Contacts of the helix formed by residues 132 - 145 (chain A) in PDB entry 4ES7
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 ARG 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASN* 5.1 1.0 - - - +
103A GLU* 3.0 41.5 + - - +
131A LEU* 1.3 77.0 - - - +
133A GLU* 1.3 65.8 + - - +
134A THR* 3.5 31.5 + - + +
135A LEU* 3.0 32.4 + - + +
136A LEU* 3.5 8.8 + - - +
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Residues in contact with GLU 133 (chain A).
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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131A LEU 3.6 1.0 + - - -
132A ARG* 1.3 71.3 - - - +
134A THR* 1.3 58.7 + - + +
136A LEU* 2.9 30.7 + - - +
137A GLN* 2.9 54.2 + - + +
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Residues in contact with THR 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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132A ARG* 3.5 31.6 + - + +
133A GLU* 1.3 79.1 - - + +
135A LEU* 1.3 57.9 + - - +
137A GLN* 3.3 10.0 + - - +
138A ASP* 2.9 36.3 + - - +
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Residues in contact with LEU 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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103A GLU* 3.8 27.6 - - - +
104A TYR* 3.9 38.4 - - + -
106A ILE* 5.4 0.3 - - - +
124A LEU* 4.2 6.8 - - + +
131A LEU* 3.8 36.1 - - + -
132A ARG* 3.0 29.8 + - + +
134A THR* 1.3 79.5 + - - +
136A LEU* 1.3 62.2 + - - +
138A ASP* 3.3 22.2 + - + +
139A PHE* 2.9 29.8 + - - +
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Residues in contact with LEU 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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21A LEU* 5.4 6.7 - - + -
22A ALA* 5.6 3.6 - - + -
124A LEU* 3.8 24.9 - - + -
131A LEU* 4.6 15.3 - - + +
132A ARG 3.5 8.3 + - - +
133A GLU* 2.9 38.9 + - - +
135A LEU* 1.3 76.2 - - - +
137A GLN* 1.3 61.3 + - - +
139A PHE* 3.3 5.7 + - - +
140A ARG* 2.9 30.1 + - - +
155A THR* 4.6 30.3 - - + +
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Residues in contact with GLN 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 GLU* 2.9 40.4 + - + +
134A THR* 3.5 11.2 - - - +
136A LEU* 1.3 75.6 - - - +
138A ASP* 1.3 66.9 + - - +
140A ARG* 2.2 49.0 + - - +
141A VAL* 3.0 24.6 + - - +
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Residues in contact with ASP 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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104A TYR* 5.6 2.3 + - + -
106A ILE* 4.7 8.5 - - + -
134A THR* 2.9 21.8 + - - +
135A LEU* 3.4 32.1 - - + +
137A GLN* 1.3 75.3 - - - +
139A PHE* 1.3 63.1 + - - +
141A VAL* 3.1 14.0 - - - +
142A VAL* 3.0 28.7 + - + +
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Residues in contact with PHE 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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22A ALA* 3.7 26.2 - - + -
23A ILE* 3.9 8.5 - - - -
24A GLY 4.0 1.6 - - - -
106A ILE* 3.9 25.5 - - + +
122A ALA* 3.2 43.5 - - + -
123A LYS 3.6 6.7 - - - -
124A LEU* 3.6 41.7 - - + -
135A LEU 2.9 14.0 + - - +
136A LEU 3.5 8.5 - - - +
137A GLN 3.1 0.2 - - - -
138A ASP* 1.3 77.4 - - - +
140A ARG* 1.3 66.1 + - + +
142A VAL* 3.0 3.2 + - - +
143A ALA* 2.9 26.0 + - + +
153A ILE* 4.0 22.4 - - + -
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Residues in contact with ARG 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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136A LEU 2.9 14.6 + - - +
137A GLN* 2.2 53.7 + - - +
139A PHE* 1.3 79.0 - - + +
141A VAL* 1.3 63.6 + - - +
143A ALA* 3.4 2.1 + - - +
144A GLN* 2.9 67.3 + - - +
150A GLU* 3.8 21.9 + - - +
153A ILE* 4.3 27.6 - - + -
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Residues in contact with VAL 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 GLN 3.0 12.8 + - - +
138A ASP* 3.1 24.9 - - - +
140A ARG* 1.3 79.6 - - - +
142A VAL* 1.3 64.5 + - + +
144A GLN* 3.8 11.3 - - + +
145A GLY* 2.9 26.3 + - - -
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Residues in contact with VAL 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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4A GLN* 5.7 4.9 - - - +
97A VAL* 4.1 15.0 - - + -
98A HIS* 3.8 26.5 - - + +
106A ILE* 4.1 28.3 - - + -
108A LEU* 4.4 11.4 - - + -
138A ASP* 3.0 24.1 + - + +
139A PHE* 3.0 6.5 + - - +
141A VAL* 1.3 80.6 - - + +
143A ALA* 1.3 63.0 + - - +
145A GLY* 3.2 10.7 + - - -
146A VAL* 3.4 13.7 + - - +
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Residues in contact with ALA 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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122A ALA* 4.1 15.7 - - + -
139A PHE* 2.9 23.3 + - + +
142A VAL* 1.3 76.2 - - - +
144A GLN* 1.3 64.2 + - - +
146A VAL* 3.2 18.1 - - - +
148A ILE* 3.1 36.2 + - + +
153A ILE* 3.7 25.1 - - + -
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Residues in contact with GLN 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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140A ARG* 2.9 53.1 + - - +
141A VAL* 3.9 9.2 - - + +
143A ALA* 1.3 74.9 - - - +
145A GLY* 1.3 58.0 + - - +
146A VAL 3.0 0.2 - - - -
147A GLY* 2.9 20.8 + - - -
148A ILE 3.3 18.7 + - - +
150A GLU* 3.2 32.2 - - - +
153A ILE* 4.0 8.4 - - + +
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Residues in contact with GLY 145 (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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141A VAL* 2.9 18.6 + - - -
142A VAL 3.2 4.0 + - - -
143A ALA 3.2 0.4 - - - -
144A GLN* 1.3 76.7 - - - +
146A VAL* 1.3 58.0 + - - +
147A GLY 3.5 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