Contacts of the helix formed by residues 583 - 588 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLN* 5.0 2.3 + - - -
465B ARG* 6.3 0.2 - - - -
579B LEU* 2.7 25.1 + - + +
580B ALA* 3.6 6.3 + - - -
581B ALA 3.1 0.2 - - - -
582B ALA* 1.3 82.2 - - - +
584B SER* 1.3 64.6 + - - +
585B TYR* 3.1 10.5 - - + -
586B SER* 3.1 7.3 + - - -
587B THR* 3.1 29.4 + - - -
617B GLN* 3.2 52.3 + - + +
618B GLN 4.1 1.8 - - - +
619B ALA* 3.7 14.6 - - - -
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Residues in contact with SER 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B PHE* 3.9 7.0 - - - -
211B LEU* 4.0 1.9 - - - +
580B ALA 3.2 11.6 + - - -
581B ALA 3.2 14.9 + - - -
583B THR* 1.3 78.4 - - - +
585B TYR* 1.3 61.9 + - - +
587B THR* 4.0 1.6 - - - +
588B ASN* 3.0 44.2 + - - +
590B LEU* 2.7 33.5 + - - +
592B MET* 3.6 15.8 - - - +
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Residues in contact with TYR 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ARG* 3.4 7.6 + - - -
466B GLN* 3.1 18.9 + - - -
467B PRO 3.3 24.7 - - - -
469B PHE* 3.4 35.4 - + + +
581B ALA 4.7 0.2 + - - -
582B ALA 3.2 27.8 - - - -
583B THR* 3.1 9.1 - - + -
584B SER* 1.3 78.8 - - - +
586B SER* 1.3 67.2 + - - +
589B ASN* 3.2 8.3 - - - -
590B LEU 3.6 1.2 + - - -
591B PRO* 3.7 24.9 - - + +
592B MET 4.6 0.8 - - - +
618B GLN* 2.6 34.3 + - - +
620B ARG* 3.4 30.7 - - + -
678B TYR* 3.8 11.7 - + + -
684B ASN* 3.3 13.7 + - - -
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 5.0 4.0 - - - -
188B GLN* 5.5 0.9 + - - +
465B ARG* 3.4 30.9 + - - +
466B GLN* 2.7 48.3 + - - +
583B THR* 3.1 8.2 + - - -
584B SER 3.1 0.2 - - - -
585B TYR* 1.3 101.4 - - - +
587B THR* 1.3 68.0 + - - +
588B ASN 3.4 0.6 + - - -
589B ASN 3.8 0.7 + - - -
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Residues in contact with THR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 4.9 4.5 - - - -
133B GLY* 3.3 22.2 - - - +
136B LEU* 3.4 39.7 - - + -
188B GLN* 4.5 12.4 + - - +
189B PHE* 4.1 20.1 - - + -
204B GLN* 4.6 6.0 + - - +
580B ALA 6.0 0.2 - - - -
583B THR* 3.1 21.7 + - - -
584B SER* 4.5 0.9 - - - -
586B SER* 1.3 81.6 + - - +
588B ASN* 1.3 74.7 + - - +
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Residues in contact with ASN 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASP* 5.7 0.4 - - - -
133B GLY* 4.6 4.9 + - - +
204B GLN* 4.9 4.8 - - - +
207B PHE* 4.9 1.4 - - - -
208B LEU* 3.7 16.4 - - - +
211B LEU* 3.8 13.6 - - + +
217B LYS* 3.5 41.4 + - + +
222B GLN* 3.6 20.0 + - - +
584B SER* 3.0 37.1 + - - +
587B THR* 1.3 92.9 - - - +
589B ASN* 1.3 72.6 + - - +
590B LEU* 3.0 4.0 + - + +
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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