Contacts of the helix formed by residues 129 - 141 (chain A) in PDB entry 4Y99
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A THR* 4.7 9.9 - - + +
128A ILE* 1.3 76.2 - - - +
130A GLU* 1.3 64.2 + - - +
131A ASP* 3.4 14.8 + - - +
132A ASP* 3.0 48.9 + - - +
133A ILE* 3.4 10.9 - - - +
41C ILE* 5.3 0.7 - - - +
45C ARG* 5.2 4.6 + - - +
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Residues in contact with GLU 130 (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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128A ILE 4.1 0.2 + - - -
129A THR* 1.3 72.4 - - - +
131A ASP* 1.3 61.5 + - - +
133A ILE* 3.2 15.6 + - + +
134A GLU* 3.0 51.0 + - + +
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Residues in contact with ASP 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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129A THR* 3.2 12.4 + - - +
130A GLU* 1.3 77.8 - - - +
132A ASP* 1.3 64.4 + - - +
134A GLU* 4.6 5.6 - - - +
135A GLU* 3.1 32.4 + - + +
40C LYS* 3.4 49.2 + - + +
41C ILE* 4.3 5.6 - - + +
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Residues in contact with ASP 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 LEU* 4.7 0.9 - - + -
127A THR 3.5 2.1 - - - +
128A ILE* 3.6 11.7 - - + +
129A THR* 3.0 40.3 + - - +
131A ASP* 1.3 75.7 - - - +
133A ILE* 1.3 61.9 + - - +
136A LEU* 3.3 33.3 + - - +
41C ILE* 3.7 20.2 - - - +
45C ARG* 2.8 46.2 + - - -
49C LEU* 3.8 17.7 - - + +
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Residues in contact with ILE 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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114A LEU* 3.7 26.9 - - + -
117A LEU* 3.8 7.3 - - + +
118A LYS* 4.0 43.7 - - + -
121A LEU* 4.2 16.8 - - + -
122A GLN* 5.7 1.1 - - - +
128A ILE* 3.5 24.0 - - + +
129A THR 3.4 17.0 - - - +
130A GLU* 3.2 16.1 + - + +
131A ASP 3.2 0.4 - - - -
132A ASP* 1.3 76.8 - - - +
134A GLU* 1.3 65.0 + - + +
137A MET* 3.2 23.7 + - - +
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Residues in contact with GLU 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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114A LEU* 4.1 22.5 - - - +
130A GLU* 3.0 38.9 + - + +
131A ASP* 4.3 6.3 - - - +
133A ILE* 1.3 77.7 - - + +
135A GLU* 1.3 58.4 + - + +
137A MET* 3.6 4.7 + - - +
138A LYS* 3.0 52.0 + - - +
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Residues in contact with GLU 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 ASP* 3.1 23.3 + - + +
134A GLU* 1.3 77.4 - - + +
136A LEU* 1.3 61.4 + - - +
138A LYS* 3.4 23.2 + - - +
139A ASP* 2.8 31.6 + - - +
38C LYS 4.0 6.6 - - - +
39C SER* 3.6 21.0 + - - +
40C LYS* 2.7 41.1 + - + +
41C ILE* 3.8 21.1 - - + -
46C LYS* 4.1 6.4 + - - -
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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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117A LEU* 4.3 9.6 - - + -
121A LEU* 3.7 34.1 - - + -
132A ASP 3.3 20.8 + - - +
133A ILE 4.0 2.5 - - - +
134A GLU 3.4 0.2 - - - -
135A GLU* 1.3 79.2 - - - +
137A MET* 1.3 56.9 + - - +
139A ASP* 3.3 2.9 + - + +
140A GLY* 2.9 24.1 + - - -
148A ILE* 4.6 0.2 - - - +
156A PHE* 3.2 32.6 - - + -
41C ILE* 4.8 0.7 - - + -
46C LYS* 4.0 37.2 - - + +
49C LEU* 3.9 17.9 - - + -
50C LYS* 4.2 10.5 - - + -
53C LEU* 4.5 9.4 - - + -
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Residues in contact with MET 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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112A ILE* 3.8 8.3 - - + +
113A ASP 3.6 32.8 - - - +
114A LEU* 3.6 22.2 - - + +
117A LEU* 3.9 19.0 - - + +
133A ILE 3.2 17.9 + - - +
134A GLU* 3.8 5.8 - - - +
136A LEU* 1.3 74.7 - - - +
138A LYS* 1.3 56.2 + - + +
140A GLY 3.3 0.2 + - - -
141A ASP* 2.8 43.2 + - + +
146A GLY* 3.6 31.6 - - - +
147A ARG* 4.0 0.9 - - - -
148A ILE* 3.7 22.9 - - + -
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Residues in contact with LYS 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 GLU* 3.0 39.6 + - - +
135A GLU* 3.8 25.0 + - - +
137A MET* 1.3 77.3 - - + +
139A ASP* 1.3 62.2 + - - +
140A GLY 3.5 0.2 + - - -
141A ASP* 3.8 16.4 - - - +
142A LYS* 5.6 0.2 - - - -
37C LYS* 5.0 10.7 + - - +
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Residues in contact with ASP 139 (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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2A ASP* 5.4 2.4 - - - +
3A ASP* 3.5 20.8 - - - +
135A GLU 2.8 21.5 + - - +
136A LEU* 3.3 8.9 + - - +
138A LYS* 1.3 74.8 - - - +
140A GLY* 1.3 58.9 + - - +
142A LYS* 3.5 24.1 + - - -
156A PHE* 3.3 11.6 - - + +
46C LYS* 3.7 21.6 + - + +
50C LYS* 3.1 27.3 + - - -
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Residues in contact with GLY 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 12.3 + - - -
137A MET 3.8 1.8 - - - -
139A ASP* 1.3 78.5 - - - +
141A ASP* 1.3 57.4 + - - +
142A LYS* 3.2 12.2 + - - +
148A ILE* 3.9 14.4 - - - -
152A GLU* 3.3 24.9 - - - +
156A PHE* 3.3 26.4 - - - -
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Residues in contact with ASP 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 MET* 2.8 32.5 + - + +
138A LYS* 3.8 13.2 - - - +
139A ASP 3.6 0.6 - - - -
140A GLY* 1.3 68.2 - - - +
142A LYS* 1.3 61.5 + - - +
143A ASN* 3.1 5.9 - - - +
144A ASN* 3.2 20.5 + - - -
145A ASP* 3.1 7.8 + - - +
146A GLY* 2.5 33.8 + - - -
147A ARG 3.4 11.2 - - - +
148A ILE* 4.0 0.6 - - - +
152A GLU* 4.0 2.0 - - - -
202A CA 2.4 27.8 - - - -
37C LYS* 5.6 1.2 + - - -
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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