Contacts of the strand formed by residues 135 - 142 (chain C) in PDB entry 4JZJ
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 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C ASP 4.7 2.7 - - - +
134C VAL* 1.3 82.8 + - - +
136C TYR* 1.3 68.6 + - - +
159C GLY 3.2 22.8 + - - -
160C THR* 3.8 0.6 - - - +
161C ARG* 2.8 50.5 + - - +
185C GLY* 3.3 3.6 - - - -
186C ARG* 2.8 74.4 + - + +
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA 2.8 24.8 + - - -
106C GLY* 3.4 10.9 + - - -
107C ALA* 3.7 19.7 - - + -
124C TRP* 3.5 24.2 - + + +
126C VAL* 3.6 18.7 - - + +
127C GLY 3.4 10.6 + - - -
130C ALA* 3.9 2.4 - - - +
134C VAL* 3.9 13.0 - - + -
135C GLN* 1.3 79.6 + - - +
137C ASP* 1.3 64.6 + - - +
138C LEU 4.3 0.2 - - - -
153C TYR* 4.2 1.7 - - - -
160C THR* 3.8 21.1 - - + -
161C ARG* 3.1 46.0 + - - +
183C VAL* 3.8 15.0 - - + -
184C ARG 3.2 15.0 - - - +
185C GLY* 3.6 15.5 - - - -
192C ILE* 4.3 0.2 - - + -
193C PRO 5.7 0.2 - - - -
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Residues in contact with ASP 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C TYR* 1.3 75.1 - - - +
138C LEU* 1.3 60.6 + - - +
139C TYR* 3.6 27.9 + - + +
149C GLU* 3.8 18.1 - - - +
153C TYR* 3.6 4.3 - - - -
161C ARG* 3.0 27.2 + - - -
183C VAL* 3.4 5.2 - - - -
184C ARG* 2.9 37.3 + - + +
185C GLY 5.9 0.2 - - - -
186C ARG* 3.1 35.0 + - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C CYS* 4.0 24.9 - - + -
124C TRP* 4.0 10.0 - - + -
137C ASP* 1.3 71.1 - - - +
139C TYR* 1.3 65.6 + - - +
149C GLU* 3.7 4.0 - - - +
150C CYS* 3.2 30.9 + - + -
153C TYR* 3.3 17.2 + - + -
164C CYS* 3.5 25.4 - - + +
166C PHE* 3.4 31.4 - - + -
181C ILE* 3.5 29.4 - - + -
182C LEU 3.5 1.8 - - - -
183C VAL* 3.6 20.4 - - + +
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Residues in contact with TYR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASP* 3.6 37.1 + - + +
138C LEU* 1.3 76.8 - - - +
140C LEU* 1.3 60.1 + - - +
141C ASN 4.0 0.4 - - - +
147C GLN* 3.4 39.9 - - + +
148C TYR 3.5 1.3 - - - -
149C GLU* 3.5 42.9 + - + -
166C PHE* 4.1 5.2 - - - -
180C HIS 3.7 0.5 - - - +
181C ILE* 3.4 7.8 - - - +
182C LEU* 2.6 54.0 + - + +
184C ARG* 4.0 28.3 - - + -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 4.1 10.3 - - + -
139C TYR* 1.3 72.4 - - - +
141C ASN* 1.3 59.8 + - - +
142C VAL* 4.1 22.4 - - + -
146C GLN 4.0 0.5 - - - +
147C GLN* 3.3 2.6 - - - +
148C TYR* 2.7 45.2 + - + +
166C PHE* 3.6 18.2 - - + -
169C ILE* 3.8 23.6 - - + -
172C LEU* 4.3 18.6 - - + -
173C SER* 4.5 7.2 - - - -
179C SER* 3.5 25.6 - - - +
180C HIS 3.8 1.3 - - - +
181C ILE* 3.6 24.2 - - + -
201C PHE* 4.6 2.0 - - + -
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Residues in contact with ASN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR 4.0 1.1 + - - +
140C LEU* 1.3 74.1 - - - +
142C VAL* 1.3 61.0 + - - +
143C ALA 3.7 1.4 + - - -
144C LYS* 3.2 33.7 + - - +
145C ARG 5.8 0.2 - - - -
146C GLN 3.5 6.7 + - - +
147C GLN* 3.5 31.8 + - - +
179C SER* 3.6 3.5 - - - -
180C HIS* 2.9 55.8 + - + +
182C LEU* 5.7 3.6 - - + -
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 4.1 11.7 - - + -
141C ASN* 1.3 72.3 - - - +
143C ALA* 1.3 75.9 + - + +
144C LYS 3.1 2.3 + - - -
145C ARG* 3.2 12.6 + - - +
146C GLN* 2.8 21.0 + - + +
148C TYR* 3.9 28.5 - - + -
172C LEU 4.0 0.4 - - - +
173C SER* 3.6 31.9 - - - +
174C SER* 5.0 5.2 - - - -
176C SER* 3.5 24.9 - - - +
179C SER* 4.6 5.4 - - - -
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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