Contacts of the helix formed by residues 122 - 136 (chain A) in PDB entry 1G5J
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 THR 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A HIS* 4.3 17.9 - - + +
119A THR* 2.8 29.4 + - - +
120A PRO 4.6 1.4 + - - -
121A GLY* 1.3 75.9 - - - +
123A ALA* 1.3 56.4 + - - +
124A TYR* 2.9 7.9 - - + -
125A GLN* 2.7 46.3 + - + +
126A SER* 3.6 4.0 + - - -
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Residues in contact with ALA 123 (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 HIS 5.1 1.1 - - - -
118A ILE* 4.6 11.7 - - + -
119A THR 3.1 9.3 + - - +
121A GLY 5.2 0.4 - - - +
122A THR* 1.3 76.9 - - - +
124A TYR* 1.3 62.1 + - - +
126A SER* 3.2 12.8 + - - -
127A PHE* 3.0 23.2 + - - +
166A LEU* 3.5 37.9 - - + -
170A ILE* 5.5 3.8 - - + -
173A TRP* 4.1 15.8 - - + -
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Residues in contact with TYR 124 (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 GLY 3.2 26.4 - - - +
122A THR* 2.8 4.1 + - + +
123A ALA* 1.3 80.2 - - - +
125A GLN* 1.3 108.7 + - + +
127A PHE* 3.8 2.7 - - - +
128A GLU* 3.0 38.3 + - + +
169A ARG* 6.0 2.7 - - - +
173A TRP* 4.1 21.0 - - + -
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Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 2.7 26.8 + - + +
124A TYR* 1.3 110.4 + - + +
126A SER* 1.3 64.7 + - - +
128A GLU* 3.8 6.8 - - - +
129A GLN* 3.2 39.8 + - - +
302B LEU* 4.7 17.0 - - + +
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Residues in contact with SER 126 (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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116A LEU* 2.7 37.2 - - - +
117A HIS 4.2 4.0 + - - -
118A ILE* 4.2 4.7 - - - +
122A THR 3.9 6.2 + - - -
123A ALA* 3.2 13.7 + - - -
125A GLN* 1.3 73.0 - - - +
127A PHE* 1.3 68.6 + - - +
129A GLN* 2.7 14.4 + - - +
130A VAL* 2.7 21.0 + - - +
154A LEU* 5.9 4.3 - - - -
302B LEU* 3.9 8.4 - - - +
305B ALA* 3.7 12.8 - - - -
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Residues in contact with PHE 127 (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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123A ALA 3.0 12.4 + - - +
124A TYR* 3.8 4.3 - - - +
126A SER* 1.3 76.6 - - - +
128A GLU* 1.3 58.2 + - - +
130A VAL* 3.3 13.4 - - + +
131A VAL* 2.7 48.4 + - + +
147A PHE* 3.7 26.7 - + - -
150A PHE* 6.0 3.8 - + - -
151A GLY* 5.1 6.3 - - - -
154A LEU* 5.4 9.4 - - + +
170A ILE* 3.6 28.9 - - + -
173A TRP* 3.7 45.8 - + + -
174A MET* 3.5 26.9 - - + -
177A TYR* 5.1 3.6 - + - -
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Residues in contact with GLU 128 (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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124A TYR* 3.0 27.4 + - + +
125A GLN* 3.8 10.3 - - - +
127A PHE* 1.3 77.0 - - - +
129A GLN* 1.3 58.1 + - + +
131A VAL* 3.3 14.9 - - - +
132A ASN* 3.1 44.6 + - - +
177A TYR* 5.1 2.9 - - - -
181A HIS* 5.2 5.9 + - - -
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Residues in contact with GLN 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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125A GLN* 3.2 26.7 + - - +
126A SER 2.7 14.3 + - - +
128A GLU* 1.3 71.0 - - + +
130A VAL* 1.3 59.7 + - - +
132A ASN* 2.6 39.8 + - - +
133A GLU* 3.2 10.4 + - - +
302B LEU* 5.0 10.1 - - + -
305B ALA* 3.3 18.8 - - + -
306B GLN* 3.4 31.2 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 2.7 36.8 + - - +
127A PHE* 3.3 17.9 - - + +
129A GLN* 1.3 72.0 - - - +
131A VAL* 1.3 60.6 + - + +
133A GLU 3.5 0.7 + - - -
134A LEU* 2.9 38.4 + - + +
147A PHE* 6.0 2.5 - - + -
150A PHE* 3.3 45.1 - - + -
154A LEU* 5.6 4.3 - - + -
305B ALA* 3.2 31.2 - - + +
306B GLN 5.4 0.2 - - - -
308B TYR* 5.1 2.0 - - + -
309B GLY* 3.9 5.4 - - - +
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Residues in contact with VAL 131 (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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127A PHE* 2.7 27.5 + - + +
128A GLU* 3.3 27.1 - - - +
130A VAL* 1.3 79.1 - - + +
132A ASN* 1.3 66.6 + - - +
134A LEU* 3.6 4.4 - - - +
135A PHE* 3.0 23.7 + - + +
147A PHE* 4.0 24.2 - - + -
177A TYR* 3.1 61.1 + - + +
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Residues in contact with ASN 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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128A GLU* 3.2 25.5 + - - +
129A GLN* 2.6 27.4 + - - +
131A VAL* 1.3 78.0 - - - +
133A GLU* 1.3 63.2 + - + +
134A LEU 3.0 0.6 + - - -
135A PHE 3.6 0.2 - - - -
136A ARG* 2.7 49.5 + - - +
177A TYR* 5.1 1.5 + - - -
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Residues in contact with GLU 133 (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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129A GLN* 3.2 12.5 + - - +
130A VAL 4.4 1.6 - - - +
132A ASN* 1.3 85.5 + - + +
134A LEU* 1.3 61.6 + - - +
136A ARG* 3.2 42.4 + - - +
306B GLN* 3.7 43.7 + - + +
309B GLY 4.2 2.7 - - - +
310B ARG* 4.1 18.6 + - + +
313B ARG* 4.0 19.9 + - - +
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Residues in contact with LEU 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 VAL* 2.9 24.9 + - + +
131A VAL* 3.6 6.1 - - - +
132A ASN 3.0 0.2 - - - -
133A GLU* 1.3 79.9 - - - +
135A PHE* 1.3 83.9 + - + +
136A ARG 3.5 0.6 + - - -
143A ARG* 3.3 30.8 + - + +
146A ALA* 5.9 0.4 - - + -
147A PHE* 4.2 18.4 - - + +
150A PHE* 4.0 25.4 - - + -
309B GLY* 4.0 9.6 - - - +
312B LEU* 3.9 33.9 - - + +
313B ARG* 4.1 12.1 - - - +
316B SER* 5.6 1.1 - - - -
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Residues in contact with PHE 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 VAL* 3.0 17.2 + - + +
132A ASN 3.6 1.6 - - - -
134A LEU* 1.3 106.9 - - + +
136A ARG* 1.3 67.5 + - - +
137A ASP 3.6 1.3 - - - -
138A GLY 3.4 13.2 + - - +
139A VAL* 3.5 45.8 - - + +
143A ARG* 3.0 45.1 - - + -
144A ILE* 3.8 2.5 - - - -
147A PHE* 3.6 22.4 - + + -
177A TYR* 4.1 22.2 - + + +
182A LEU* 3.6 13.7 - - + -
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Residues in contact with ARG 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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132A ASN* 2.7 31.7 + - - +
133A GLU* 3.2 35.6 + - - +
134A LEU 3.5 2.4 - - - -
135A PHE* 1.3 81.2 - - - +
137A ASP* 1.3 61.9 + - + +
138A GLY 3.8 1.0 + - - -
313B ARG* 6.0 3.6 - - - +
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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