Contacts of the helix formed by residues 131 - 136 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 1.3 73.5 - - - +
132B ASP* 1.3 79.2 + - - +
133B THR* 2.6 27.7 + - - -
134B PHE* 2.6 16.8 + - - +
135B TYR* 4.2 2.0 - - - -
157B MET* 4.1 7.4 - - - -
128D GLN 3.4 5.0 + - - +
129D ASP 3.0 8.4 + - - +
130D PHE 2.7 37.4 + - - -
131D ASN* 3.5 17.6 - - + +
153D TRP* 5.2 2.8 - - - -
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Residues in contact with ASP 132 (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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131B ASN* 1.3 79.0 - - - +
133B THR* 1.3 76.3 + - - -
134B PHE 2.8 1.6 + - - -
135B TYR* 2.9 13.9 + - - +
136B ARG* 2.9 32.9 + - - +
157B MET* 3.4 26.4 - - + +
160B SER* 5.2 1.8 - - - +
161B LEU* 3.6 22.4 - - + -
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Residues in contact with THR 133 (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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131B ASN* 2.6 21.3 + - - -
132B ASP* 1.3 82.4 + - - +
134B PHE* 1.3 62.6 + - - +
136B ARG* 3.7 21.1 + - - +
137B GLN* 4.1 6.6 + - - +
126D LYS* 4.5 16.4 - - - +
128D GLN* 3.7 19.4 + - + +
129D ASP* 3.7 12.3 - - - +
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Residues in contact with PHE 134 (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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76B HIS* 4.9 0.7 - + - -
78B ILE* 3.6 20.9 - - + -
123B HIS* 4.0 21.1 - + - -
130B PHE* 3.1 52.9 - + + -
131B ASN 2.6 16.2 + - - +
133B THR* 1.3 75.1 - - - +
135B TYR* 1.3 70.4 + + - +
137B GLN* 2.9 49.5 - - - +
138B PHE* 3.7 23.9 - + - -
125D ASN* 3.8 15.5 - - - -
129D ASP* 4.0 25.8 + - + +
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Residues in contact with TYR 135 (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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52B LEU* 3.7 31.6 - - + -
54B ILE* 4.5 9.9 - - + -
78B ILE* 4.2 1.9 - - + +
127B ILE* 2.5 41.3 + - - +
130B PHE* 3.5 29.0 - - + -
131B ASN 4.1 6.1 - - - -
132B ASP 2.9 7.4 + - - +
134B PHE* 1.3 79.7 - + - +
136B ARG* 1.3 64.1 + - - +
137B GLN 2.9 7.2 + - - -
138B PHE* 3.2 22.6 + - - +
141B ILE* 4.2 18.0 - - + +
153B TRP* 3.6 7.0 - + - -
154B ILE* 4.5 6.1 - - + -
157B MET* 3.5 35.2 - - + -
158B LEU* 4.9 1.6 - - + -
161B LEU* 4.2 15.0 - - + +
175B VAL* 5.0 1.4 - - - +
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Residues in contact with ARG 136 (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* 2.9 38.8 + - - +
133B THR* 3.8 11.6 - - - +
134B PHE 3.3 0.2 - - - -
135B TYR* 1.3 76.2 - - - +
137B GLN* 1.3 63.1 + - - +
138B PHE 3.4 7.8 + - - +
160B SER 4.4 4.8 + - - -
161B LEU* 3.8 55.6 + - + +
173B SER* 6.3 0.2 - - - +
175B VAL* 5.3 2.9 - - - +
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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