Contacts of the helix formed by residues 203 - 207 (chain H) in PDB entry 1R4N
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 203 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H ARG* 2.5 35.5 + - - -
198H ALA* 4.7 8.5 - - + -
199H CYS 3.4 6.5 + - - -
200H ILE 3.6 3.2 - - - +
202H CYS* 1.3 76.0 - - + +
204H LEU* 1.3 62.3 + - - +
205H GLU 3.2 3.8 + - - -
206H LEU* 3.4 34.6 + - + +
207H TYR* 4.6 5.4 - - - -
321H TYR* 4.7 2.5 - - + -
337H ALA* 3.5 31.6 - - + -
338H GLU 4.8 3.8 - - - +
149L GLN* 4.1 16.4 - - - +
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Residues in contact with LEU 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H ILE* 4.6 7.6 - - + -
152H ARG* 4.1 21.8 - - + +
200H ILE* 3.4 10.2 + - + +
201H GLU* 3.3 37.9 - - - +
202H CYS 2.8 5.0 + - - +
203H THR* 1.3 77.5 - - - +
205H GLU* 1.3 61.2 + - + +
206H LEU 3.2 1.8 + - - -
207H TYR* 3.6 28.8 + - + +
372H ALA 4.9 1.3 - - - +
373H SER* 4.2 18.6 - - - +
374H LEU 4.1 18.8 - - - +
375H GLN* 3.8 26.9 + - - +
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Residues in contact with GLU 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H CYS 4.6 0.8 + - - +
203H THR* 3.2 1.4 - - - +
204H LEU* 1.3 77.1 - - + +
206H LEU* 1.3 61.3 + - - +
207H TYR 3.0 11.8 + - - +
340H LYS* 3.4 25.5 + - - +
372H ALA* 3.2 44.7 - - + +
373H SER* 4.5 4.1 - - - -
375H GLN* 5.0 4.5 - - - +
142L ARG* 3.2 30.7 + - - +
149L GLN* 4.3 13.9 + - - +
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Residues in contact with LEU 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H ARG* 5.5 0.2 - - - +
203H THR* 3.6 30.1 - - + +
204H LEU 3.2 2.0 - - - -
205H GLU* 1.3 78.0 - - - +
207H TYR* 1.3 61.0 + - - +
208H PRO 3.7 1.0 - - - -
321H TYR* 3.6 35.9 - - + +
335H PHE* 4.1 12.8 - - + -
142L ARG* 4.0 17.9 - - + +
144L ILE* 4.3 6.7 - - + -
149L GLN* 3.7 24.9 + - + +
170L VAL* 3.8 22.9 - - + -
171L LEU* 3.8 9.7 - - - +
172L ALA* 3.1 33.0 + - + +
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Residues in contact with TYR 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H ILE* 3.9 46.0 - - + -
151H ARG* 3.5 24.7 + - - -
179H ASP* 4.5 0.5 + - - -
188H ASN* 4.8 1.2 + - - -
190H ARG* 3.0 27.2 + - - -
200H ILE* 5.1 8.0 - - + +
203H THR 4.6 6.5 - - - -
204H LEU* 3.6 27.8 - - + +
205H GLU* 3.0 12.9 - - - +
206H LEU* 1.3 79.2 - - - +
208H PRO* 1.3 76.2 - - + +
375H GLN* 6.3 0.2 - - - +
142L ARG* 3.5 8.0 + - - -
172L ALA* 3.5 27.6 - - + -
173L LEU 3.3 27.1 + - - -
174L ARG* 4.2 5.2 - - + -
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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