Contacts of the helix formed by residues 559 - 571 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A CYS* 3.1 11.9 - - + -
545A CYS* 3.3 9.9 - - - -
547A ASP* 4.1 15.3 - - + +
548A GLU 4.0 10.1 - - - -
550A SER* 4.2 1.5 - - - -
558A THR* 1.3 80.5 + - - +
560A GLY* 1.3 71.7 + - - +
561A SER 3.7 0.4 - - - -
562A CYS* 2.9 33.0 - - - -
563A LYS* 3.2 13.0 + - - +
591A ARG* 3.2 20.4 - - - -
650A ZN 2.4 31.4 - - - -
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Residues in contact with GLY 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ASP* 5.2 2.2 + - - -
548A GLU 4.6 3.0 + - - -
550A SER* 4.0 16.6 - - - -
559A CYS* 1.3 76.9 - - - +
561A SER* 1.3 63.3 + - - +
563A LYS* 3.1 20.2 + - - +
564A VAL* 3.5 6.6 + - - +
31D T 4.1 17.6 + - - -
32D T 6.2 3.8 - - - -
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Residues in contact with SER 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A CYS* 3.4 1.4 - - - -
560A GLY* 1.3 69.8 - - - +
562A CYS* 1.3 59.7 + - - +
564A VAL* 2.7 6.4 + - - +
565A PHE* 2.4 37.1 + - - +
591A ARG* 3.1 24.0 - - - -
598A ARG* 3.4 2.6 + - - -
29D T 4.0 6.4 - - - +
30D G 2.3 45.5 + - - +
31D T 3.9 18.7 + - - +
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Residues in contact with CYS 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ILE* 3.1 30.5 - - + -
545A CYS* 3.9 2.5 - - - -
558A THR* 3.9 9.9 - - + -
559A CYS* 2.9 25.0 - - - +
561A SER* 1.3 73.8 - - - +
563A LYS* 1.3 68.0 + - - +
565A PHE* 3.4 4.2 - - - +
566A PHE* 2.8 22.7 + - - +
598A ARG* 3.4 21.8 - - - +
602A CYS* 5.6 3.6 - - - -
607A MET* 5.5 2.6 - - + +
650A ZN 2.2 32.5 - - - -
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Residues in contact with LYS 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A HIS* 3.4 33.4 - - + +
554A TYR* 3.4 33.1 - - + +
558A THR* 3.7 19.2 + - - +
559A CYS 3.2 3.4 + - - +
560A GLY* 3.1 12.0 + - - +
561A SER 2.8 3.6 + - - -
562A CYS* 1.3 80.6 - - - +
564A VAL* 1.3 85.2 + - - +
566A PHE* 3.2 15.1 + - - +
567A LYS 3.3 4.3 + - - -
607A MET* 6.0 0.7 - - - -
3C A 4.0 13.8 + - + +
4C G 3.4 39.1 + - - -
5C A 4.4 5.0 - - - +
32D T 4.5 4.9 + - - +
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Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A GLY 3.8 2.9 - - - +
561A SER* 2.7 9.2 + - - +
563A LYS* 1.3 91.5 - - - +
565A PHE* 1.3 68.1 + - - +
566A PHE 2.9 1.7 + - - -
567A LYS* 3.1 8.6 + - + +
568A ARG* 3.0 68.9 + - + +
5C A 5.1 4.3 - - - +
6C A 5.4 2.5 - - - +
30D G 4.9 1.8 - - + +
31D T 3.7 35.0 - - + +
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Residues in contact with PHE 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A SER* 2.4 29.3 + - - +
562A CYS 3.4 5.2 - - - +
564A VAL* 1.3 72.7 - - - +
566A PHE* 1.3 74.2 + + + +
568A ARG* 3.6 10.9 + - - +
569A ALA* 3.2 16.7 + - + +
576A TYR* 3.8 22.3 + + - -
591A ARG 5.4 0.2 - - - -
595A PRO* 4.0 11.4 - - + -
598A ARG* 3.3 67.1 - - + +
599A LEU* 3.8 25.4 - - + -
602A CYS* 5.0 4.9 - - - -
29D T 4.1 37.5 - - - -
30D G 4.9 1.6 - - - -
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Residues in contact with PHE 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A TYR* 4.6 9.0 - + + -
562A CYS 2.8 11.4 + - - +
563A LYS* 3.2 10.8 - - - +
564A VAL 2.9 0.2 + - - -
565A PHE* 1.3 84.3 - + + +
567A LYS* 1.3 74.6 + - - +
568A ARG 2.6 2.3 + - - -
569A ALA* 5.1 0.2 - - - -
570A ALA* 2.5 50.4 + - + +
599A LEU* 5.5 4.5 - - + -
602A CYS* 3.7 22.4 - - + -
603A TYR* 4.3 28.5 - + - -
607A MET* 3.4 37.9 - - + -
608A THR* 3.8 25.6 - - - -
609A LEU* 4.1 20.9 - - + -
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Residues in contact with LYS 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A TYR* 3.4 27.8 - - + +
563A LYS 3.3 3.5 + - - +
564A VAL* 3.1 11.4 + - + +
566A PHE* 1.3 81.7 - - - +
568A ARG* 1.3 69.3 + - + +
570A ALA* 3.4 14.9 - - - +
571A GLU* 3.9 5.3 + - - +
609A LEU* 3.7 24.3 - - + +
4C G 3.1 35.9 - - + +
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Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A VAL* 3.0 45.3 + - + +
565A PHE* 3.6 9.5 - - - +
566A PHE 2.6 4.4 + - - -
567A LYS* 1.3 81.6 - - + +
569A ALA* 1.3 64.7 + - - +
571A GLU 3.5 14.2 - - - +
572A GLY 4.3 0.2 + - - -
574A GLN* 4.3 5.7 + - - +
576A TYR* 5.8 1.6 - - - +
6C A 4.7 3.2 - - - +
7C C 6.0 0.2 - - - +
28D A 6.3 0.4 - - - -
29D T 3.4 41.8 + - - +
30D G 3.1 44.3 + - - -
31D T 4.5 0.8 + - - -
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Residues in contact with ALA 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A PHE* 3.6 12.3 - - + +
566A PHE 2.9 2.8 + - - -
568A ARG* 1.3 76.5 - - - +
570A ALA* 1.3 70.5 + - - +
571A GLU 3.0 1.4 + - - -
572A GLY 3.2 17.2 + - - +
574A GLN* 3.3 30.5 + - + +
576A TYR* 3.6 27.1 + - + +
599A LEU* 3.8 16.8 - - + +
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Residues in contact with ALA 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A PHE* 2.5 53.3 + - + +
567A LYS* 3.4 10.1 - - - +
569A ALA* 1.3 73.9 - - - +
571A GLU* 1.3 65.9 + - - +
572A GLY 3.7 2.3 + - - +
599A LEU* 4.2 9.0 - - - +
603A TYR* 3.2 24.5 + - - +
609A LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A LYS* 3.9 3.8 + - - +
568A ARG 3.5 9.9 + - - +
569A ALA 3.3 1.5 - - - -
570A ALA* 1.3 84.7 - - - +
572A GLY* 1.3 59.1 + - - +
603A TYR* 5.4 0.6 + - - -
609A LEU* 4.2 17.7 - - + -
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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
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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