Contacts of the strand formed by residues 158 - 162 (chain A) in PDB entry 1JPM
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 THR 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A GLU* 3.4 20.2 + - - -
132A THR 4.5 1.4 + - - +
133A ASP* 3.1 17.4 - - + -
134A TYR* 3.0 21.8 + - - +
156A PHE* 3.3 1.8 - - - +
157A GLN* 1.3 82.8 + - - +
159A LEU* 1.3 65.7 + - - +
187A LYS* 3.5 19.6 - - - +
189A ARG* 3.5 45.3 + - + +
216A GLU* 3.9 10.3 - - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 4.7 2.2 - - - -
134A TYR* 3.2 13.7 - - + +
136A VAL* 3.7 15.9 - - + -
148A ALA* 3.7 38.1 - - + +
151A TYR* 4.0 22.4 - - + -
156A PHE* 3.9 22.2 - - + +
158A THR* 1.3 82.6 - - - +
160A LYS* 1.3 60.2 + - - +
161A ILE* 4.0 1.3 + - + -
178A ILE* 4.9 1.1 - - + -
182A VAL* 5.6 0.2 - - + -
186A VAL* 4.6 21.3 - - + -
187A LYS 3.0 7.7 + - - +
188A LEU* 3.6 19.0 - - + +
189A ARG* 2.9 26.2 + - - +
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Residues in contact with LYS 160 (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 ASP* 4.0 15.7 - - - +
134A TYR 2.8 12.2 + - - +
135A THR* 3.2 31.4 + - - +
136A VAL 3.0 25.1 + - - -
158A THR 4.3 0.2 + - - -
159A LEU* 1.3 73.4 - - - +
161A ILE* 1.3 68.9 + - - +
162A LYS 4.3 0.4 - - - +
189A ARG* 3.3 17.0 - - + +
190A LEU 5.4 0.2 - - - -
191A ASP* 4.9 16.7 + - + +
219A GLU* 4.8 11.7 - - - +
293A MET* 5.7 1.3 - - + -
321A ASP* 2.9 37.4 + - - +
323A ASP* 5.0 2.8 + - - -
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Residues in contact with ILE 161 (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* 4.4 14.8 - - + -
144A MET* 4.0 20.0 - - + -
159A LEU 4.7 2.5 - - - +
160A LYS* 1.3 83.4 - - - +
162A LYS* 1.3 72.6 + - - +
163A VAL* 3.5 12.8 + - + -
174A ARG* 5.9 2.2 - - + -
175A ILE* 4.4 14.4 - - + -
178A ILE* 3.4 30.3 - - + -
188A LEU* 4.0 24.2 - - + -
189A ARG 2.7 10.4 + - - +
190A LEU* 3.3 23.6 - - + +
191A ASP 3.1 22.3 + - - -
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Residues in contact with LYS 162 (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 THR* 5.7 5.6 - - + +
136A VAL 4.9 4.4 + - - +
138A VAL* 3.8 30.3 - - + +
144A MET* 5.5 0.2 - - - +
160A LYS* 5.3 0.6 - - - +
161A ILE* 1.3 78.0 - - - +
163A VAL* 1.3 84.8 + - - +
164A GLY 4.2 1.2 - - - -
165A LYS* 3.7 24.4 - - - +
171A ASP* 4.7 1.9 - - - +
174A ARG* 5.3 3.6 + - - -
191A ASP* 3.0 14.6 - - + +
192A ALA 4.3 0.8 + - - -
193A ASN* 2.8 46.4 - - - +
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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