Contacts of the helix formed by residues 583 - 588 (chain A) in PDB entry 1L8A
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 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A GLN* 4.8 2.3 + - - -
579A LEU* 2.7 27.6 + - + +
580A ALA* 3.5 6.7 + - - -
582A ALA* 1.3 82.9 - - - +
584A SER* 1.3 59.7 + - - +
585A TYR* 3.2 9.0 - - + -
586A SER* 3.2 8.0 + - - -
587A THR* 3.0 34.2 + - - -
617A GLN* 3.1 52.0 + - - +
618A GLN 4.2 1.3 - - - +
619A ALA* 3.7 13.7 - - - -
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Residues in contact with SER 584 (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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207A PHE* 3.9 8.2 - - - -
211A LEU* 4.0 4.3 - - - +
580A ALA 3.2 12.5 + - - -
581A ALA 3.3 15.6 + - - -
583A THR* 1.3 76.0 - - - +
585A TYR* 1.3 65.2 + - - +
587A THR* 4.5 1.6 - - - +
588A ASN* 3.0 45.2 + - - +
590A LEU* 2.8 28.1 + - - +
592A MET* 3.5 15.9 - - - +
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Residues in contact with TYR 585 (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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465A ARG* 3.5 4.8 + - - -
466A GLN* 4.8 0.7 + - - -
467A PRO 3.1 25.4 - - - -
468A ASN 4.5 0.5 - - - -
469A PHE* 3.4 39.8 - + + +
582A ALA 3.3 27.8 - - - -
583A THR* 4.0 7.2 - - - -
584A SER* 1.3 79.2 - - - +
586A SER* 1.3 68.4 + - - +
589A ASN* 3.1 21.0 - - - -
590A LEU 3.4 1.2 + - - -
591A PRO* 3.7 25.6 - - + +
592A MET 4.6 0.8 - - - +
618A GLN* 2.6 33.2 + - - +
620A ARG* 3.3 32.8 - - + -
678A TYR* 3.8 11.4 - - + -
684A ASN* 3.1 14.2 + - - -
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Residues in contact with SER 586 (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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128A ARG* 5.3 3.6 + - - -
188A GLN* 5.5 0.9 + - - +
465A ARG* 3.4 31.3 + - - +
466A GLN* 2.7 43.5 + - - +
468A ASN 5.5 0.2 - - - -
583A THR* 3.2 8.6 + - - -
585A TYR* 1.3 99.8 - - - +
587A THR* 1.3 67.6 + - - +
588A ASN 3.3 0.9 + - - -
589A ASN* 3.5 6.6 + - - -
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Residues in contact with THR 587 (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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128A ARG* 5.0 4.7 - - - -
133A GLY* 3.3 21.7 - - - +
136A LEU* 3.5 42.4 - - + -
188A GLN* 4.5 14.1 + - - +
189A PHE* 4.1 20.9 - - + -
204A GLN* 4.6 5.0 + - - +
583A THR* 3.0 22.5 + - - -
584A SER* 4.5 0.4 - - - -
586A SER* 1.3 81.9 + - - +
588A ASN* 1.3 69.9 + - - +
617A GLN* 5.3 0.2 + - - -
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Residues in contact with ASN 588 (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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132A ASP 5.7 0.4 - - - -
133A GLY* 4.6 7.4 + - - +
204A GLN* 5.0 3.6 - - - +
207A PHE* 5.0 1.4 - - - -
208A LEU* 3.8 14.5 - - - +
211A LEU* 3.8 16.4 - - + +
217A LYS* 3.3 38.7 + - + -
222A GLN* 3.7 21.7 + - - +
584A SER* 3.0 37.0 + - - +
587A THR* 1.3 90.8 - - - +
589A ASN* 1.3 71.9 + - - +
590A LEU* 3.1 4.7 + - + +
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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