Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 1WKM
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 ILE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL 3.7 1.3 + - - -
127A GLU* 1.3 71.8 - - - +
129A LYS* 1.3 63.4 + - - +
130A GLU 3.0 0.2 - - - -
131A LEU* 2.9 28.4 + - + +
132A GLY* 3.3 3.9 + - - -
164A ILE* 3.5 25.6 - - + -
165A SER 3.3 27.8 - - - +
166A ILE* 4.0 22.0 - - + -
167A PRO* 4.3 7.9 - - + -
174A ASP* 3.8 14.5 + - + +
176A TYR* 3.0 33.3 + - + +
178A LEU* 4.3 14.1 - - + -
184A PHE* 4.0 12.8 - - + -
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Residues in contact with LYS 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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127A GLU* 3.1 31.0 + - + -
128A ILE* 1.3 76.6 - - - +
130A GLU* 1.3 71.7 + - - +
131A LEU 3.3 0.2 - - - -
132A GLY* 3.3 4.5 + - - +
133A LYS 2.9 24.3 + - - -
167A PRO* 6.5 0.2 - - - -
169A ILE 5.7 0.7 - - - -
170A TYR* 3.2 41.5 + - + +
171A ARG 3.3 26.0 - - - +
172A PRO* 3.6 8.1 + - - +
174A ASP* 3.0 23.2 + - + +
175A ASN* 2.7 28.4 - - - +
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Residues in contact with GLU 130 (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 VAL* 4.5 9.1 - - + +
126A VAL* 3.6 21.3 - - + -
127A GLU* 2.9 22.3 + - + +
128A ILE 2.9 0.2 + - - -
129A LYS* 1.3 95.6 - - + +
131A LEU* 1.3 65.4 + - + +
133A LYS* 3.4 33.1 + - - +
134A ALA* 3.0 24.0 + - - +
170A TYR* 4.5 1.7 + - - -
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Residues in contact with LEU 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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118A ALA* 3.7 18.3 - - + +
121A VAL* 4.2 11.0 - - + -
122A ALA* 4.0 26.9 - - + -
126A VAL* 4.4 12.3 - - + -
127A GLU 4.6 1.8 - - - +
128A ILE* 2.9 14.5 + - - +
130A GLU* 1.3 76.7 - - - +
132A GLY* 1.3 55.2 + - - +
134A ALA* 3.2 3.6 + - - +
135A ILE* 2.8 40.8 + - - +
166A ILE* 3.9 31.9 - - + -
178A LEU* 4.1 18.4 - - + -
186A ILE* 3.7 29.4 - - + -
283A ILE* 5.5 1.1 - - + -
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Residues in contact with GLY 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 ILE 3.3 4.5 + - - -
129A LYS* 3.3 8.4 + - - -
130A GLU 3.2 0.4 - - - -
131A LEU* 1.3 77.0 - - - +
133A LYS* 1.3 58.6 + - - +
135A ILE* 3.2 4.4 + - - +
136A GLU* 2.8 32.4 + - - +
166A ILE* 5.2 0.2 - - - +
167A PRO* 3.6 24.4 + - - -
168A ASN 4.0 0.5 - - - +
169A ILE 3.7 18.8 - - - -
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Residues in contact with LYS 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 LYS 2.9 11.0 + - - +
130A GLU* 3.5 32.1 + - - +
131A LEU 3.3 0.2 - - - -
132A GLY* 1.3 75.2 - - - +
134A ALA* 1.3 64.5 + - - +
136A GLU* 3.3 1.7 + - - -
137A ASN* 3.0 51.3 + - - +
170A TYR* 3.4 49.7 + - + +
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Residues in contact with ALA 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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117A ALA* 3.9 19.2 - - + +
121A VAL* 4.0 25.4 - - + -
130A GLU 3.0 9.9 + - - +
131A LEU 3.2 10.7 + - - +
133A LYS* 1.3 81.7 - - - +
135A ILE* 1.3 61.9 + - - +
137A ASN* 4.1 4.6 - - - +
138A GLU* 3.2 29.3 + - - +
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Residues in contact with ILE 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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114A ALA* 3.7 15.7 - - + +
118A ALA* 3.7 24.5 - - + -
131A LEU 2.8 27.2 + - - +
132A GLY* 3.5 4.3 - - - +
134A ALA* 1.3 75.6 - - - +
136A GLU* 1.3 65.4 + - - +
138A GLU* 3.2 12.3 + - - +
139A ILE* 3.3 20.6 + - + +
166A ILE* 4.5 7.0 - - + -
167A PRO 4.0 12.6 - - - +
168A ASN* 3.5 42.0 - - - +
186A ILE* 4.2 13.9 - - + -
188A PRO* 3.6 17.5 - - + -
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Residues in contact with GLU 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 GLY 2.8 19.5 + - - +
133A LYS 3.7 3.6 - - - +
135A ILE* 1.3 73.4 - - - +
137A ASN* 1.3 65.4 + - - +
139A ILE* 3.4 1.2 + - - +
140A ARG* 2.8 77.1 + - + +
146A PRO* 4.0 9.2 - - + -
168A ASN 3.6 12.3 + - - +
169A ILE* 3.9 8.6 - - - +
170A TYR* 2.8 39.9 + - - +
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Residues in contact with ASN 137 (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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133A LYS* 3.0 40.4 + - - +
134A ALA* 4.1 4.6 - - - +
136A GLU* 1.3 86.3 - - - +
138A GLU* 1.3 61.9 + - + +
140A ARG* 4.7 3.9 - - - +
141A LYS* 2.8 38.4 + - + +
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Residues in contact with GLU 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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110A ALA* 4.2 3.2 - - - +
113A GLU* 3.8 13.5 - - - +
114A ALA* 3.6 16.6 - - - +
117A ALA* 3.5 22.9 - - + +
134A ALA 3.2 15.5 + - - +
135A ILE 3.2 9.5 + - - +
137A ASN* 1.3 79.0 - - + +
139A ILE* 1.3 60.5 + - - +
141A LYS* 3.3 19.8 + - - +
142A ARG* 2.7 69.6 + - - +
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Residues in contact with ILE 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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110A ALA* 3.9 10.8 - - - +
111A ALA* 5.2 0.4 - - - -
114A ALA* 3.9 14.6 - - + -
135A ILE* 3.3 30.9 + - + +
136A GLU 3.7 3.8 - - - +
137A ASN 3.2 0.4 - - - -
138A GLU* 1.3 78.3 - - - +
140A ARG* 1.3 62.7 + - - +
142A ARG* 3.4 8.8 + - - +
144A PHE* 3.1 32.4 + - + +
145A LYS 3.7 3.6 - - - -
146A PRO* 3.5 38.4 - - + -
168A ASN* 5.1 0.4 - - + -
188A PRO* 4.6 2.9 - - + -
189A PHE 3.7 23.8 - - - +
190A ALA* 3.9 20.9 - - + -
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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 GLU* 2.8 59.9 + - + +
137A ASN* 4.6 3.4 - - - +
139A ILE* 1.3 71.4 - - - +
141A LYS* 1.3 57.7 + - - +
142A ARG 2.8 5.2 - - - -
143A GLY* 2.6 27.0 + - - -
144A PHE 3.3 10.5 + - - +
145A LYS* 4.5 15.2 - - - +
146A PRO* 3.7 34.1 + - + +
148A VAL* 6.0 1.8 - - - +
169A ILE* 4.4 5.5 - - - +
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Residues in contact with LYS 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 ASN* 2.8 21.7 + - + +
138A GLU* 3.3 25.4 + - - +
140A ARG* 1.3 78.6 - - - +
142A ARG* 1.3 90.6 + - + +
143A GLY 3.3 1.3 + - - -
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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