Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 1JZO
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 3.6 1.6 - - - +
87A LYS* 1.3 89.4 + - + +
89A VAL* 1.3 68.1 + - - +
90A ILE* 4.2 1.1 - - + -
115A GLY 2.9 2.6 + - - +
116A ILE* 4.0 11.2 - - + -
117A THR* 2.8 26.7 + - - -
203A LYS* 3.9 21.5 - - + -
206A LEU* 3.5 56.4 - - + +
207A ASP* 2.8 26.3 + - - -
210A GLN* 3.1 30.2 + - - -
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Residues in contact with VAL 89 (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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86A GLU* 3.2 40.4 - - + +
88A HIS* 1.3 74.4 - - - +
90A ILE* 1.3 66.9 + - - +
117A THR* 3.6 8.5 - - + +
119A ARG* 4.0 37.2 - - + +
186A VAL 4.9 0.3 - - - +
187A LEU* 5.3 0.2 - - - -
188A SER* 4.8 16.7 + - - -
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Residues in contact with ILE 90 (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 HIS* 5.1 0.2 - - + -
89A VAL* 1.3 82.8 - - - +
91A THR* 1.3 61.8 + - - +
92A VAL* 3.8 22.0 - - + -
104A LEU* 6.3 0.4 - - + -
111A TYR* 5.9 1.3 - - + -
116A ILE* 4.0 16.6 - - + -
117A THR 3.0 16.2 + - - +
118A VAL* 4.3 9.9 - - + -
119A ARG* 2.9 26.3 + - - +
185A VAL* 3.6 22.9 - - + -
186A VAL 4.0 3.1 - - - -
187A LEU* 4.5 5.6 - - + -
202A MET* 4.2 23.3 - - + -
206A LEU* 3.8 33.9 - - + -
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Residues in contact with THR 91 (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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71A LEU* 4.2 15.2 - - + +
78A MET* 4.0 22.4 - - + -
89A VAL* 5.5 0.2 - - - +
90A ILE* 1.3 72.7 - - - +
92A VAL* 1.3 61.8 + - - +
93A PHE* 5.0 4.0 - - + -
119A ARG* 2.8 46.6 + - - +
121A LEU* 4.1 20.2 - - + -
184A ALA 3.8 0.7 - - - +
185A VAL* 3.5 1.7 - - - -
186A VAL* 2.8 41.6 + - - +
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Residues in contact with VAL 92 (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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90A ILE* 3.8 27.4 - - + -
91A THR* 1.3 80.3 - - - +
93A PHE* 1.3 75.9 + - - +
94A THR* 3.4 2.4 + - - -
104A LEU* 4.5 10.3 - - + -
118A VAL* 3.9 13.2 - - + -
119A ARG 2.7 9.3 + - - -
120A TYR* 3.3 28.3 - - + -
121A LEU 3.1 21.6 + - - -
183A PRO* 3.8 20.6 - - + -
184A ALA 3.3 8.5 - - - +
185A VAL* 4.1 11.4 - - + -
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Residues in contact with PHE 93 (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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71A LEU* 5.1 1.6 - - + -
91A THR* 5.0 3.6 - - + -
92A VAL* 1.3 73.8 - - - +
94A THR* 1.3 57.8 + - - +
121A LEU* 3.5 41.3 - - + -
122A ALA 4.3 2.0 - - - -
123A PHE* 3.9 26.0 - + + -
170A HIS 3.4 23.6 - - - -
173A LEU* 4.2 4.5 - - + -
174A GLY* 3.5 21.1 - - - -
177A LEU* 3.7 16.4 - - + -
179A VAL* 3.8 19.5 - - + -
182A THR* 3.7 5.7 - - + +
183A PRO* 3.5 6.8 - - - +
184A ALA* 2.9 34.3 + - + +
186A VAL* 3.5 33.0 - - + -
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Residues in contact with THR 94 (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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92A VAL* 4.6 2.9 - - - -
93A PHE* 1.3 75.4 - - - +
95A ASP* 1.3 68.8 + - - +
96A ILE 4.2 0.2 - - - -
101A SER* 3.1 25.3 + - - -
120A TYR* 3.5 39.0 - - + -
121A LEU 3.1 11.1 + - - +
122A ALA 3.7 0.2 - - - -
123A PHE 2.8 24.9 + - - -
136A MET* 3.6 5.7 - - - +
140A TRP* 4.3 4.5 - - + -
149A PHE* 3.7 30.3 - - + -
153A MET* 4.5 0.5 - - - +
182A THR* 4.3 2.0 - - - -
183A PRO* 5.4 0.4 - - - -
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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