEU* 1.3 75.3 - - - +
615F GLU* 1.3 67.2 + - - +
616F GLU* 3.9 23.1 - - + +
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Residues in contact with GLU 615 (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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611F PHE 2.9 2.4 + - - -
612F VAL 3.3 19.0 - - - +
613F LEU* 3.1 14.9 - - - +
614F THR* 1.3 82.0 - - - +
616F GLU* 1.3 56.8 + - - +
617F LEU* 3.3 29.6 + - - +
647F LYS* 4.1 23.2 + - - +
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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