Contacts of the helix formed by residues 128 - 135 (chain A) in PDB entry 1BKX
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 MET 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A GLY 3.8 0.4 + - - -
127A GLU* 1.3 66.8 - - - +
129A PHE* 1.3 55.9 + - - +
130A SER 2.6 17.3 + - - -
131A HIS* 3.0 12.3 + - - -
132A LEU* 3.1 12.7 + - + +
138A PHE* 4.3 19.7 - - + -
146A TYR* 3.5 41.7 - - + -
150A ILE* 5.8 1.1 - - + -
169A PRO* 3.3 19.5 + - - +
172A LEU* 2.6 48.8 + - + +
174A ILE* 3.5 20.2 - - + -
180A ILE* 4.9 5.4 - - + -
227A LEU* 5.2 5.6 - - + -
231A MET* 4.3 15.0 - - - +
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Residues in contact with PHE 129 (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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127A GLU* 3.6 19.5 - - - +
128A MET* 1.3 73.7 - - - +
130A SER* 1.3 65.8 + - - +
132A LEU* 3.7 6.0 - - - +
133A ARG* 3.0 72.7 + - + +
169A PRO* 3.0 41.0 + - + +
170A GLU* 3.6 27.6 - - + +
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Residues in contact with SER 130 (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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127A GLU* 3.1 23.2 + - - +
128A MET 2.6 6.3 + - - -
129A PHE* 1.3 84.2 - - - +
131A HIS* 1.3 83.3 + - - -
132A LEU 3.0 1.3 - - - -
133A ARG* 2.8 5.4 + - - +
134A ARG* 2.8 25.5 + - - +
326A ASN 4.7 9.5 + - - -
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Residues in contact with HIS 131 (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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125A GLY 2.8 29.4 + - - -
126A GLY* 3.9 1.8 + - - -
127A GLU 3.5 15.7 + - - -
128A MET 3.0 3.6 + - - +
130A SER* 1.3 82.9 + - - +
132A LEU* 1.3 66.5 + - - +
134A ARG* 2.9 27.6 + - - +
135A ILE* 2.7 38.2 + - + +
138A PHE* 4.7 7.2 - - + -
174A ILE* 3.4 29.5 - - + +
314A PHE* 3.5 32.9 - + + -
316A PRO* 4.4 11.0 - - + +
326A ASN* 4.6 8.7 - - + -
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Residues in contact with LEU 132 (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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128A MET* 3.1 20.5 + - + +
129A PHE 3.7 6.1 - - - +
131A HIS* 1.3 80.6 - - - +
133A ARG* 1.3 67.0 + - - +
136A GLY 2.9 29.5 + - - +
137A ARG* 3.9 25.5 + - - -
138A PHE* 4.1 20.9 - - + -
169A PRO* 4.7 13.9 - - + -
230A GLU* 3.9 39.9 - - + +
231A MET* 4.0 20.9 - - + +
234A GLY* 4.4 3.6 - - - +
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Residues in contact with ARG 133 (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 PHE* 3.0 63.8 + - + +
130A SER* 2.8 10.5 + - - +
132A LEU* 1.3 79.1 - - - +
134A ARG* 1.3 67.9 - - - +
136A GLY* 4.0 6.8 + - - +
169A PRO* 5.4 0.2 - - - +
230A GLU* 2.5 30.5 + - - -
234A GLY* 5.0 9.1 + - - -
235A TYR* 5.7 0.4 - - - +
236A PRO* 5.3 7.3 - - - +
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Residues in contact with ARG 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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130A SER* 2.8 11.1 + - - +
131A HIS* 3.3 29.2 + - - +
133A ARG* 1.3 83.6 - - - +
135A ILE* 1.3 88.4 + - - +
136A GLY* 3.3 1.0 + - - -
314A PHE* 3.8 21.4 - - - -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A HIS* 2.7 20.4 + - + +
132A LEU 4.3 0.9 - - - +
134A ARG* 1.3 94.4 - - - +
136A GLY* 1.4 54.7 + - - +
137A ARG 3.5 22.2 + - - +
138A PHE* 3.8 24.5 - - + -
142A HIS* 4.8 2.5 - - + -
314A PHE* 3.6 33.9 - - + -
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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