Contacts of the helix formed by residues 588 - 594 (chain A) in PDB entry 1E7U
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 ALA 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A ILE* 3.4 42.8 - - + +
575A LEU* 6.1 0.7 - - + -
582A SER* 3.7 16.6 - - - +
585A ASP* 2.8 15.8 + - + +
587A LYS* 1.3 77.3 - - - +
589A TYR* 1.3 61.3 + - - +
590A PRO 3.4 1.8 - - - -
591A LYS* 3.3 7.6 + - - +
592A LEU* 2.8 29.8 + - + +
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Residues in contact with TYR 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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582A SER 4.8 1.1 - - - -
583A LEU* 2.9 60.9 + - + +
585A ASP 3.4 5.2 - - - -
586A PRO* 2.9 36.0 + - + +
588A ALA* 1.3 77.1 - - - +
590A PRO* 1.3 67.2 - - + +
592A LEU* 4.2 3.6 - - + -
593A PHE* 2.9 56.3 + + + -
611A LEU* 5.0 3.4 - - + -
614A ARG* 5.0 3.1 - - - +
616A VAL* 4.6 0.9 - - - +
617A TRP* 3.5 56.0 + + + +
630A LEU* 4.3 8.1 - - + -
643A ILE* 4.3 10.8 - - + -
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Residues in contact with PRO 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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587A LYS 3.8 11.4 - - - +
588A ALA 3.6 2.9 - - - -
589A TYR* 1.3 94.0 - - + +
591A LYS* 1.3 63.8 + - + +
594A SER* 3.1 25.2 + - - -
626A LEU* 3.8 19.7 - - + -
629A GLN* 3.7 33.0 - - + +
630A LEU* 3.8 15.7 - - + -
635A PHE* 3.3 21.6 - - + -
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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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558A ILE* 4.0 15.8 + - + +
559A ILE* 4.1 12.3 + - + +
561A THR* 3.1 28.7 + - - -
562A ASP 3.4 18.7 + - - -
563A PRO* 4.4 8.6 - - - +
565A ASN* 4.0 11.4 - - - +
567A LEU* 3.5 31.1 - - + +
575A LEU* 3.4 18.4 - - + -
587A LYS 5.3 3.2 + - - +
588A ALA* 3.3 11.1 + - + +
590A PRO* 1.3 83.3 - - + +
592A LEU* 1.3 56.1 + - - +
594A SER* 2.6 22.4 + - - +
595A SER* 2.7 20.6 + - - -
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Residues in contact with LEU 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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575A LEU* 3.5 37.2 - - + +
576A TRP* 4.6 7.4 - - + -
579A ARG* 4.2 24.0 - - + +
582A SER* 4.1 22.0 - - - +
583A LEU* 4.3 12.1 - - + +
588A ALA 2.8 22.2 + - - +
589A TYR* 3.6 6.7 - - + +
591A LYS* 1.3 72.9 - - - +
593A PHE* 1.3 78.5 + - + +
595A SER* 2.9 24.1 + - - -
596A VAL* 3.6 7.0 + - + +
610A LEU* 4.3 15.9 - - + -
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Residues in contact with PHE 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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583A LEU* 5.0 4.5 - - + -
589A TYR* 2.9 66.1 + + + +
592A LEU* 1.3 87.2 - - + +
594A SER* 1.3 55.9 + - - +
595A SER 3.1 1.9 + - - -
596A VAL* 3.7 9.7 - - + +
598A TRP* 3.0 33.1 + + + -
607A THR* 3.9 20.2 - - + -
610A LEU* 5.0 7.2 - - + -
611A LEU* 3.5 44.0 - - + -
630A LEU* 5.0 1.3 - - + -
635A PHE* 3.6 23.4 - - + -
640A VAL* 3.7 22.9 - - + -
643A ILE* 4.8 3.6 - - + -
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Residues in contact with SER 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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392A GLN* 5.6 1.7 - - - +
567A LEU* 3.4 11.6 - - - +
572A LYS* 3.7 22.6 + - - -
590A PRO 3.1 13.8 + - - -
591A LYS* 2.6 25.0 + - - +
592A LEU 3.0 0.4 - - - -
593A PHE* 1.3 76.4 - - - +
595A SER* 1.3 56.1 + - - +
596A VAL 3.4 5.9 - - - +
598A TRP* 5.0 1.6 - - - +
634A ASN* 5.9 6.1 - - - -
635A PHE* 4.4 10.8 - - - -
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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