Contacts of the helix formed by residues 128 - 144 (chain A) in PDB entry 5J3S
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 ASN 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU 3.5 2.2 + - - -
127A ASN* 1.3 81.8 - - - +
129A LEU* 1.3 58.8 - - - +
130A SER* 3.2 4.0 - - - +
131A GLU* 3.1 8.4 + - + +
132A ARG* 3.0 29.2 + - - +
342A CYS* 3.8 38.0 + - - +
344A ARG* 4.9 8.5 - - + +
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Residues in contact with LEU 129 (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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122A ASP 4.7 0.7 - - - +
123A GLY* 3.3 28.7 - - - +
125A ASP 3.4 18.8 - - - +
126A LEU* 3.6 17.7 + - + +
127A ASN 3.0 3.4 + - - -
128A ASN* 1.3 78.1 - - - +
130A SER* 1.3 58.0 + - - +
132A ARG* 4.0 10.3 - - - +
133A ALA* 2.9 37.2 + - + +
154A ILE* 3.9 14.1 - - + -
156A PRO* 5.5 4.5 - - + -
157A TYR* 3.8 39.7 - - + +
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASN* 3.2 1.4 - - - -
129A LEU* 1.3 81.8 - - - +
131A GLU* 1.3 57.9 + - - +
133A ALA* 4.1 4.1 + - - +
134A ARG* 3.6 18.0 + - - +
160A TYR* 4.6 11.0 - - - -
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASN* 3.1 12.0 + - + +
130A SER* 1.3 77.4 - - - +
132A ARG* 1.3 65.2 + - - +
133A ALA 3.3 1.6 - - - -
134A ARG* 3.2 8.7 + - + +
135A GLY* 3.0 17.0 + - - -
340A LEU* 3.6 10.5 - - + +
341A ASP* 3.3 22.0 + - - +
342A CYS* 3.2 47.5 + - - +
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Residues in contact with ARG 132 (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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121A ILE 3.3 14.8 + - - -
122A ASP* 2.9 35.4 + - - +
125A ASP* 2.7 49.7 + - - +
127A ASN 3.3 13.9 + - - -
128A ASN* 3.0 27.2 + - + +
129A LEU* 4.0 9.5 - - + +
131A GLU* 1.3 75.3 - - - +
133A ALA* 1.3 58.4 + - - +
135A GLY* 3.0 2.4 + - - -
136A VAL* 2.8 32.7 + - - +
157A TYR* 4.2 5.9 - - - +
304A ASN* 5.0 3.7 - - - +
340A LEU* 3.6 14.1 - - + -
342A CYS* 5.2 1.6 - - - -
344A ARG* 4.8 8.5 - - + +
345A PHE 3.5 20.5 + - - +
346A PRO* 3.3 20.4 + - + +
347A SER* 4.4 2.2 - - - +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 2.9 22.9 + - + +
130A SER* 4.4 4.3 - - - +
132A ARG* 1.3 77.9 - - - +
134A ARG* 1.3 58.1 + - - +
136A VAL* 4.0 1.5 - - - +
137A CYS* 3.2 33.1 + - - +
157A TYR* 3.4 36.8 + - + -
160A TYR* 3.9 22.3 - - + -
161A LEU* 5.7 0.2 - - - +
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Residues in contact with ARG 134 (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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130A SER 3.6 13.5 + - - +
131A GLU* 3.2 13.1 + - + +
133A ALA* 1.3 77.3 - - - +
135A GLY* 1.3 58.9 + - - +
137A CYS* 4.1 2.5 - - - +
138A SER* 3.3 23.2 + - - -
160A TYR* 3.5 24.0 + - - +
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Residues in contact with GLY 135 (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 GLU 3.0 9.5 + - - -
132A ARG 3.0 6.5 + - - -
134A ARG* 1.3 76.1 - - - +
136A VAL* 1.3 63.2 + - - +
137A CYS 3.3 0.2 - - - -
138A SER* 2.6 24.8 + - - -
139A TYR* 3.0 17.7 + - - -
340A LEU* 4.3 21.8 - - - -
346A PRO* 4.9 2.2 - - - -
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Residues in contact with VAL 136 (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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119A TRP* 4.3 24.9 - - + -
121A ILE* 4.1 24.9 - - + -
132A ARG 2.8 20.1 + - - +
133A ALA 4.0 2.9 - - - +
134A ARG 3.5 0.2 - - - -
135A GLY* 1.3 77.2 - - - +
137A CYS* 1.3 63.5 + - - +
139A TYR* 3.1 5.2 + - - +
140A LEU* 3.0 35.4 + - + +
150A LEU* 5.2 3.1 - - + -
157A TYR* 3.4 22.4 - - + +
161A LEU* 5.3 5.2 - - + -
346A PRO* 3.6 25.4 - - + +
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Residues in contact with CYS 137 (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 ALA* 3.2 13.6 + - - +
134A ARG* 4.2 4.5 - - - +
136A VAL* 1.3 78.5 - - - +
138A SER* 1.3 58.5 + - - +
140A LEU* 3.1 9.6 + - - +
141A ALA* 2.8 31.9 + - - +
160A TYR* 3.6 31.2 - - + +
161A LEU* 3.6 28.5 - - - -
164A ARG* 3.8 16.8 - - + -
165A SER* 4.4 6.1 - - - +
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Residues in contact with SER 138 (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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134A ARG 3.3 14.9 + - - -
135A GLY* 2.6 23.9 + - - -
137A CYS* 1.3 77.8 - - - +
139A TYR* 1.3 66.5 + - - +
141A ALA* 4.0 5.9 - - - +
142A LEU* 3.4 34.0 + - - +
340A LEU* 5.9 0.5 - - - +
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Residues in contact with TYR 139 (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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119A TRP* 4.1 22.4 - + + -
135A GLY 3.0 24.4 + - - -
136A VAL 3.1 6.3 + - - +
138A SER* 1.3 86.2 + - - +
140A LEU* 1.3 65.3 + - + +
142A LEU* 4.3 4.6 - - + -
143A TYR* 3.3 42.4 + + - +
335A LEU* 4.5 16.6 - - + +
336A GLY* 3.7 28.6 - - - -
337A LEU 3.9 1.0 + - - -
338A GLU* 3.3 40.6 + - - +
340A LEU* 5.1 6.5 - - + -
346A PRO* 4.3 11.0 - - + -
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Residues in contact with LEU 140 (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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117A ILE* 3.7 33.0 - - + -
119A TRP* 5.3 6.3 - - + -
136A VAL* 3.0 25.5 + - + +
137A CYS* 3.6 8.5 - - - +
139A TYR* 1.3 77.6 - - + +
141A ALA* 1.3 58.5 + - - +
144A SER* 2.8 30.0 + - - -
145A PRO* 3.5 5.3 - - + +
148A ILE* 3.6 42.2 - - + -
150A LEU* 5.3 4.0 - - + -
161A LEU* 4.4 22.9 - - + -
165A SER* 4.8 8.7 - - - +
168A TYR* 5.0 2.7 + - + +
183A MET* 4.7 3.8 - - - -
335A LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 141 (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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137A CYS 2.8 16.6 + - - +
138A SER* 4.0 8.1 - - - +
139A TYR 3.2 0.2 - - - -
140A LEU* 1.3 79.3 - - - +
142A LEU* 1.3 66.7 + - + +
144A SER* 3.7 12.4 + - - +
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Residues in contact with LEU 142 (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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138A SER* 3.4 22.2 + - - +
139A TYR* 4.3 4.7 - - + +
141A ALA* 1.3 80.0 - - + +
143A TYR* 1.3 67.2 + - + +
144A SER* 4.6 1.4 - - - -
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Residues in contact with TYR 143 (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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117A ILE* 4.5 14.6 - - + -
139A TYR* 3.3 35.7 + + - +
140A LEU 4.4 0.7 - - - +
142A LEU* 1.3 82.0 - - + +
144A SER* 1.3 70.6 + - - +
145A PRO* 4.5 2.8 - - + +
333A ASP* 6.1 0.9 - - - +
334A LEU 5.3 2.3 + - - -
335A LEU* 4.3 28.0 - - + +
353A LEU* 3.6 31.2 - - + +
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Residues in contact with SER 144 (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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115A SER* 4.7 1.4 + - - -
140A LEU 2.8 19.7 + - - -
141A ALA* 3.8 12.1 - - - +
142A LEU 3.5 1.3 - - - -
143A TYR* 1.3 77.0 - - - +
145A PRO* 1.3 69.8 + - - +
167A ASN* 5.3 5.5 + - - -
168A TYR* 4.1 6.4 + - - -
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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