Contacts of the strand formed by residues 154 - 158 (chain A) in PDB entry 1JX6
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 LYS 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ASP 3.1 17.1 + - - +
130A TYR* 3.4 19.2 + - + +
131A LEU 2.9 26.0 + - - +
152A ASN 4.2 9.1 + - - +
153A THR* 1.3 76.7 - - - +
155A LEU* 1.3 60.6 + - - +
173A PHE* 3.6 30.3 - - + -
326A ASP* 2.9 39.8 + - - +
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Residues in contact with LEU 155 (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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131A LEU* 3.5 23.1 - - + -
133A PHE* 3.7 26.0 - - + -
144A VAL* 3.6 39.7 - - + +
147A VAL* 3.5 39.7 - - + -
148A LEU* 4.2 12.4 - - + +
153A THR* 4.4 0.4 - - + +
154A LYS* 1.3 73.6 - - - +
156A ILE* 1.3 62.2 + - - +
157A LEU* 4.0 4.5 - - + -
172A PRO* 3.9 13.2 - - + +
173A PHE* 3.2 12.0 + - - +
174A LEU 3.1 23.7 + - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 4.6 7.9 - - + -
131A LEU 3.0 7.9 + - - +
132A ILE* 3.3 31.0 - - + +
133A PHE 3.1 25.1 + - - +
154A LYS 5.3 0.4 - - - +
155A LEU* 1.3 75.6 - - - +
157A LEU* 1.3 64.3 + - - +
173A PHE* 3.8 22.2 - - + -
174A LEU* 3.3 15.5 - - + +
176A VAL* 3.7 17.9 - - + -
319A MET* 3.4 35.2 - - + +
323A ILE* 4.3 26.0 - - + -
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Residues in contact with LEU 157 (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 PHE* 3.2 31.6 - - + +
134A THR* 5.3 0.2 - - - -
135A LEU* 3.1 36.1 - - + -
144A VAL* 4.9 2.7 - - + -
155A LEU* 4.8 5.2 - - + -
156A ILE* 1.3 76.9 - - - +
158A GLN* 1.3 60.6 + - - +
160A ILE* 3.2 23.4 - - + +
167A TRP* 4.2 8.3 - - + -
172A PRO* 4.0 29.4 - - + -
174A LEU 2.8 14.7 + - - +
175A TYR* 4.0 18.4 - - + -
176A VAL* 3.0 26.8 + - - -
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Residues in contact with GLN 158 (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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73A TYR* 3.4 33.0 + - + +
81A TYR* 2.5 33.3 + - + -
82A TRP* 3.6 18.4 - - + -
85A ASN* 3.4 10.6 + - - +
132A ILE* 4.6 2.2 - - + -
133A PHE 2.8 7.7 + - - +
134A THR* 2.6 30.0 + - - -
156A ILE 3.7 1.4 + - - -
157A LEU* 1.3 73.6 - - - +
159A ASN* 1.3 64.5 + - - +
160A ILE* 3.5 2.4 + - - +
176A VAL* 3.4 25.8 - - + +
177A GLY* 3.8 2.6 - - - -
315A THR* 4.0 1.9 + - - -
319A MET* 3.1 34.2 - - - +
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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