Contacts of the helix formed by residues 133 - 142 (chain A) in PDB entry 2BPF
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLY* 5.3 0.7 - - - +
131A LYS 3.8 1.2 + - - -
132A LEU* 1.3 78.8 - - - +
134A HIS* 1.3 61.0 + - - +
135A HIS* 3.1 12.5 - - - +
136A GLN* 2.7 58.9 - - - +
137A ARG* 2.7 29.5 + - - +
10T C 4.3 31.8 - - - +
11T G 4.3 15.9 + - - +
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Residues in contact with HIS 134 (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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133A ASN* 1.3 75.0 - - - +
135A HIS* 1.3 64.1 + - + +
137A ARG* 2.8 50.8 + - - +
138A ILE* 2.9 38.2 + - + +
226A ASP* 5.8 1.1 - - + -
227A THR* 3.0 30.3 + - - -
228A LEU* 4.6 9.4 - - - -
10T C 4.3 13.9 + - - +
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Residues in contact with HIS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 3.3 40.9 + - + -
105A GLY* 3.7 9.0 - - - -
133A ASN* 3.1 11.9 - - - +
134A HIS* 1.3 83.2 - - + +
136A GLN* 1.3 63.0 + - - +
138A ILE* 2.8 17.6 + - - +
139A GLY 2.8 12.3 + - - -
228A LEU* 3.5 43.5 - - + +
236A MET* 4.9 9.6 - - + +
5P G 6.4 0.7 - - - -
6P C 4.3 15.8 - - - -
10T C 5.3 2.3 + - - +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 4.3 3.3 - - - +
104A THR 3.8 7.9 - - - -
105A GLY* 3.4 32.5 - - - +
106A ILE* 4.2 14.1 - - + -
110A ALA* 3.9 19.5 - - - +
114A LEU* 6.1 0.4 - - - +
131A LYS 4.4 2.8 + - - -
132A LEU* 3.4 27.3 - - + +
133A ASN* 2.7 61.8 - - - +
135A HIS* 1.3 74.5 - - - +
137A ARG* 1.3 54.2 + - - +
140A LEU* 2.6 40.3 + - - +
5P G 5.3 1.0 - - - +
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Residues in contact with ARG 137 (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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129A GLU* 4.0 35.4 + - + +
130A ASP* 5.6 2.6 + - - +
132A LEU* 2.9 34.8 + - + -
133A ASN* 2.7 15.7 + - - +
134A HIS* 2.8 49.7 + - - +
136A GLN* 1.3 77.3 - - - +
138A ILE* 1.3 56.5 + - + +
140A LEU* 3.3 5.5 + - - +
141A LYS* 2.6 35.7 + - - +
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Residues in contact with ILE 138 (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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134A HIS* 2.9 39.7 + - + +
135A HIS 2.8 8.3 + - - +
137A ARG* 1.3 80.5 - - + +
139A GLY* 1.4 59.9 + - - +
141A LYS* 2.7 30.6 + - + +
142A TYR* 2.9 40.9 + - + -
146A PHE* 4.3 4.7 - - + -
226A ASP* 4.0 17.3 - - + +
228A LEU* 4.0 20.6 - - + -
238A VAL* 4.1 14.6 - - + -
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Residues in contact with GLY 139 (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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103A VAL* 4.3 6.5 - - - -
104A THR* 3.0 39.1 + - - +
135A HIS 2.8 13.9 + - - -
136A GLN 3.6 2.2 - - - -
138A ILE* 1.4 71.0 - - - +
140A LEU* 1.3 63.5 + - - +
142A TYR 3.6 1.0 - - - -
143A PHE* 2.9 28.2 + - - +
146A PHE* 4.4 6.0 - - - -
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Residues in contact with LEU 140 (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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103A VAL* 4.1 12.2 - - + +
122A LEU* 4.5 12.6 - - + -
125A LEU* 3.5 34.8 - - + -
126A ARG* 3.1 48.3 + - + +
129A GLU* 5.4 8.7 - - - +
132A LEU* 3.9 15.5 - - + -
136A GLN 2.6 18.7 + - - +
137A ARG* 3.6 5.6 - - - +
139A GLY* 1.3 79.1 - - - +
141A LYS* 1.3 66.1 + - - +
143A PHE* 3.1 23.4 + - + +
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Residues in contact with LYS 141 (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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126A ARG* 5.1 7.4 + - - +
129A GLU* 5.8 2.2 + - - +
137A ARG 2.6 18.8 + - - +
138A ILE* 2.7 18.8 + - + +
140A LEU* 1.3 73.4 - - - +
142A TYR* 1.3 98.4 + - + +
143A PHE 3.6 1.4 + - - -
144A GLU* 5.4 2.8 - - - +
226A ASP* 4.4 6.7 + - - +
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Residues in contact with TYR 142 (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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138A ILE* 2.9 36.4 + - + +
139A GLY 3.6 2.2 - - - -
141A LYS* 1.3 101.6 + - + +
143A PHE* 1.3 58.0 + - - +
144A GLU* 3.5 2.9 - - - -
145A ASP* 3.0 16.0 - - + +
146A PHE* 2.9 52.9 + + + -
225A THR* 3.9 1.0 + - - -
226A ASP* 3.1 38.5 + - - -
238A VAL* 4.1 2.2 - - + -
252A HIS* 3.1 48.9 + + + -
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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