Contacts of the helix formed by residues 564 - 577 (chain A) in PDB entry 5I4E
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 THR 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A LYS 3.8 10.0 + - - +
563A ALA* 1.3 80.5 - - - +
565A ASP* 1.3 66.7 + - - +
566A LYS* 3.8 10.5 + - - +
567A SER* 2.6 42.6 + - - -
568A PHE* 3.1 5.7 + - - +
611A LEU* 3.6 9.9 - - - +
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Residues in contact with ASP 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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564A THR* 1.3 73.1 - - - +
566A LYS* 1.4 55.6 + - - +
568A PHE* 3.3 8.9 + - - +
569A VAL* 3.2 32.3 + - + +
607A ALA* 3.4 22.6 - - + +
608A ASN* 4.3 2.8 - - - +
609A GLU* 3.1 22.0 + - - +
610A TRP* 3.3 4.5 + - - +
611A LEU* 3.3 37.2 + - - +
612A MET* 5.9 0.3 - - - +
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Residues in contact with LYS 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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564A THR* 3.0 10.2 + - - +
565A ASP* 1.4 74.6 - - - +
567A SER* 1.4 59.8 + - - +
569A VAL* 3.3 11.2 + - + +
570A GLU* 2.9 61.3 + - + +
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Residues in contact with SER 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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557A GLU* 2.5 26.8 + - - +
562A LYS 5.5 1.3 - - - -
563A ALA* 3.7 2.7 - - - -
564A THR* 2.6 34.5 + - - -
566A LYS* 1.4 73.8 - - - +
568A PHE* 1.4 58.9 + - - +
570A GLU* 3.6 19.1 - - - +
571A LYS* 3.0 28.2 + - - +
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Residues in contact with PHE 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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550A LEU* 4.0 8.7 - - + -
553A LEU 4.2 5.6 - - - -
554A LEU* 3.5 52.0 - - + -
557A GLU* 3.5 22.9 - - + -
564A THR 3.1 7.5 + - - +
565A ASP* 3.4 12.6 - - - +
566A LYS 3.2 0.2 - - - -
567A SER* 1.4 75.3 + - - +
569A VAL* 1.4 57.5 + - + +
571A LYS* 3.1 5.2 + - + +
572A VAL* 2.8 70.6 + - + +
594A PHE* 4.3 9.4 - + - -
607A ALA* 4.1 15.9 - - + -
610A TRP* 3.7 34.3 - + + -
611A LEU* 4.0 6.5 - - + -
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Residues in contact with VAL 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 ASP 3.2 15.6 + - - +
566A LYS* 3.3 13.0 + - + +
568A PHE* 1.4 79.2 - - + +
570A GLU* 1.4 55.5 + - + +
572A VAL* 3.6 4.0 + - - +
573A ALA* 3.0 31.5 + - + +
582A PHE* 5.8 0.3 - - - -
585A PRO* 5.9 1.1 - - + -
593A ASP* 2.8 58.3 - - + +
594A PHE* 5.1 5.1 - - + -
607A ALA* 3.7 11.7 - - + -
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Residues in contact with GLU 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 LYS* 2.9 44.4 + - + +
567A SER* 3.6 21.0 + - - +
569A VAL* 1.4 73.8 - - + +
571A LYS* 1.3 58.0 + - - +
573A ALA* 3.5 5.2 + - - +
574A GLN* 3.1 31.5 + - - +
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Residues in contact with LYS 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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553A LEU* 4.2 26.5 - - + +
556A GLU* 5.2 8.7 - - - -
557A GLU* 4.1 18.2 - - - +
567A SER 3.0 18.8 + - - +
568A PHE* 3.1 8.5 + - + +
570A GLU* 1.3 74.0 - - - +
572A VAL* 1.3 57.5 + - + +
574A GLN* 3.4 10.1 + - - +
575A GLU* 2.8 55.0 + - + +
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Residues in contact with VAL 572 (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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550A LEU* 3.2 32.8 - - + -
553A LEU* 4.1 23.3 - - + -
568A PHE* 2.8 55.0 + - + +
569A VAL* 4.1 4.7 - - - +
571A LYS* 1.3 74.6 - - + +
573A ALA* 1.3 60.3 + - - +
575A GLU 4.6 0.2 - - - +
576A GLN* 3.1 28.4 + - + +
582A PHE* 3.5 18.2 - - + -
594A PHE* 4.8 8.3 - - + -
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Residues in contact with ALA 573 (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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569A VAL* 3.0 21.3 + - + +
570A GLU* 3.9 5.8 - - - +
572A VAL* 1.3 76.4 - - - +
574A GLN* 1.3 59.5 + - - +
577A GLY* 3.3 22.9 + - - -
582A PHE* 4.1 12.3 - - + -
584A ARG* 3.5 30.6 + - + -
585A PRO* 5.5 6.5 - - + -
593A ASP 5.8 1.1 - - - +
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Residues in contact with GLN 574 (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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570A GLU 3.1 18.6 + - - +
571A LYS* 3.5 10.3 - - - +
573A ALA* 1.3 79.0 - - - +
575A GLU* 1.3 81.6 + - - +
577A GLY* 4.2 2.9 + - - -
578A GLY 5.5 0.3 + - - -
584A ARG* 5.1 2.4 + - - +
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Residues in contact with GLU 575 (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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548A PRO* 5.4 8.0 - - + +
553A LEU* 4.1 24.1 - - + +
571A LYS* 2.8 42.8 + - + +
574A GLN* 1.3 99.4 + - + +
576A GLN* 1.3 64.2 + - + +
577A GLY 3.6 0.2 - - - -
578A GLY 5.1 1.4 + - - -
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Residues in contact with GLN 576 (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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540A LEU* 3.1 24.2 - - + +
547A PRO* 5.0 7.9 + - - +
548A PRO* 2.9 31.1 + - - +
549A GLY* 4.1 4.0 - - - -
550A LEU* 3.9 20.2 - - + -
553A LEU* 3.9 14.5 - - + +
572A VAL 3.1 14.3 + - - +
575A GLU* 1.3 81.4 + - - +
577A GLY* 1.3 65.2 + - - +
578A GLY 3.1 3.4 - - - -
579A HIS* 3.0 26.2 + - - +
582A PHE* 3.3 31.1 - - + +
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Residues in contact with GLY 577 (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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572A VAL 3.8 1.0 + - - -
573A ALA 3.3 22.8 + - - -
574A GLN 4.2 1.7 + - - -
575A GLU 3.6 1.8 - - - -
576A GLN* 1.3 76.5 - - - +
578A GLY* 1.3 57.1 + - - +
579A HIS 3.7 1.0 + - - +
582A PHE* 3.9 21.6 - - - +
583A GLN* 5.3 0.2 - - - -
584A ARG* 3.4 33.4 + - - +
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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