Contacts of the helix formed by residues 147 - 154 (chain A) in PDB entry 1P1B
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 GLN 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A TYR* 3.8 19.0 - - + -
135A THR* 3.3 26.3 + - + -
144A HIS 3.8 11.8 + - - +
145A THR 3.9 0.8 - - - -
146A HIS* 1.3 78.1 - - - +
148A PHE* 1.3 78.7 + - + +
149A ASN 3.1 2.3 + - - -
150A PHE 3.4 2.6 + - - -
151A ILE* 3.3 23.0 + - + +
167A TYR* 3.8 21.8 - - + -
169A ASN* 2.8 43.6 + - - +
172A SER* 5.2 0.3 + - - -
173A TRP* 4.3 1.2 + - - -
192A GLN* 3.0 24.1 + - - +
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Residues in contact with PHE 148 (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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144A HIS 4.2 7.9 - - - -
145A THR* 2.9 30.0 + - + +
146A HIS 2.8 1.0 + - - -
147A GLN* 1.3 89.6 - - + +
149A ASN* 1.3 61.7 + - - +
150A PHE 3.4 0.2 - - - -
151A ILE* 3.8 18.4 - - + -
152A LYS* 3.1 49.3 + - + +
167A TYR* 3.7 14.6 - - - -
191A THR 3.8 13.0 - - - -
192A GLN* 3.3 38.4 - - - -
195A ALA* 3.5 25.8 - - + -
196A LEU* 3.8 18.4 - - + -
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Residues in contact with ASN 149 (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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116A TRP* 3.6 21.1 - - + -
138A LEU* 5.9 0.2 - - - +
142A THR* 5.0 5.3 + - - -
145A THR 4.3 4.9 - - - +
146A HIS* 2.9 39.6 + - - +
148A PHE* 1.3 80.3 - - - +
150A PHE* 1.3 60.1 + - - +
152A LYS* 5.1 1.0 + - - -
153A THR* 2.7 31.8 + - - -
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Residues in contact with PHE 150 (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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64A LEU* 3.9 13.2 - - + -
66A VAL* 3.7 24.2 - - + -
88A ILE* 5.2 0.9 - - + -
116A TRP* 3.5 43.3 - + + -
120A ALA* 4.5 9.2 - - + -
131A ILE* 3.7 28.7 - - + -
133A TYR* 3.6 43.3 - + + -
146A HIS 4.4 0.2 + - - -
147A GLN 3.4 1.6 + - - -
149A ASN* 1.3 79.1 - - - +
151A ILE* 1.3 65.0 - - + +
154A HIS* 2.6 43.9 + - + -
155A ALA* 3.0 23.2 + - + -
158A LEU* 4.6 1.8 - - + -
165A LEU* 5.0 1.1 - - + -
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Residues in contact with ILE 151 (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 TYR* 4.8 2.2 - - + -
147A GLN* 3.3 19.6 + - + +
148A PHE* 3.8 22.4 - - + -
150A PHE* 1.3 87.0 - - + +
152A LYS* 1.3 64.4 + - - +
155A ALA* 3.2 36.5 + - + +
156A PHE* 3.4 9.4 + - - +
165A LEU* 4.2 8.1 - - + -
167A TYR* 3.9 39.3 - - + -
196A LEU* 3.9 15.7 - - + -
199A ALA* 3.8 19.5 - - + +
201A PHE* 4.2 7.4 - - + -
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Residues in contact with LYS 152 (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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148A PHE* 3.1 35.8 + - + +
149A ASN* 5.1 0.8 + - - -
151A ILE* 1.3 79.5 - - + +
153A THR* 1.3 63.8 + - - +
156A PHE* 4.9 4.2 - - - +
195A ALA* 3.7 22.3 - - - +
198A GLU* 3.6 42.7 + - + +
199A ALA* 3.7 31.9 - - + +
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Residues in contact with THR 153 (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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116A TRP* 5.3 0.2 - - - -
149A ASN* 2.7 25.6 + - - -
151A ILE 3.2 0.4 - - - -
152A LYS* 1.3 82.3 - - - +
154A HIS* 1.3 83.1 + - + +
157A ARG* 3.4 21.8 - - - +
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Residues in contact with HIS 154 (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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116A TRP* 3.4 35.1 - + - -
117A GLU 4.9 1.1 - - - -
120A ALA* 3.5 26.9 - - + +
121A PRO* 3.6 21.2 - - + +
150A PHE* 2.6 24.0 + - + +
151A ILE 3.7 0.2 + - - -
153A THR* 1.3 97.0 - - + +
155A ALA* 1.3 65.9 + - - +
156A PHE 3.4 2.2 - - - -
157A ARG* 2.9 34.0 - - - +
158A LEU* 2.8 45.2 + - + +
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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