Contacts of the helix formed by residues 198 - 204 (chain A) in PDB entry 1R4L
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 ASP 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A ASN* 3.4 6.5 - - - +
191A ALA* 3.2 14.8 - - - +
192A ARG* 3.5 11.9 - - - -
196A TYR* 3.2 5.5 - - - +
197A GLU* 1.3 85.8 - - - +
199A TYR* 1.3 63.0 + - - +
200A GLY* 2.7 11.6 + - - -
201A ASP* 2.5 37.2 + - - +
202A TYR 3.3 11.4 + - - -
204A ARG* 4.3 0.9 + - - -
461A TRP 5.3 0.2 - - - -
464A PHE* 3.4 21.1 - - - +
465A LYS* 3.2 41.9 - - - -
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Residues in contact with TYR 199 (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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183A TYR* 3.6 12.3 - - - -
187A LYS* 3.3 53.5 + - + +
188A ASN* 3.2 12.6 + - - +
190A MET* 4.2 7.2 - - + -
191A ALA* 3.4 11.1 - - + +
198A ASP* 1.3 73.4 - - - +
200A GLY* 1.3 58.3 + - - +
202A TYR* 2.7 58.3 + + + +
203A TRP* 2.9 48.0 + + - +
464A PHE* 3.2 32.3 - + + -
509A ASP* 3.4 10.6 + - - +
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Residues in contact with GLY 200 (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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198A ASP* 2.7 12.5 + - - -
199A TYR* 1.3 71.8 - - - +
201A ASP* 1.3 61.3 + - - -
202A TYR 3.0 0.2 + - - -
203A TRP* 3.1 8.8 + - - +
204A ARG* 2.9 32.7 + - - +
461A TRP* 3.9 18.9 + - - -
464A PHE* 3.2 23.5 - - - -
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Residues in contact with ASP 201 (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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196A TYR* 3.2 7.7 - - - +
197A GLU* 2.8 44.8 + - + +
198A ASP* 2.5 24.6 + - - +
200A GLY* 1.3 70.8 - - - -
202A TYR* 1.3 59.2 + - - +
204A ARG* 3.2 24.1 + - - +
205A GLY 3.3 2.8 + - - -
219A ARG* 2.6 77.5 + - - +
220A GLY 5.4 0.2 + - - -
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Residues in contact with TYR 202 (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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102A GLN* 5.6 3.4 - - - -
190A MET* 5.0 14.9 - - + +
191A ALA* 4.6 5.6 - - + -
194A ASN* 6.1 2.2 - - + -
196A TYR* 3.5 42.8 - + + -
198A ASP 3.3 7.4 + - - +
199A TYR* 2.7 46.5 + + + +
201A ASP* 1.3 75.1 - - - +
203A TRP* 1.3 61.8 + + - -
204A ARG 2.9 4.0 - - - -
205A GLY* 2.4 31.2 + - - -
206A ASP 3.8 1.6 + - - -
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Residues in contact with TRP 203 (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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183A TYR* 4.0 10.8 - - - -
199A TYR* 2.9 59.2 + + - +
200A GLY* 3.9 7.9 - - - +
202A TYR* 1.3 82.4 - + - +
204A ARG* 1.3 59.1 + - - +
205A GLY 2.9 1.6 + - - -
206A ASP* 3.7 18.8 + - - +
207A TYR* 4.5 4.7 - - - -
398A GLU* 4.4 7.2 - - - +
457A GLU* 3.8 16.6 - - - +
460A ARG* 3.3 55.2 - - + -
461A TRP* 5.4 4.5 - + - +
464A PHE* 3.9 15.0 - + - -
509A ASP* 4.1 17.7 - - - +
510A TYR 4.1 1.4 - - - +
511A SER* 3.8 26.8 - - - +
513A ILE* 5.6 2.5 - - + +
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Residues in contact with ARG 204 (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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197A GLU* 4.7 6.1 + - - -
198A ASP* 4.5 0.2 + - - -
200A GLY* 2.9 15.1 + - - +
201A ASP* 3.2 43.0 + - - +
202A TYR 2.9 0.4 + - - -
203A TRP* 1.3 75.0 - - - +
205A GLY* 1.3 68.4 + - - +
207A TYR* 3.4 16.8 + - - +
208A GLU 3.9 0.5 + - - -
219A ARG* 3.7 34.6 + - + +
220A GLY* 4.8 2.2 - - - +
222A LEU* 3.9 22.9 - - + +
223A ILE* 3.4 30.4 - - - +
461A TRP* 3.2 48.0 - - + +
465A LYS* 3.3 32.8 - - - +
513A ILE* 6.4 0.7 - - + -
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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