Contacts of the helix formed by residues 616 - 631 (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 GLU 616 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587F ILE* 5.6 1.0 - - - +
611F PHE* 2.9 35.8 + - + +
614F THR* 3.9 27.9 - - + +
615F GLU* 1.3 76.7 - - - +
617F LEU* 1.3 58.4 + - - +
618F ASP 3.4 2.5 - - - -
619F LYS* 3.3 23.9 + - + +
620F ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 617 (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 4.3 0.9 + - - -
612F VAL* 5.3 5.2 - - + +
615F GLU* 3.3 23.4 - - + +
616F GLU* 1.3 75.0 - - - +
618F ASP* 1.3 74.2 + - + +
620F ALA* 3.4 8.1 + - - +
621F LEU* 3.0 24.2 + - - +
644F ILE* 3.5 26.1 - - + +
647F LYS* 5.2 14.1 - - + +
648F GLN* 3.9 26.9 - - + +
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Residues in contact with ASP 618 (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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616F GLU 3.4 0.8 - - - -
617F LEU* 1.3 87.0 - - + +
619F LYS* 1.3 66.0 + - - +
621F LEU* 3.4 26.5 + - - +
622F ALA* 3.8 5.4 + - - +
648F GLN* 3.3 21.9 + - - -
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Residues in contact with LYS 619 (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* 3.5 36.3 - - + -
616F GLU* 3.3 31.4 + - + +
618F ASP* 1.3 77.8 - - - +
620F ALA* 1.3 61.1 + - - +
622F ALA* 3.4 16.0 + - - +
623F CYS* 3.4 17.4 - - - -
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Residues in contact with ALA 620 (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 3.7 10.8 - - - +
611F PHE* 3.2 32.9 - - + +
612F VAL* 3.7 7.4 - - + +
616F GLU 2.9 12.2 + - - +
617F LEU* 3.4 8.5 - - - +
618F ASP 3.3 0.2 - - - -
619F LYS* 1.3 74.0 - - - +
621F LEU* 1.3 64.3 + - - +
623F CYS* 3.2 4.9 + - - +
624F PHE* 3.1 27.5 + - - -
644F ILE* 3.7 14.6 - - + -
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Residues in contact with LEU 621 (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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617F LEU 3.0 15.5 + - - +
618F ASP* 3.4 19.1 - - - +
619F LYS 3.3 0.4 - - - -
620F ALA* 1.3 73.9 - - - +
622F ALA* 1.3 64.5 + - - +
624F PHE* 3.1 7.4 + - - +
625F ARG* 2.9 28.6 + - + +
641F LEU* 4.2 11.0 - - + +
644F ILE* 3.6 26.4 - - + +
645F TYR* 3.8 41.7 - - + +
648F GLN* 3.9 26.2 - - - +
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Residues in contact with ALA 622 (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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618F ASP 3.8 4.1 + - - +
619F LYS* 3.4 13.4 + - - +
621F LEU* 1.3 78.8 - - - +
623F CYS* 1.3 57.5 + - - +
625F ARG* 3.1 9.3 + - - +
626F ASN* 2.9 38.8 + - - +
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Residues in contact with CYS 623 (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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604F TYR* 3.9 14.7 - - + +
607F LEU* 4.0 13.2 - - + -
608F GLY* 3.9 18.4 - - - +
611F PHE* 3.4 34.3 - - - -
619F LYS* 3.4 17.9 - - - -
620F ALA 3.2 5.8 + - - +
622F ALA* 1.3 73.5 - - - +
624F PHE* 1.3 60.4 + - - +
626F ASN* 3.1 10.7 + - - +
627F ALA* 2.9 26.2 + - - +
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Residues in contact with PHE 624 (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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605F THR* 3.6 21.8 - - - -
608F GLY* 3.5 13.9 - - - -
609F HIS* 3.5 36.3 - + - -
612F VAL* 3.8 7.9 - - + -
620F ALA 3.1 16.6 + - - -
621F LEU 3.1 7.3 + - - +
623F CYS* 1.3 76.7 - - - +
625F ARG* 1.3 59.3 + - - +
627F ALA* 2.7 23.9 + - - +
628F ILE* 2.9 16.8 + - - +
637F ALA* 3.5 30.5 - - + +
640F GLY* 3.6 25.1 - - - -
641F LEU* 3.8 17.0 - - + -
644F ILE* 3.3 27.1 - - + -
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Residues in contact with ARG 625 (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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621F LEU* 2.9 22.4 + - + +
622F ALA* 3.5 9.2 - - - +
624F PHE* 1.3 75.5 - - - +
626F ASN* 1.3 60.1 + - - +
628F ILE* 3.1 27.8 + - - +
629F ARG* 2.9 34.5 + - - +
638F TRP* 4.7 7.7 - - - -
641F LEU* 3.9 27.8 - - + +
645F TYR* 4.7 5.3 + - - -
657F HIS* 3.4 31.3 - - - -
526Y GLN 5.4 0.4 + - - -
529Y MET* 3.8 24.8 + - - +
530Y ASP* 4.8 6.3 + - - +
533Y SER* 3.6 28.0 + - - +
549Y MET* 3.7 29.3 - - - +
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Residues in contact with ASN 626 (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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604F TYR* 3.6 30.5 + - + -
622F ALA* 2.9 23.6 + - - +
623F CYS* 3.4 11.2 - - - +
624F PHE 3.1 0.2 - - - -
625F ARG* 1.3 72.8 - - - +
627F ALA* 1.3 64.4 + - - +
629F ARG* 3.5 41.5 + - + +
630F VAL* 3.4 27.2 + - - +
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Residues in contact with ALA 627 (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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601F ALA* 4.4 7.5 - - - +
604F TYR* 3.8 19.3 - - + -
605F THR* 3.8 14.1 - - - +
623F CYS 2.9 10.7 + - - +
624F PHE* 2.7 13.3 + - - +
626F ASN* 1.3 74.3 - - - +
628F ILE* 1.3 59.0 + - - +
630F VAL* 3.2 3.9 + - - +
631F ASN* 3.0 29.8 + - - +
634F HIS* 4.9 2.9 - - - +
637F ALA* 3.2 24.2 - - + -
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Residues in contact with ILE 628 (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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624F PHE 2.9 12.1 + - - +
625F ARG* 3.1 18.4 + - - +
627F ALA* 1.3 76.5 - - - +
629F ARG* 1.3 62.4 + - - +
631F ASN 3.0 22.5 - - - +
632F PRO* 3.0 20.4 - - + +
634F HIS 4.6 1.1 - - - +
637F ALA* 3.6 22.4 - - + -
638F TRP* 3.6 61.0 - - + +
641F LEU* 3.8 17.5 - - + -
530Y ASP* 4.9 9.2 - - - +
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Residues in contact with ARG 629 (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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127F LYS* 5.7 2.3 - - - +
625F ARG* 2.9 18.6 + - - +
626F ASN* 3.5 43.9 + - + +
627F ALA 3.2 0.4 - - - -
628F ILE* 1.3 77.6 - - + +
630F VAL* 1.3 62.0 + - + +
632F PRO* 4.7 4.5 - - - +
533Y SER* 3.7 31.7 + - - +
534Y ILE* 4.8 17.7 - - + -
536Y LEU* 4.3 9.7 + - - +
537Y SER* 3.5 40.1 - - - +
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Residues in contact with VAL 630 (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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598F PRO 3.6 21.3 - - - +
599F ASN* 3.4 43.4 + - - +
601F ALA* 3.5 24.0 - - + +
604F TYR* 3.9 9.4 - - + -
626F ASN 3.4 16.3 + - - +
627F ALA 3.2 5.1 + - - +
629F ARG* 1.3 80.2 - - + +
631F ASN* 1.3 62.5 + - - +
632F PRO* 4.3 2.4 - - - +
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Residues in contact with ASN 631 (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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157F GLU* 4.2 22.4 + - - +
601F ALA* 3.7 13.6 - - + +
627F ALA 3.0 13.2 + - - +
628F ILE* 3.0 11.5 - - - +
630F VAL* 1.3 79.6 - - - +
632F PRO* 1.4 74.1 - - - +
633F ARG* 3.1 16.3 + - - +
634F HIS* 3.3 41.3 + - + +
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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