Contacts of the helix formed by residues 131 - 136 (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 ASN 131 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLN 3.5 7.0 + - - +
129F ASP 3.1 6.2 + - - +
130F PHE 2.8 36.4 + - - -
131F ASN* 3.6 18.2 - - + +
153F TRP* 5.3 2.8 - - - -
130H PHE* 1.3 74.5 - - - +
132H ASP* 1.3 78.4 + - - +
133H THR* 2.6 27.9 + - - -
134H PHE* 2.6 17.3 + - - +
135H TYR* 4.2 2.0 - - - -
157H MET* 4.0 7.0 - - - -
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Residues in contact with ASP 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ASN* 1.3 81.0 - - - +
133H THR* 1.3 75.6 + - - -
134H PHE 2.8 1.6 + - - -
135H TYR* 3.0 3.2 + - - +
136H ARG* 2.9 43.0 + - - +
157H MET* 3.4 32.8 - - + +
160H SER* 5.1 1.8 - - - +
161H LEU* 3.7 15.7 - - + -
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Residues in contact with THR 133 (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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126F LYS* 4.4 17.3 - - - +
128F GLN* 3.8 15.1 + - + +
129F ASP* 3.7 17.3 - - - +
131H ASN* 2.6 20.4 + - - -
132H ASP* 1.3 83.6 + - - +
134H PHE* 1.3 61.3 + - - +
136H ARG* 3.7 20.4 + - - +
137H GLN* 4.1 7.4 + - - +
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Residues in contact with PHE 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ASN* 3.8 15.9 - - - -
129F ASP* 3.9 25.8 - - - +
52H LEU* 5.0 0.2 - - + -
76H HIS* 4.9 0.4 - + - -
78H ILE* 3.7 20.9 - - + -
123H HIS* 4.1 20.9 - + - -
130H PHE* 3.1 54.5 - + + -
131H ASN 2.6 15.5 + - - +
133H THR* 1.3 72.3 - - - +
135H TYR* 1.3 73.1 + + - +
137H GLN* 2.9 48.2 - - - +
138H PHE* 3.7 22.7 - + - -
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Residues in contact with TYR 135 (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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52H LEU* 3.7 30.7 - - + -
54H ILE* 4.5 11.2 - - + -
78H ILE* 4.3 1.2 - - + +
127H ILE* 2.5 41.2 + - - +
130H PHE* 3.5 34.1 - - + -
131H ASN 4.1 5.8 - - - -
132H ASP 3.0 4.4 + - - +
134H PHE* 1.3 79.7 - + - +
136H ARG* 1.3 63.7 + - - +
137H GLN 2.8 7.0 + - - -
138H PHE* 3.2 22.8 + - - +
141H ILE* 4.2 17.3 - - + +
153H TRP* 3.6 7.9 - + - -
154H ILE* 4.5 6.3 - - + -
157H MET* 3.5 34.5 - - + -
158H LEU* 4.9 1.6 - - + -
161H LEU* 4.2 13.3 - - + +
175H VAL* 5.0 1.6 - - - +
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Residues in contact with ARG 136 (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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132H ASP* 2.9 39.1 + - - +
133H THR* 3.8 11.9 - - - +
134H PHE 3.3 0.4 - - - -
135H TYR* 1.3 76.3 - - - +
137H GLN* 1.3 62.8 + - - +
138H PHE 3.3 7.3 + - - +
160H SER 4.4 4.8 + - - -
161H LEU* 3.8 55.7 + - + +
173H SER* 6.3 0.2 - - - +
175H VAL* 5.4 3.3 - - - +
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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