Contacts of the helix formed by residues 588 - 598 (chain A) in PDB entry 5ID6
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 GLY 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A LEU 3.7 0.6 + - - -
587A PRO* 1.3 74.8 - - - +
589A PRO* 1.3 75.3 - - - +
590A ASN* 3.2 13.3 + - - -
591A LYS* 3.2 7.1 + - - +
592A MSE 3.0 17.8 + - - +
674A GLU* 5.0 6.8 + - - +
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Residues in contact with PRO 589 (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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586A LEU* 4.3 9.0 - - + +
587A PRO 3.7 2.6 - - - +
588A GLY* 1.3 87.8 - - - +
590A ASN* 1.3 63.2 + - - +
592A MSE 4.4 2.0 - - + +
593A LEU* 2.7 45.1 + - + +
670A TYR* 3.8 19.2 - - + +
673A VAL* 3.7 24.9 - - + -
674A GLU* 3.6 50.7 - - + +
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Residues in contact with ASN 590 (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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588A GLY* 3.9 12.5 - - - -
589A PRO* 1.3 83.2 - - - +
591A LYS* 1.3 90.5 + - - +
594A PRO* 3.3 18.0 - - - +
670A TYR* 3.6 40.4 + - + +
674A GLU* 5.6 1.2 - - - +
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Residues in contact with LYS 591 (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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588A GLY* 3.2 8.3 + - - +
589A PRO 3.2 0.2 - - - -
590A ASN* 1.3 97.1 - - - +
592A MSE 1.3 61.9 + - + +
593A LEU 3.7 0.4 - - - -
594A PRO* 3.4 11.4 - - - +
595A LYS* 3.3 32.8 - - - +
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Residues in contact with MSE 592 (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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586A LEU* 3.7 15.9 - - + -
587A PRO* 3.6 26.5 - - + +
588A GLY 3.0 15.4 + - - +
589A PRO* 4.2 2.0 - - + +
591A LYS* 1.3 81.1 - - + +
593A LEU* 1.3 67.4 + - - +
594A PRO 3.4 0.4 - - - -
595A LYS* 3.7 23.1 - - - +
596A VAL* 3.1 39.9 + - + +
649A TRP* 3.5 31.0 - - + +
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Residues in contact with LEU 593 (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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586A LEU* 4.4 5.4 - - + -
589A PRO* 2.7 33.1 + - + +
592A MSE 1.3 73.8 - - - +
594A PRO* 1.3 61.4 - - + +
596A VAL* 4.0 0.2 - - - +
597A PHE* 3.0 39.5 + - + +
639A PHE* 4.0 22.9 - - + -
643A ILE* 4.4 9.0 - - + -
649A TRP* 3.5 33.0 - - + -
669A PHE* 4.0 26.5 - - + -
670A TYR* 4.4 10.3 - - + -
673A VAL* 4.2 24.0 - - + -
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Residues in contact with PRO 594 (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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589A PRO 3.6 1.1 - - - +
590A ASN 3.3 26.9 - - - +
591A LYS* 3.4 10.5 - - - +
593A LEU* 1.3 95.7 - - + +
595A LYS* 1.3 59.0 + - - +
596A VAL 3.3 0.2 - - - -
598A PHE* 3.3 41.9 + - + +
616A TYR* 3.6 39.9 - - + +
639A PHE* 4.3 6.5 - - + -
670A TYR* 4.3 10.5 - - - +
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Residues in contact with LYS 595 (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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591A LYS* 3.3 29.2 + - - +
592A MSE 3.4 28.3 + - - +
593A LEU 3.2 1.0 - - - -
594A PRO* 1.3 79.3 - - - +
596A VAL* 1.3 61.7 + - - +
598A PHE 4.6 0.3 - - - -
599A SER* 3.6 17.3 - - - -
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Residues in contact with VAL 596 (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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592A MSE 3.1 30.5 + - + +
593A LEU 4.0 2.2 - - - +
595A LYS* 1.3 79.4 - - + +
597A PHE* 1.3 82.2 + - + +
598A PHE 3.2 1.7 + - - -
599A SER* 2.4 32.6 + - - +
602A TRP* 3.5 5.3 - - + +
646A TYR* 4.0 27.1 - - + +
649A TRP* 3.7 22.2 - - + -
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Residues in contact with PHE 597 (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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593A LEU* 3.0 24.2 + - + +
596A VAL* 1.3 96.1 - - + +
598A PHE* 1.3 67.2 + - - +
599A SER 3.6 1.1 - - - -
602A TRP* 3.1 56.1 - + + +
603A MSE 4.0 5.0 - - - +
638A PHE* 3.7 18.2 - - + -
639A PHE* 3.8 17.7 - + + -
642A SER* 3.6 29.8 - - - -
643A ILE* 4.1 14.1 - - + -
646A TYR* 3.9 14.8 - + + -
649A TRP* 3.7 31.2 - + - -
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Residues in contact with PHE 598 (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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594A PRO* 3.3 37.8 + - + +
595A LYS 4.6 0.9 - - - -
596A VAL 3.2 0.8 - - - -
597A PHE* 1.3 83.0 - - - +
599A SER* 1.3 58.2 - - - +
600A LYS 3.4 3.6 + - - -
603A MSE 3.9 31.8 - - + +
608A PRO* 5.0 1.1 - - + -
612A ILE* 3.6 28.0 - - + -
613A GLN* 4.6 13.9 - - + -
616A TYR* 3.7 45.3 - + + -
635A LEU* 4.2 5.2 - - + -
638A PHE* 3.7 22.0 - + - -
639A PHE* 4.3 12.1 - + - -
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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