Contacts of the helix formed by residues 130 - 143 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B GLN* 3.5 21.8 - - + +
122B PHE* 4.1 4.5 - - + -
128B ALA 3.5 5.3 - - - +
129B PRO* 1.3 83.8 - - + +
131B LEU* 1.3 57.9 + - - +
133B ILE* 3.3 12.5 + - + +
134B LYS* 3.1 45.1 + - + +
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Residues in contact with LEU 131 (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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115B LEU* 4.5 6.7 - - + -
121B GLN* 5.0 4.0 - - - +
129B PRO* 3.2 0.8 - - - +
130B PRO* 1.3 78.4 - - + +
132B LEU* 1.3 65.7 + - - +
134B LYS* 3.4 23.6 + - - +
135B LEU* 3.1 29.8 + - + +
164B LEU 4.4 14.1 - - - +
165B LEU* 3.7 35.2 - - + +
167B CYS* 4.6 14.8 - - - -
174B LEU* 4.6 12.3 - - + -
189B TYR* 3.8 28.9 - - + -
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Residues in contact with LEU 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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129B PRO* 3.1 21.7 + - + +
131B LEU* 1.3 77.8 - - - +
133B ILE* 1.3 58.1 + - - +
135B LEU* 3.5 7.6 + - + +
136B VAL* 2.9 35.0 + - + +
186B PHE* 3.8 31.0 - - + -
189B TYR* 3.8 35.1 + - + +
190B LEU* 5.2 0.9 - - + -
239B THR* 3.7 30.5 - - + -
242B TYR* 3.9 20.6 - - + -
243B LEU* 3.8 18.4 - - + -
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Residues in contact with ILE 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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127B ILE* 4.6 10.3 - - + -
128B ALA* 3.7 33.0 - - + +
129B PRO 3.2 11.0 + - - +
130B PRO* 3.5 10.5 - - + +
132B LEU* 1.3 77.3 - - - +
134B LYS* 1.3 58.6 + - + +
137B GLU* 3.0 51.1 + - - +
242B TYR* 3.4 30.2 + - + +
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Residues in contact with LYS 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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130B PRO* 3.1 28.1 + - + +
131B LEU* 3.6 27.4 - - - +
132B LEU 3.3 0.2 - - - -
133B ILE* 1.3 75.0 - - + +
135B LEU* 1.3 64.1 + - - +
137B GLU* 4.0 4.5 - - - +
138B ALA* 3.1 26.2 + - - +
167B CYS* 4.3 20.4 - - - -
174B LEU* 3.5 21.9 - - + +
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Residues in contact with LEU 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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131B LEU* 3.1 26.3 + - + +
132B LEU* 3.7 10.5 - - + +
134B LYS* 1.3 75.5 - - - +
136B VAL* 1.3 62.6 + - - +
138B ALA* 3.3 3.9 + - - +
139B ILE* 3.0 30.6 + - + +
164B LEU* 5.9 1.6 - - + -
165B LEU* 4.0 24.0 - - + -
174B LEU* 3.9 14.7 - - + +
182B LEU* 4.3 24.6 - - + +
185B ALA* 4.2 20.9 - - + -
186B PHE* 4.1 26.7 - - + -
189B TYR* 4.2 14.1 - - + -
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Residues in contact with VAL 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 LEU* 2.9 28.2 + - + +
135B LEU* 1.3 71.1 - - - +
137B GLU* 1.3 59.6 + - + +
139B ILE* 3.5 6.1 + - - +
140B GLU* 2.9 39.7 + - - +
186B PHE* 3.7 28.5 - - + -
242B TYR* 3.8 31.4 - - + +
243B LEU* 4.9 1.6 - - + -
246B HIS* 3.6 34.1 - - + +
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Residues in contact with GLU 137 (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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133B ILE* 3.0 41.6 + - + +
134B LYS* 4.1 4.6 - - - +
136B VAL* 1.3 76.5 - - + +
138B ALA* 1.3 62.6 + - - +
140B GLU* 3.4 6.1 + - - +
141B LYS* 3.0 25.3 + - - +
175B GLU* 6.3 0.2 - - - -
242B TYR* 4.3 7.6 + - - +
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Residues in contact with ALA 138 (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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134B LYS 3.1 18.5 + - - +
135B LEU* 3.7 3.6 - - - +
137B GLU* 1.3 74.3 - - - +
139B ILE* 1.3 62.7 + - - +
141B LYS* 3.3 6.6 + - - +
142B LYS* 3.2 28.8 + - - +
174B LEU* 4.1 23.1 - - + +
175B GLU* 4.5 13.7 - - + +
182B LEU* 3.7 22.4 - - + -
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Residues in contact with ILE 139 (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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135B LEU* 3.0 23.3 + - + +
136B VAL* 3.9 5.6 - - - +
138B ALA* 1.3 75.2 - - - +
140B GLU* 1.3 56.6 + - - +
143B GLY* 2.7 30.4 + - - +
149B LEU* 3.9 30.3 - - + -
150B TYR* 3.3 28.3 - - - +
179B VAL* 4.9 5.8 - - + +
182B LEU* 3.8 33.7 - - + +
183B ALA* 4.1 4.5 - - - +
186B PHE* 3.7 29.4 - - + -
246B HIS* 4.2 7.9 - - + -
250B LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 140 (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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136B VAL* 2.9 29.1 + - - +
137B GLU* 4.2 5.7 - - - +
139B ILE* 1.3 73.2 - - - +
141B LYS* 1.3 66.4 + - - +
143B GLY 4.3 0.2 - - - -
144B LEU* 3.4 42.3 - - + +
246B HIS* 2.7 47.9 + - + +
249B LYS* 3.1 36.6 + - + +
250B LEU* 5.0 1.1 - - + -
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Residues in contact with LYS 141 (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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155A SER* 4.2 21.5 - - - -
137B GLU 3.0 17.6 + - - +
138B ALA* 3.3 8.0 + - - +
140B GLU* 1.3 77.5 - - - +
142B LYS* 1.3 92.1 + - - +
175B GLU* 3.0 42.7 + - - +
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Residues in contact with LYS 142 (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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178A ASP* 3.9 23.6 + - - +
181A VAL* 5.6 0.8 - - - +
138B ALA* 3.2 19.1 + - + +
139B ILE 4.3 0.4 - - - +
141B LYS* 1.3 100.8 - - - +
143B GLY* 1.3 57.1 + - - +
144B LEU 3.8 2.0 - - - -
146B CYS* 5.1 1.7 - - - +
174B LEU 5.2 0.2 - - - +
175B GLU* 2.9 27.9 + - - +
177B ILE 3.0 25.6 + - - -
179B VAL* 3.3 31.2 - - + +
182B LEU* 3.9 13.0 - - + -
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Residues in contact with GLY 143 (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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139B ILE 2.7 19.5 + - - -
142B LYS* 1.3 73.9 - - - +
144B LEU* 1.3 64.7 + - - +
145B GLU 3.1 3.4 - - - -
146B CYS* 2.9 29.6 + - - +
149B LEU* 3.6 18.3 - - - +
179B VAL* 3.9 13.2 - - - +
250B LEU* 4.7 0.4 - - - +
257B ASN* 4.9 0.2 - - - +
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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