Contacts of the helix formed by residues 559 - 572 (chain B) in PDB entry 1R4I
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 CYS 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542B CYS* 3.4 1.2 - - - -
545B CYS* 3.5 8.7 - - - -
547B ASP* 4.4 5.4 - - + +
548B GLU* 3.1 20.0 - - + +
550B SER* 4.1 1.9 - - - -
558B THR* 1.3 89.5 + - - +
560B GLY* 1.3 69.5 + - - +
561B SER* 2.9 17.0 - - - -
562B CYS* 2.9 30.3 - - - -
563B LYS* 3.2 6.4 + - - +
591B ARG* 3.2 13.2 - - - +
652B ZN 2.5 34.4 - - - -
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Residues in contact with GLY 560 (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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548B GLU* 4.5 1.2 + - - +
550B SER* 3.6 18.5 + - - -
559B CYS* 1.3 75.6 - - - +
561B SER* 1.3 60.8 + - - +
563B LYS* 3.2 17.4 - - - +
564B VAL* 3.2 13.3 - - - +
14C A 4.0 14.0 + - - -
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Residues in contact with SER 561 (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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559B CYS* 2.9 21.2 - - - -
560B GLY* 1.3 71.1 - - - +
562B CYS* 1.3 55.7 + - - +
563B LYS 2.9 2.9 + - - -
564B VAL* 2.9 9.7 + - - +
565B PHE* 2.5 35.9 + - - +
591B ARG* 3.3 12.2 + - - +
598B ARG* 3.0 10.3 + - - -
13C G 2.9 50.0 - - - -
14C A 3.8 4.8 + - - -
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Residues in contact with CYS 562 (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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544B ILE* 3.1 29.6 - - + -
545B CYS* 3.8 3.6 - - - -
558B THR* 3.9 10.5 - - + -
559B CYS* 2.9 26.3 - - - +
561B SER* 1.3 71.1 + - - +
563B LYS* 1.3 66.4 + - - +
565B PHE* 4.0 5.3 - - - -
566B PHE* 3.0 21.8 + - - +
598B ARG* 3.3 22.2 - - - +
602B CYS* 5.2 1.8 - - - -
607B MET* 5.1 2.9 - - + +
652B ZN 2.1 37.9 - - - -
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Residues in contact with LYS 563 (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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553B HIS* 3.6 32.3 - - + +
554B TYR* 4.0 30.4 + - + +
558B THR* 3.4 19.4 + - - +
559B CYS 3.2 5.9 + - - +
560B GLY* 3.2 12.3 - - - +
561B SER 2.9 1.0 + - - -
562B CYS* 1.3 83.7 - - - +
564B VAL* 1.3 86.2 + - + +
565B PHE 3.0 0.2 + - - -
566B PHE* 3.0 11.3 + - - +
567B LYS* 3.4 8.6 + - - +
15C A 5.7 0.4 - - - +
20D T 4.0 27.8 - - - -
21D G 3.4 33.9 + - - -
22D T 4.4 13.3 + - - +
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Residues in contact with VAL 564 (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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560B GLY 3.2 20.0 - - - +
561B SER* 2.9 9.6 + - - +
563B LYS* 1.3 89.0 - - + +
565B PHE* 1.3 63.0 + - - +
567B LYS* 3.6 5.2 + - - +
568B ARG* 2.9 66.3 + - + +
13C G 4.9 1.1 - - + +
14C A 4.1 26.7 - - - +
15C A 5.2 4.0 - - - +
22D T 4.7 15.3 - - + +
23D T 5.0 1.3 - - - +
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Residues in contact with PHE 565 (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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561B SER 2.5 20.7 + - - +
562B CYS* 3.8 5.4 - - - +
564B VAL* 1.3 71.8 - - - +
566B PHE* 1.3 83.7 + - + +
567B LYS 3.0 0.7 + - - -
568B ARG* 3.3 6.6 + - - +
569B ALA* 2.8 44.1 + - + +
576B TYR* 5.2 2.7 - + - -
595B PRO* 3.9 35.4 - - + -
598B ARG* 3.4 61.0 - - + +
599B LEU* 3.7 21.1 - - + -
602B CYS* 4.8 6.1 - - - -
12C A 4.6 18.2 - - + -
13C G 5.0 1.3 - - - +
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Residues in contact with PHE 566 (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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554B TYR* 4.2 15.3 - + + -
562B CYS 3.0 19.1 + - - +
563B LYS* 3.6 4.7 - - - +
565B PHE* 1.3 83.4 - - - +
567B LYS* 1.3 68.1 + - - +
569B ALA* 4.3 1.6 - - - -
570B ALA* 3.0 31.9 + - + +
599B LEU* 4.3 5.4 - - + -
602B CYS* 3.5 24.5 - - + -
603B TYR* 3.9 28.5 - + - -
607B MET* 3.4 33.0 - - + -
608B THR* 3.6 45.3 - - - -
609B LEU* 4.3 11.7 - - + -
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Residues in contact with LYS 567 (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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554B TYR* 3.5 29.2 - - + +
563B LYS* 3.4 6.3 + - + +
564B VAL* 4.0 8.5 - - - +
565B PHE 3.0 1.6 + - - -
566B PHE* 1.3 85.0 - - - +
568B ARG* 1.3 82.2 + - - +
569B ALA 2.7 5.7 + - - -
571B GLU* 3.0 49.4 + - - +
609B LEU* 4.1 17.4 - - + +
21D G 3.5 22.4 - - + +
22D T 4.2 30.5 + - - -
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Residues in contact with ARG 568 (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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564B VAL* 2.9 44.6 + - + +
565B PHE* 3.3 5.7 + - + +
567B LYS* 1.3 94.1 - - - +
569B ALA* 1.3 61.4 + - - +
571B GLU* 4.4 2.2 - - - -
572B GLY* 3.6 14.9 + - - -
574B GLN* 6.1 0.5 - - - +
576B TYR* 4.8 4.0 + - - -
12C A 4.0 28.0 + - - +
13C G 2.7 49.3 + - - -
22D T 6.3 1.3 - - + -
23D T 4.2 13.1 + - - +
24D C 4.8 2.8 - - - +
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Residues in contact with ALA 569 (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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565B PHE* 2.8 47.7 + - + +
566B PHE* 3.7 3.6 - - - +
567B LYS 2.7 4.2 + - - -
568B ARG* 1.3 74.1 - - - +
570B ALA* 1.3 64.7 + - - +
571B GLU 3.2 3.0 + - - -
572B GLY 3.7 6.1 + - - -
573B LYS* 3.7 10.0 + - - -
574B GLN* 4.3 4.7 + - - +
576B TYR* 4.2 25.7 + - + +
599B LEU* 4.4 10.2 - - + +
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Residues in contact with ALA 570 (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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566B PHE* 3.0 32.4 + - + +
567B LYS 4.4 0.2 - - - +
569B ALA* 1.3 76.3 - - - +
571B GLU* 1.3 60.6 + - - +
573B LYS* 4.0 9.1 + - - +
599B LEU* 4.6 6.0 - - + +
603B TYR* 2.9 34.5 + - + +
609B LEU* 4.5 12.5 - - + +
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Residues in contact with GLU 571 (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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567B LYS* 3.0 48.2 + - - +
568B ARG* 4.6 1.8 - - - +
570B ALA* 1.3 76.7 - - - +
572B GLY* 1.3 60.5 + - - +
573B LYS* 3.0 13.0 + - - +
609B LEU* 4.4 19.3 - - + +
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Residues in contact with GLY 572 (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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568B ARG 3.6 15.6 + - - -
569B ALA 3.7 1.8 + - - -
571B GLU* 1.3 76.0 - - - +
573B LYS* 1.3 69.6 + - - +
574B GLN* 2.9 22.4 + - - +
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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