Contacts of the helix formed by residues 130 - 143 (chain A) in PDB entry 1PBW
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 PRO 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLN* 3.4 23.8 - - + +
122A PHE* 3.9 5.4 - - + -
126A ASP* 5.0 7.9 - - - +
128A ALA 3.4 6.0 - - - +
129A PRO* 1.3 85.3 - - + +
131A LEU* 1.3 62.0 + - - +
133A ILE* 3.3 12.0 + - + +
134A LYS* 3.1 43.1 + - - +
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Residues in contact with LEU 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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115A LEU* 4.2 8.7 - - + -
121A GLN* 5.1 4.7 + - - +
129A PRO* 3.3 1.4 - - - +
130A PRO* 1.3 80.3 - - - +
132A LEU* 1.3 57.0 + - - +
134A LYS* 3.5 14.2 + - + +
135A LEU* 3.0 35.7 + - + +
164A LEU 4.5 1.6 - - - +
165A LEU* 3.9 30.5 - - + -
166A ASP* 3.4 45.5 - - + +
174A LEU* 5.2 2.0 - - + -
189A TYR* 3.7 32.8 - - + -
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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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129A PRO* 3.0 19.9 + - + +
131A LEU* 1.3 75.5 - - - +
133A ILE* 1.3 66.8 + - - +
135A LEU* 3.8 4.7 - - + +
136A VAL* 2.9 34.2 + - + +
186A PHE* 3.6 33.0 - - + -
189A TYR* 3.7 40.1 - - + +
190A LEU* 5.0 1.3 - - + -
239A THR* 4.0 24.9 - - + -
242A TYR* 3.9 17.0 - - + -
243A LEU* 3.9 20.2 - - + -
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Residues in contact with ILE 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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127A ILE* 4.5 10.5 - - + +
128A ALA* 3.6 35.4 - - + +
129A PRO 3.1 9.4 + - - +
130A PRO* 3.3 11.4 + - + +
132A LEU* 1.3 75.8 - - - +
134A LYS* 1.3 59.2 + - + +
137A GLU* 2.9 61.6 + - - +
242A TYR* 3.4 27.1 - - + +
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Residues in contact with LYS 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 PRO* 3.1 35.8 + - - +
131A LEU* 3.6 15.8 - - + +
133A ILE* 1.3 80.3 - - + +
135A LEU* 1.3 62.8 + - - +
137A GLU* 3.6 4.6 + - - +
138A ALA* 3.2 24.8 + - - +
141A LYS* 5.7 0.2 + - - -
166A ASP* 4.4 13.1 + - - +
174A LEU* 4.1 28.3 - - + +
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Residues in contact with LEU 135 (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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131A LEU* 3.0 24.6 + - + +
132A LEU* 3.8 6.5 - - + +
134A LYS* 1.3 80.8 - - - +
136A VAL* 1.3 62.2 + - - +
138A ALA* 3.9 3.8 - - - +
139A ILE* 3.1 30.7 + - + +
164A LEU* 6.0 0.4 - - + -
165A LEU* 4.3 10.3 - - + -
174A LEU* 4.7 13.5 - - + -
182A LEU* 4.3 22.8 - - + +
185A ALA* 4.1 26.7 - - + +
186A PHE* 3.7 36.8 - - + -
189A TYR* 4.2 18.4 - - + -
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Residues in contact with VAL 136 (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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132A LEU* 2.9 22.9 + - + +
135A LEU* 1.3 77.8 - - - +
137A GLU* 1.3 58.0 + - + +
139A ILE* 3.4 7.0 + - - +
140A GLU* 3.0 39.5 + - - +
186A PHE* 3.8 28.7 - - + -
242A TYR* 3.6 33.9 - - + +
243A LEU* 4.9 1.6 - - + -
246A HIS* 3.6 33.4 - - + +
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Residues in contact with GLU 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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133A ILE* 2.9 38.1 + - - +
134A LYS* 4.1 4.6 - - - +
136A VAL* 1.3 76.3 - - + +
138A ALA* 1.3 57.2 + - - +
140A GLU* 3.5 9.9 + - - +
141A LYS* 3.0 45.5 + - - +
242A TYR* 4.2 9.7 + - - +
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Residues in contact with ALA 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 LYS 3.2 18.9 + - - +
135A LEU 3.9 2.7 - - - +
137A GLU* 1.3 72.8 - - - +
139A ILE* 1.3 66.4 + - - +
141A LYS* 3.3 17.4 + - - +
142A LYS* 2.9 34.9 + - + +
174A LEU* 4.2 22.4 - - + +
175A GLU 4.6 0.2 - - - +
182A LEU* 3.8 20.4 - - + -
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Residues in contact with ILE 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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135A LEU* 3.1 23.2 + - + +
136A VAL* 3.7 5.4 - - - +
138A ALA* 1.3 77.5 - - - +
140A GLU* 1.3 54.5 + - - +
142A LYS* 5.0 1.1 - - - -
143A GLY* 2.6 34.1 + - - +
149A LEU* 3.9 27.8 - - + -
150A TYR* 3.6 28.3 - - + +
179A VAL* 5.0 4.3 - - - +
182A LEU* 3.7 42.8 - - + +
183A ALA* 4.1 5.4 - - - +
186A PHE* 3.8 17.5 - - + -
246A HIS* 4.1 9.4 - - + +
250A LEU* 5.5 0.7 - - + -
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Residues in contact with GLU 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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136A VAL* 3.0 27.4 + - - +
137A GLU* 3.9 9.8 - - - +
138A ALA 3.3 0.2 - - - -
139A ILE* 1.3 76.2 - - - +
141A LYS* 1.3 62.2 + - - +
142A LYS 3.4 0.2 + - - -
144A LEU* 3.4 43.9 + - + +
246A HIS* 2.7 46.8 + - + +
249A LYS* 3.3 39.6 + - + +
250A LEU* 5.6 0.2 - - - -
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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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134A LYS 5.7 0.2 + - - -
137A GLU* 3.0 39.7 + - - +
138A ALA* 3.5 13.6 - - - +
139A ILE 3.3 0.2 - - - -
140A GLU* 1.3 76.6 - - - +
142A LYS* 1.3 60.3 + - - +
175A GLU* 3.0 48.1 + - - +
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Residues in contact with LYS 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 ALA* 2.9 23.2 + - - +
141A LYS* 1.3 82.0 - - + +
143A GLY* 1.3 55.9 + - - +
144A LEU 3.9 1.1 - - - -
146A CYS* 5.0 2.4 - - - +
174A LEU 4.0 0.7 - - - -
175A GLU* 2.9 48.9 + - - +
177A ILE 3.1 27.3 + - - -
179A VAL* 3.3 29.9 - - + +
182A LEU* 3.6 15.0 - - - -
178B ASP* 3.5 20.4 + - - -
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Residues in contact with GLY 143 (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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139A ILE 2.6 20.7 + - - -
142A LYS* 1.3 75.6 - - - +
144A LEU* 1.3 65.1 + - - +
145A GLU 3.2 3.1 - - - -
146A CYS* 3.1 28.0 + - - +
149A LEU* 3.6 21.1 - - - +
179A VAL* 3.8 8.0 - - - +
250A LEU* 5.4 0.2 - - - -
257A ASN* 4.9 0.5 - - - +
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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