Contacts of the helix formed by residues 514 - 529 (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 514 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482F LYS* 4.2 12.1 + - - -
509F TYR* 3.2 34.3 + - + +
512F LEU* 3.6 26.9 - - - +
513F SER* 1.3 77.3 - - - +
515F TYR* 1.3 50.9 + - - +
516F MET* 3.3 3.6 - - - -
517F GLN* 3.0 19.5 + - + +
518F ALA* 2.8 33.4 + - - +
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Residues in contact with TYR 515 (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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510F PHE* 3.2 54.2 + + - -
513F SER* 3.4 28.9 + - - -
514F GLU* 1.3 75.0 - - - +
516F MET* 1.3 56.8 + - - +
518F ALA* 3.4 6.4 - - + +
519F GLU* 2.8 33.3 + - - +
542F THR* 3.7 6.5 - - + +
545F HIS* 3.5 48.7 + + + -
546F LEU* 3.7 20.7 - - + +
496R GLN* 3.8 16.8 + - - -
497R GLY* 4.3 3.5 - - - -
498R ILE* 4.3 10.6 + - - -
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Residues in contact with MET 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514F GLU 3.3 0.8 - - - -
515F TYR* 1.3 77.2 - - - +
517F GLN* 1.3 61.6 + - - +
519F GLU* 3.8 10.5 - - - +
520F ARG* 3.4 28.4 + - - +
546F LEU* 3.5 31.0 - - + +
548F LYS* 5.4 6.7 - - - +
88J GLN* 3.8 35.9 - - + +
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Residues in contact with GLN 517 (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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509F TYR* 3.7 40.9 + - + -
514F GLU* 3.0 24.7 + - + +
516F MET* 1.3 78.6 - - - +
518F ALA* 1.3 55.2 + - - +
520F ARG* 3.1 29.4 - - - +
521F ILE* 3.3 17.5 + - - +
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Residues in contact with ALA 518 (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 4.3 4.9 - - - +
509F TYR* 3.9 21.7 - - + +
510F PHE* 4.1 14.8 - - + +
514F GLU 2.8 15.8 + - - +
515F TYR* 3.1 14.3 + - - +
517F GLN* 1.3 71.9 - - - +
519F GLU* 1.3 59.4 - - - +
521F ILE* 2.9 21.8 + - - +
522F PHE* 2.9 19.4 + - + +
542F THR* 3.9 12.6 - - + +
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Residues in contact with GLU 519 (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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515F TYR 2.8 9.5 + - - +
516F MET* 3.8 14.4 - - - +
518F ALA* 1.3 68.7 - - - +
520F ARG* 1.3 93.4 + - - +
522F PHE* 4.0 0.6 - - - +
523F SER* 3.1 30.7 + - - -
539F TYR* 4.2 8.9 + - + +
542F THR* 3.5 14.9 - - + +
543F LEU* 3.7 25.8 - - + +
546F LEU* 3.4 30.1 - - + +
548F LYS* 3.6 25.6 + - + +
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Residues in contact with ARG 520 (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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516F MET* 3.4 17.6 + - - +
517F GLN* 3.1 27.4 - - - +
519F GLU* 1.3 90.1 + - - +
521F ILE* 1.3 61.1 + - + +
523F SER* 2.6 33.6 + - - -
524F GLU* 3.3 38.3 + - - +
58J HIS* 5.6 8.1 - - - -
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Residues in contact with ILE 521 (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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496F TYR* 4.2 17.3 - - - +
502F LEU* 3.6 20.5 - - + +
505F ILE* 3.7 13.7 - - + -
506F GLY* 3.5 30.1 - - - +
509F TYR* 3.7 28.3 - - + -
517F GLN* 3.6 18.8 - - - +
518F ALA* 2.9 13.3 + - - +
520F ARG* 1.3 77.7 - - + +
522F PHE* 1.3 58.8 + - - +
524F GLU* 3.1 32.7 + - - +
525F VAL* 3.3 8.8 + - + +
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Residues in contact with PHE 522 (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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503F CYS* 3.7 33.4 - - - -
506F GLY* 3.7 16.8 - - - -
507F ARG* 3.5 20.2 - - + -
510F PHE* 5.1 0.7 - - + -
518F ALA* 2.9 24.0 + - + +
519F GLU 4.0 0.2 - - - +
521F ILE* 1.3 68.6 - - - +
523F SER* 1.3 64.4 + - - +
524F GLU 3.1 1.5 + - - -
525F VAL* 3.3 17.3 - - + +
526F ARG* 3.1 24.8 + - - +
535F GLY 4.3 6.7 - - - -
536F MET* 4.8 5.8 - - - -
538F ILE* 3.6 29.8 - - + -
539F TYR* 3.0 52.5 - + + -
542F THR* 4.1 9.2 - - - -
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Residues in contact with SER 523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519F GLU* 3.1 19.4 + - - -
520F ARG* 2.6 35.2 + - - -
522F PHE* 1.3 75.6 - - - +
524F GLU* 1.3 63.7 + - - +
526F ARG* 3.3 7.6 + - - +
527F ARG* 3.1 22.9 + - - +
539F TYR* 4.0 17.6 - - - -
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Residues in contact with GLU 524 (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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496F TYR* 5.8 0.2 + - - -
502F LEU* 4.7 13.0 - - + +
520F ARG* 3.3 54.7 + - - +
521F ILE* 3.1 16.0 + - - +
522F PHE 3.1 0.8 - - - -
523F SER* 1.3 81.2 + - - +
525F VAL* 1.3 63.8 + - - +
527F ARG* 3.1 29.0 - - + +
528F ILE* 3.4 17.4 + - + +
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Residues in contact with VAL 525 (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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499F GLY* 3.7 27.6 - - - +
502F LEU* 3.2 39.2 - - + +
503F CYS* 3.6 18.2 - - + +
521F ILE 3.5 13.0 - - - +
522F PHE* 3.3 17.5 - - + +
524F GLU* 1.3 76.9 - - - +
526F ARG* 1.3 52.5 + - + +
528F ILE* 2.7 22.3 + - - +
529F GLU* 2.8 19.6 + - + +
532F ARG* 4.6 4.5 - - + -
536F MET* 4.5 17.0 - - + -
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Residues in contact with ARG 526 (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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522F PHE 3.1 15.0 + - - +
523F SER* 3.3 9.2 + - - +
524F GLU 3.3 0.6 - - - -
525F VAL* 1.3 74.5 - - - +
527F ARG* 1.3 62.2 + - - +
529F GLU 3.9 16.5 + - - +
530F ASN* 3.1 43.0 + - - +
532F ARG 4.6 1.4 + - - -
536F MET* 3.6 37.4 - - + +
539F TYR* 4.1 18.2 - - + +
555F LEU* 3.8 20.6 - - - +
558F ASP* 2.7 36.1 + - - +
559F LEU* 3.9 20.0 - - - +
562F MET* 5.5 1.2 - - - +
59H ARG* 5.1 1.6 - - - +
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Residues in contact with ARG 527 (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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523F SER 3.1 11.7 + - - +
524F GLU* 3.1 27.6 + - + +
525F VAL 3.2 0.4 - - - -
526F ARG* 1.3 77.6 - - - +
528F ILE* 1.3 91.4 - - - +
530F ASN* 3.9 8.8 - - - +
259K GLU* 4.3 22.3 + - - -
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Residues in contact with ILE 528 (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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497F ASN* 3.5 28.7 - - + +
498F THR* 4.8 0.9 - - - -
499F GLY* 4.1 9.0 - - - +
502F LEU* 3.5 22.9 - - + -
524F GLU* 3.4 17.8 + - + +
525F VAL* 2.7 10.2 + - - +
527F ARG* 1.3 114.2 - - - +
529F GLU* 1.3 73.3 + - + +
530F ASN* 3.6 7.3 + - - +
531F TYR* 4.8 3.6 - - - -
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Residues in contact with GLU 529 (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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498F THR* 4.7 2.4 - - - -
499F GLY* 3.2 24.0 + - - -
525F VAL* 2.8 15.3 + - + +
526F ARG* 3.9 14.4 + - - +
528F ILE* 1.3 85.3 - - + +
530F ASN* 1.3 62.0 + - - +
531F TYR* 2.9 42.6 + - + +
532F ARG* 3.1 53.1 + - + +
536F MET* 5.2 0.5 - - - +
29H GLU* 3.1 20.4 - - - +
48H TYR* 4.6 0.5 + - - -
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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