Contacts of the strand formed by residues 130 - 134 (chain A) in PDB entry 1PJX
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 LEU 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLN* 4.0 1.3 - - + -
86A PHE* 3.8 32.1 - - + -
94A LEU* 3.9 27.8 - - + -
122A CYS* 3.8 18.8 - - + -
123A ALA 3.7 5.2 - - - +
124A PHE* 3.7 49.1 - - + +
129A ASN* 1.3 73.9 - - - +
131A TRP* 1.3 60.4 + - - +
132A ILE* 3.7 14.4 - - + +
157A CYS* 3.3 3.1 - - - -
158A PHE* 2.8 47.9 + - + +
422A EDO 4.8 0.2 - - - +
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Residues in contact with TRP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A CYS* 3.1 4.2 - - - +
123A ALA 2.8 44.2 + - - +
125A ASP* 2.8 28.1 + - - +
129A ASN* 3.7 10.1 + - + +
130A LEU* 1.3 71.9 - - - +
132A ILE* 1.3 58.9 + - - +
155A ILE* 5.2 0.4 - - + -
156A TYR 3.4 8.5 - - - +
157A CYS* 3.8 27.4 - - + -
167A VAL* 4.3 12.1 - - + -
177A ILE* 3.8 11.3 - - + +
179A VAL* 3.7 16.2 - - + +
190A LEU* 3.7 33.2 - - + -
205A ILE* 4.0 22.5 - - + +
207A GLY 4.0 2.7 - - - -
208A PRO* 4.8 2.0 - - + -
209A ALA* 3.5 31.9 - - - -
210A LYS 3.9 3.8 - - - -
211A ILE* 3.7 30.5 - - + -
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Residues in contact with ILE 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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88A ALA* 4.7 2.5 - - + -
94A LEU* 4.0 21.1 - - + -
119A CYS* 3.4 33.9 - - + -
121A ASP 3.4 11.9 - - - +
122A CYS* 3.9 13.2 - - + -
130A LEU* 3.7 12.6 - - + +
131A TRP* 1.3 79.3 - - - +
133A THR* 1.3 67.8 + - - +
155A ILE* 3.3 7.4 - - - +
156A TYR* 2.8 42.2 + - + +
158A PHE* 3.9 27.4 - - + -
164A MET* 4.0 19.5 - - + -
177A ILE* 3.9 3.2 - - - +
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Residues in contact with THR 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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119A CYS* 3.2 8.7 - - - +
120A ASN* 2.9 25.3 + - - +
121A ASP 2.9 19.6 + - - -
132A ILE* 1.3 73.8 - - - +
134A ALA* 1.4 59.8 + - - +
135A PRO* 3.6 1.1 - - - -
154A SER 3.9 3.4 - - - -
155A ILE* 4.1 2.5 - - + -
174A PRO* 3.7 22.9 + - + -
175A ASN* 2.7 38.9 + - - +
176A GLY 4.0 2.7 - - - +
177A ILE* 3.9 27.6 - - + +
192A VAL* 4.1 6.7 - - + -
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Residues in contact with ALA 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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117A GLN* 3.4 14.4 + - + -
118A GLY 3.2 15.5 - - - +
119A CYS* 4.0 5.6 - - - -
133A THR* 1.4 73.8 - - - +
135A PRO* 1.3 63.4 - - - +
153A GLY* 3.3 2.9 - - - -
154A SER 2.8 34.1 + - - +
156A TYR* 3.4 35.7 - - + -
174A PRO* 4.0 1.3 - - - +
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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