Contacts of the helix formed by residues 150 - 158 (chain B) in PDB entry 1PJS
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 HIS 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASP* 5.4 4.8 + - - -
254A ASP* 4.3 11.7 - - - -
414A VAL* 4.3 12.3 - - + +
148B PRO* 3.3 3.0 - - - +
149B GLN* 1.3 101.6 + - + +
151B LEU* 1.3 62.7 + - - +
152B GLY 3.1 3.1 - - - -
153B GLN* 3.0 27.9 + - + +
189B ALA* 3.5 30.8 - - + +
190B GLN* 3.3 35.8 + - + -
193B ALA* 3.7 23.8 - - + +
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Residues in contact with LEU 151 (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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135A LEU* 3.9 23.6 - - + -
139A LEU* 4.7 4.7 - - + -
505A PGE 5.0 5.4 - - - +
119B ARG* 4.4 10.1 - - + +
122B LEU* 3.5 37.2 - - + -
147B LEU* 4.9 9.2 - - + -
148B PRO* 3.1 37.2 + - + +
149B GLN 3.4 1.0 - - - -
150B HIS* 1.3 76.8 - - - +
152B GLY* 1.3 62.5 + - - +
154B VAL* 3.0 37.8 - - + +
155B ALA* 3.3 5.0 + - - +
183B PHE 3.9 17.5 - - - +
189B ALA* 5.3 1.3 - - - -
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Residues in contact with GLY 152 (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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119B ARG* 3.1 30.1 + - - +
120B SER 3.5 13.2 - - - -
121B PRO* 3.6 4.2 - - - +
149B GLN 4.8 0.8 + - - -
150B HIS* 3.1 2.0 - - - +
151B LEU* 1.3 80.0 - - - +
153B GLN* 1.3 61.6 + - - +
155B ALA* 3.2 7.5 + - - +
156B ARG* 3.0 25.3 + - - +
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Residues in contact with GLN 153 (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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150B HIS* 3.0 29.1 + - + +
152B GLY* 1.3 78.2 - - - +
154B VAL* 1.3 58.7 + - - +
156B ARG* 3.5 6.9 + - - +
157B TYR* 3.0 26.3 + - - +
189B ALA* 3.7 23.8 - - - +
192B LEU* 3.8 20.4 + - + +
193B ALA* 3.8 25.5 - - + +
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Residues in contact with VAL 154 (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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150B HIS 4.0 0.4 + - - +
151B LEU* 3.0 38.8 - - + +
153B GLN* 1.3 75.0 - - - +
155B ALA* 1.3 65.7 + - - +
156B ARG 3.2 0.4 - - - -
157B TYR* 4.1 5.4 - - - -
158B ALA* 3.0 20.4 + - - +
182B PHE* 3.2 25.1 - - + +
183B PHE* 3.8 17.7 - - + +
185B ASN 4.3 6.3 - - - +
188B LEU* 4.2 20.6 - - + -
189B ALA* 3.9 32.1 - - + +
192B LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 155 (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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128A SEP 5.8 2.0 - - - -
131A THR* 2.8 17.2 - - + +
132A SER* 2.7 27.9 + - - +
135A LEU* 3.6 22.7 - - + -
121B PRO* 4.0 16.2 - - + -
122B LEU* 4.7 5.2 - - + -
151B LEU 3.3 9.3 + - - +
152B GLY* 3.2 12.9 + - - +
154B VAL* 1.3 78.2 - - - +
156B ARG* 1.3 57.3 + - - +
158B ALA* 3.7 5.4 + - - +
183B PHE* 3.9 4.9 - - - -
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Residues in contact with ARG 156 (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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2A ASP* 4.2 14.3 + - - +
107A LYS* 5.3 10.9 - - - +
131A THR* 3.3 31.0 + - - +
11B ARG* 5.7 2.0 - - - +
121B PRO* 3.8 29.8 - - + +
152B GLY 3.0 15.1 + - - +
153B GLN* 3.7 8.5 - - - +
155B ALA* 1.3 80.5 - - - +
157B TYR* 1.3 60.6 + - - +
158B ALA 3.6 0.3 + - - -
159B GLY* 3.8 9.0 + - - -
160B GLN* 4.9 4.5 + - - +
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Residues in contact with TYR 157 (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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153B GLN 3.0 18.3 + - - +
154B VAL* 3.3 5.3 + - - +
156B ARG* 1.3 74.2 - - - +
158B ALA* 1.3 65.0 + - - +
159B GLY 3.0 2.9 - - - -
160B GLN* 2.9 50.0 + - + +
161B LEU* 3.9 23.4 + - + +
182B PHE* 3.9 18.6 - + - -
188B LEU* 4.0 14.1 - - + -
192B LEU* 3.6 30.1 - - + -
200B VAL* 4.0 12.0 - - + +
201B ASN* 5.6 1.9 + - - -
204B THR* 2.8 36.6 + - - +
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Residues in contact with ALA 158 (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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131A THR 4.5 3.8 - - - +
132A SER* 3.5 25.1 - - - +
154B VAL 3.0 14.0 + - - +
155B ALA 3.7 1.3 - - - +
156B ARG 3.4 0.4 - - - -
157B TYR* 1.3 75.8 - - - +
159B GLY* 1.3 61.6 + - - +
161B LEU* 3.0 12.8 + - - +
162B ARG* 3.1 17.2 + - - +
179B TRP* 3.6 29.1 - - + -
182B PHE* 3.8 12.5 - - + -
183B PHE* 4.2 3.8 - - + -
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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