Contacts of the helix formed by residues 597 - 616 (chain B) in PDB entry 1FGI
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 597 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B SER* 1.3 74.6 - - - +
598B LYS* 1.3 61.8 + - - +
600B LEU* 3.3 12.1 + - - +
601B VAL* 3.2 24.4 + - - +
694B PHE* 5.1 1.1 - - - -
761B THR* 3.6 17.9 - - - +
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Residues in contact with LYS 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B SER* 3.1 8.3 + - - +
597B SER* 1.3 76.9 - - - +
599B ASP* 1.3 56.1 + - - +
601B VAL* 3.1 6.9 - - - +
602B SER* 2.7 37.3 + - - -
758B VAL* 2.7 45.9 + - + +
759B ALA* 3.3 14.1 + - - +
761B THR* 2.9 36.3 + - - +
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Residues in contact with ASP 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B GLN 4.6 2.4 - - - +
595B LEU* 3.7 28.0 - - + +
596B SER* 2.9 40.9 + - - +
598B LYS* 1.3 75.5 - - - +
600B LEU* 1.3 63.6 + - - +
602B SER* 3.6 7.2 - - - -
603B CYS* 3.1 22.3 + - - +
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Residues in contact with LEU 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LEU* 4.3 2.0 - - + -
595B LEU* 3.9 25.4 - - + +
596B SER 3.0 16.1 + - - +
597B SER* 3.6 12.3 - - - +
598B LYS 3.1 0.2 - - - -
599B ASP* 1.3 74.3 - - - +
601B VAL* 1.3 64.1 + - - +
603B CYS* 3.2 8.0 + - + +
604B ALA* 3.2 17.3 + - - +
693B ILE* 3.8 24.8 - - + +
694B PHE* 3.6 34.9 - - + -
696B LEU* 3.8 31.0 - - + -
724B ASN* 5.4 4.0 - - + +
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Residues in contact with VAL 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B SER 3.2 14.7 + - - +
598B LYS* 3.1 23.6 - - + +
600B LEU* 1.3 74.0 - - - +
602B SER* 1.3 61.3 + - - +
604B ALA* 3.0 6.6 + - - +
605B TYR* 2.8 28.6 + - - +
694B PHE* 4.1 6.7 - - + -
729B LEU* 3.8 29.4 - - + -
754B LEU* 5.0 4.1 - - + +
757B ILE* 3.8 24.7 - - + -
758B VAL* 3.7 21.9 - - + +
761B THR* 3.8 19.7 - - + +
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Residues in contact with SER 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B LYS* 2.7 22.6 + - - -
599B ASP* 3.6 9.4 - - - -
601B VAL* 1.3 73.7 - - - +
603B CYS* 1.3 62.0 + - - +
605B TYR* 3.1 8.4 + - - +
606B GLN* 2.9 39.1 + - - +
758B VAL* 4.1 17.5 - - - -
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Residues in contact with CYS 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LEU* 3.7 29.4 - - - -
572B TYR* 6.2 1.1 - - + -
573B LEU* 5.4 1.8 - - + -
599B ASP 3.1 11.5 + - - +
600B LEU* 3.4 12.3 - - + +
601B VAL 3.2 0.4 - - - -
602B SER* 1.3 79.3 - - - +
604B ALA* 1.3 61.8 + - - +
606B GLN* 3.5 5.2 + - - +
607B VAL* 3.1 29.6 + - - +
637B MET* 3.7 38.3 - - + +
693B ILE* 4.0 17.5 - - + -
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Residues in contact with ALA 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B LEU 3.2 8.9 + - - +
601B VAL* 3.0 12.0 + - - +
603B CYS* 1.3 75.3 - - - +
605B TYR* 1.3 65.1 + - - +
607B VAL* 4.5 3.1 - - - -
608B ALA 3.1 17.7 + - - -
686B PHE* 3.4 12.6 - - - -
690B LEU* 3.5 30.3 - - + -
693B ILE* 4.0 13.7 - - + -
694B PHE* 4.8 5.4 - - + -
754B LEU* 3.4 13.6 - - + +
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Residues in contact with TYR 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B VAL 2.8 12.3 + - - +
602B SER* 3.3 12.8 - - - +
604B ALA* 1.3 76.5 - - - +
606B GLN* 1.3 63.9 + - + +
608B ALA* 3.1 4.9 + - - +
609B ARG* 2.9 73.5 + - + +
751B VAL* 3.6 32.9 - - + +
754B LEU* 3.9 12.8 - - + +
755B ASP* 3.7 39.0 + - + -
758B VAL* 4.1 16.4 - - + -
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Residues in contact with GLN 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ASN* 3.0 44.1 + - - +
602B SER* 2.9 34.3 + - - +
603B CYS* 3.7 5.5 - - - +
605B TYR* 1.3 83.6 - - + +
607B VAL* 1.3 61.7 + - - +
609B ARG* 3.1 6.0 + - - +
610B GLY 3.0 20.1 + - - -
635B ASN 3.6 18.4 + - - -
636B VAL* 3.6 11.0 - - - +
637B MET* 3.3 28.8 + - + +
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Residues in contact with VAL 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ASN* 5.4 0.7 - - - -
569B LEU* 4.7 0.9 - - + -
603B CYS* 3.1 24.7 + - - +
604B ALA* 3.8 4.7 - - - +
606B GLN* 1.3 75.5 - - - +
608B ALA* 1.3 61.3 + - - +
610B GLY 3.5 0.5 + - - -
611B MET* 3.1 23.8 + - + +
624B LEU* 4.5 2.9 - - + -
629B VAL* 4.2 17.0 - - + -
637B MET* 4.1 18.8 - - + -
639B ILE* 3.6 19.5 - - + +
686B PHE* 3.5 21.5 - - + -
689B LEU* 3.8 29.2 - - + -
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Residues in contact with ALA 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B ALA 3.1 18.9 + - - +
605B TYR 3.1 4.7 + - - +
607B VAL* 1.3 72.7 - - - +
609B ARG* 1.3 55.4 + - - +
611B MET* 3.2 3.2 + - - +
612B GLU* 2.7 34.5 + - - +
686B PHE* 3.7 15.5 - - + -
747B PHE* 4.1 14.4 - - + -
750B LEU* 4.6 3.6 - - + -
751B VAL* 3.7 14.7 - - + +
754B LEU* 3.6 19.3 - - + -
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Residues in contact with ARG 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B HIS* 4.2 14.3 + - + +
543B ASN* 3.8 14.6 - - - +
605B TYR* 2.9 66.1 + - + +
606B GLN* 3.5 7.9 - - - +
608B ALA* 1.3 73.6 - - - +
610B GLY* 1.3 60.5 + - - +
612B GLU* 2.9 13.8 + - - +
613B TYR* 2.8 29.8 + - - +
751B VAL* 3.9 21.3 - - + +
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Residues in contact with GLY 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B HIS* 4.1 5.2 - - - -
543B ASN* 3.8 30.0 - - - +
544B ILE* 3.8 6.7 - - - +
606B GLN 3.0 11.6 + - - -
607B VAL 3.9 1.8 - - - -
608B ALA 3.4 0.2 - - - -
609B ARG* 1.3 75.1 - - - +
611B MET* 1.3 56.4 + - - +
613B TYR* 3.3 3.5 + - - +
614B LEU* 3.0 31.4 + - - +
639B ILE* 4.2 7.6 - - - -
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Residues in contact with MET 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B VAL* 3.1 19.7 + - + +
608B ALA 3.5 8.1 - - - +
609B ARG 3.1 0.2 - - - -
610B GLY* 1.3 75.2 - - - +
612B GLU* 1.3 55.0 + - - +
614B LEU* 3.2 24.8 + - + +
615B ALA* 2.8 37.9 + - + +
619B CYS 5.1 2.2 - - - +
621B HIS* 4.1 12.1 - - + +
624B LEU* 3.8 34.8 - - + -
639B ILE* 4.0 12.1 - - + -
682B ASP* 3.5 28.0 - - + +
747B PHE* 3.6 34.5 - - + -
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Residues in contact with GLU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ALA 2.7 17.8 + - - +
609B ARG* 2.9 20.2 + - - +
611B MET* 1.3 71.9 - - - +
613B TYR* 1.3 58.1 + - - +
615B ALA* 3.7 3.6 - - - +
616B SER* 3.0 29.2 + - - -
747B PHE* 4.0 12.3 - - - +
748B LYS* 3.7 32.9 - - + +
751B VAL* 3.3 35.2 - - + +
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Residues in contact with TYR 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B ILE* 2.8 37.5 + - + -
539B GLY* 3.4 19.7 - - - -
540B LYS 3.2 20.0 + - - -
541B HIS* 3.5 43.1 - + + +
544B ILE* 4.0 10.5 - - + -
609B ARG 2.8 8.7 + - - +
610B GLY 3.4 7.6 - - - +
612B GLU* 1.3 74.4 - - - +
614B LEU* 1.3 68.3 + - + +
616B SER* 2.5 28.6 + - - -
617B LYS* 3.0 30.0 + - + +
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Residues in contact with LEU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B ILE* 4.0 17.9 - - + -
544B ILE* 4.0 14.8 - - + -
610B GLY 3.0 18.3 + - - +
611B MET* 3.5 32.1 - - + +
613B TYR* 1.3 76.1 - - - +
615B ALA* 1.3 56.5 + - - +
617B LYS* 3.0 14.8 + - - -
619B CYS* 2.8 43.3 + - + +
621B HIS* 4.9 0.9 - - + -
639B ILE* 3.8 14.8 - - + -
642B PHE* 3.6 47.8 - - + -
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Residues in contact with ALA 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B MET* 2.8 22.4 + - + +
612B GLU* 3.7 7.0 - - - +
614B LEU* 1.3 69.7 - - - +
616B SER* 1.3 65.4 + - - +
618B LYS* 3.0 11.8 + - - +
619B CYS 4.0 1.1 + - - +
679B HIS* 3.3 42.0 + - + +
747B PHE* 4.7 12.6 - - + -
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Residues in contact with SER 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B GLU* 3.0 13.0 + - - -
613B TYR* 2.5 31.5 + - - -
615B ALA* 1.3 78.1 - - - +
617B LYS* 1.3 66.6 + - - +
618B LYS* 3.2 7.7 + - - +
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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
------------------------------------------------------------
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