Contacts of the helix formed by residues 136 - 144 (chain E) in PDB entry 5JLH
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 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ASP* 5.0 0.2 - - - -
11E ASN 4.5 1.2 + - - -
12E GLY* 3.8 27.1 - - - +
105E THR* 2.9 36.7 - - + +
106E GLU* 2.9 16.9 + - - +
107E ALA* 3.9 28.3 - - - +
108E PRO* 4.9 0.4 - - + -
135E ILE* 1.3 74.9 - - - +
137E ALA* 1.3 63.9 + - - +
139E LEU* 3.3 13.1 + - - +
140E SER 3.3 8.5 + - - -
153E ASP* 3.0 31.3 - - - +
158E VAL 5.4 0.2 - - - +
160E HIS* 4.3 2.9 + - - -
338E VAL* 3.7 21.6 - - + +
401E ADP 4.4 1.1 + - - -
402E MG 3.9 10.2 - - - -
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Residues in contact with ALA 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PRO* 5.2 2.8 - - + +
135E ILE* 3.3 4.1 - - + +
136E GLN* 1.3 80.8 - - - +
138E VAL* 1.3 63.9 + - - +
140E SER* 2.6 23.2 + - - -
141E LEU* 3.0 6.1 + - - +
151E VAL* 3.7 30.1 - - + +
153E ASP* 4.4 13.7 + - + +
160E HIS* 5.9 0.2 - - + -
161E THR 5.6 0.2 - - - -
162E VAL* 3.9 34.3 - - + -
299E SER* 5.4 0.2 - - - -
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ILE* 3.2 27.6 - - + +
136E GLN 3.3 0.2 - - - -
137E ALA* 1.3 76.0 - - - +
139E LEU* 1.3 68.9 + - + +
141E LEU* 3.0 14.9 + - + +
142E TYR* 2.9 49.1 + - + -
162E VAL* 5.0 6.3 - - + -
164E ILE* 3.9 28.3 - - + -
345E LEU* 5.8 1.6 - - + -
374E PHE* 5.7 3.6 - - + -
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 5.6 1.3 - - + -
103E LEU* 4.2 10.1 - - + -
105E THR* 4.2 21.8 - - - +
134E ALA* 3.7 23.1 - - + -
135E ILE 3.2 14.4 - - - +
136E GLN 3.3 9.6 + - - +
137E ALA 3.1 0.4 - - - -
138E VAL* 1.3 82.9 - - + +
140E SER* 1.3 58.3 + - - +
142E TYR* 3.1 8.1 + - + +
143E ALA 2.9 23.0 + - - -
337E SER 4.3 0.2 - - - -
338E VAL* 3.6 25.6 - - + +
341E GLY* 3.1 17.2 - - - +
342E GLY* 3.6 24.0 - - - +
345E LEU* 4.4 15.5 - - + -
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Residues in contact with SER 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E GLN 3.3 6.6 + - - -
137E ALA 2.6 20.1 + - - -
139E LEU* 1.3 80.3 - - - +
141E LEU* 1.3 61.1 + - - +
143E ALA* 3.1 2.9 + - - +
144E SER* 2.9 25.7 + - - -
151E VAL* 3.2 18.7 - - - +
297E VAL* 4.6 4.6 - - - +
299E SER* 3.7 26.2 - - - -
337E SER* 3.7 25.8 + - - -
338E VAL* 4.3 2.2 - - - +
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E ALA 3.0 7.4 + - - +
138E VAL* 3.0 16.1 + - + +
140E SER* 1.3 82.4 + - - +
142E TYR* 1.3 65.3 + - + +
144E SER* 3.2 14.2 + - - -
145E GLY 3.2 8.0 + - - -
146E ARG* 3.2 33.3 + - + +
147E THR* 4.0 7.4 - - - +
148E THR 4.0 23.6 - - - +
149E GLY* 4.2 3.6 - - - +
151E VAL* 3.9 20.0 - - + -
164E ILE* 3.3 37.0 - - + -
167E GLY* 5.8 2.0 - - - -
297E VAL* 4.8 7.4 - - + -
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Residues in contact with TYR 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E VAL* 2.9 47.1 + - + -
139E LEU* 3.2 9.9 - - - +
141E LEU* 1.3 81.6 - - + +
143E ALA* 1.3 55.3 + - - +
145E GLY* 2.7 25.6 + - - +
146E ARG 4.8 3.1 - - - -
341E GLY* 4.3 1.1 - - - -
344E ILE* 3.7 35.3 - - + +
345E LEU* 3.3 35.3 - - + +
348E LEU* 4.7 14.8 - - + +
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LEU 2.9 6.0 + - - +
140E SER 3.1 7.8 + - - +
142E TYR* 1.3 78.0 - - - +
144E SER* 1.3 60.6 + - - +
145E GLY* 3.4 0.7 + - - -
337E SER* 3.3 34.1 - - - +
340E ILE* 3.8 21.3 - - + +
341E GLY* 3.7 13.2 - - - +
344E ILE* 5.0 3.1 - - - -
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Residues in contact with SER 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E SER 2.9 13.2 + - - -
141E LEU* 3.6 9.4 - - - -
142E TYR 3.1 0.6 - - - -
143E ALA* 1.3 74.9 - - - +
145E GLY* 1.3 63.1 + - - +
146E ARG* 3.3 26.8 + - - +
297E VAL* 3.7 20.5 - - - +
329E ILE* 5.5 6.5 - - - +
331E PRO* 4.3 16.7 - - - +
337E SER* 5.3 2.9 + - - -
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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