Contacts of the helix formed by residues 127 - 141 (chain B) 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 GLU 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLY 5.0 2.9 - - - +
126B VAL* 1.3 77.6 - - - +
128B ILE* 1.3 55.9 - - - +
129B LYS* 3.1 38.1 + - + -
130B GLU* 2.8 41.9 + - + +
131B LEU* 4.1 0.7 + - - +
174B ASP 4.1 3.1 - - - +
175B ASN* 3.5 32.3 - - - +
176B TYR 3.3 6.3 - - - +
177B VAL* 4.1 13.2 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL 3.8 1.0 + - - -
127B GLU* 1.3 71.7 - - - +
129B LYS* 1.3 63.0 + - - +
131B LEU* 2.9 28.6 + - + +
132B GLY* 3.2 4.0 + - - -
164B ILE* 3.4 25.6 - - + -
165B SER 3.3 28.0 - - - +
166B ILE* 3.9 24.2 - - + -
167B PRO* 4.0 8.7 - - + -
174B ASP* 3.7 16.7 + - + +
176B TYR* 3.0 34.4 + - + +
178B LEU* 4.4 13.5 - - + -
184B PHE* 4.1 10.3 - - + -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU* 3.0 26.6 + - + -
128B ILE* 1.3 77.0 - - - +
130B GLU* 1.3 70.6 + - - +
132B GLY* 3.2 4.2 + - - +
133B LYS 2.9 23.0 + - - -
167B PRO* 6.3 0.4 - - - -
169B ILE 5.7 0.4 - - - -
170B TYR* 3.2 36.6 + - + +
171B ARG 3.3 28.0 - - - +
172B PRO* 3.4 11.5 + - - +
174B ASP* 3.0 24.1 + - + +
175B ASN* 2.8 32.6 - - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.3 8.3 - - + +
126B VAL* 3.7 21.3 - - + -
127B GLU* 2.8 22.6 + - + +
129B LYS* 1.3 98.5 - - - +
131B LEU* 1.3 57.0 - - + +
133B LYS* 3.3 36.0 + - - +
134B ALA* 3.1 27.4 + - - +
170B TYR* 4.4 2.1 + - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA* 3.8 16.3 - - + +
121B VAL* 3.8 17.9 - - + -
122B ALA* 4.0 28.7 - - + -
126B VAL* 4.2 17.3 - - + -
127B GLU 4.2 2.9 - - - +
128B ILE* 2.9 16.4 + - + +
130B GLU* 1.3 76.9 - - - +
132B GLY* 1.3 60.6 + - - +
134B ALA* 3.3 3.0 + - - +
135B ILE* 2.9 37.1 + - - +
166B ILE* 4.0 36.6 - - + -
178B LEU* 4.3 14.4 - - + -
186B ILE* 4.1 13.5 - - + -
283B ILE* 5.5 1.1 - - + -
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE 3.2 8.3 + - - -
129B LYS* 3.2 5.3 + - - -
131B LEU* 1.3 80.9 - - - +
133B LYS* 1.3 57.0 + - - +
135B ILE* 3.6 3.5 - - - +
136B GLU* 2.9 32.2 + - - +
167B PRO* 3.4 25.1 + - - -
169B ILE* 3.8 13.3 - - - -
170B TYR 3.9 6.5 - - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LYS 2.9 11.5 + - - +
130B GLU* 3.3 34.0 + - - +
132B GLY* 1.3 74.2 - - - +
134B ALA* 1.3 66.1 + - - +
136B GLU* 3.3 2.3 + - - +
137B ASN* 3.0 49.2 + - - +
170B TYR* 3.5 45.7 + - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 4.1 31.1 - - + +
118B ALA* 4.3 1.8 - - - +
121B VAL* 4.3 13.2 - - + -
130B GLU 3.1 9.2 + - - +
131B LEU 3.5 8.5 - - - +
133B LYS* 1.3 81.1 - - - +
135B ILE* 1.3 63.6 + - - +
137B ASN* 3.5 4.6 + - - +
138B GLU* 3.2 28.1 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 3.7 13.6 - - + +
118B ALA* 3.7 24.5 - - + -
131B LEU 2.9 24.5 + - - +
132B GLY 3.6 3.4 - - - +
134B ALA* 1.3 77.6 - - - +
136B GLU* 1.3 62.9 + - - +
138B GLU* 3.4 4.2 + - - +
139B ILE* 3.3 28.3 + - + +
166B ILE* 4.4 6.7 - - + -
167B PRO 4.0 12.1 - - - +
168B ASN* 3.5 46.0 - - + +
186B ILE* 4.2 13.5 - - + -
188B PRO* 3.7 18.2 - - + -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLY 2.9 16.6 + - - +
133B LYS* 3.3 3.7 + - - +
135B ILE* 1.3 77.4 - - - +
137B ASN* 1.3 64.9 + - - +
139B ILE* 3.5 1.4 + - - +
140B ARG* 2.7 71.1 + - - +
146B PRO* 4.0 7.4 - - + -
168B ASN 3.6 10.8 - - - +
169B ILE* 3.9 8.8 - - - +
170B TYR* 2.8 35.1 + - - +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LYS* 3.0 36.7 + - - +
134B ALA* 3.9 5.5 - - - +
136B GLU* 1.3 85.2 - - - +
138B GLU* 1.3 66.5 + - - +
140B ARG* 4.7 4.3 - - - +
141B LYS* 3.0 33.6 + - + +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA 4.2 1.1 - - - +
113B GLU* 3.6 15.7 - - - +
114B ALA* 3.6 21.3 - - + +
117B ALA* 3.5 22.9 - - + +
134B ALA 3.2 13.8 + - - +
135B ILE 3.6 2.7 - - - +
137B ASN* 1.3 80.9 - - + +
139B ILE* 1.3 61.8 + - - +
141B LYS* 3.4 22.7 + - - +
142B ARG* 2.6 68.9 + - - +
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 4.1 12.1 - - - +
111B ALA* 5.3 0.2 - - - -
114B ALA* 4.0 15.9 - - + -
135B ILE* 3.3 29.6 + - + +
136B GLU 3.8 3.4 - - - +
137B ASN 3.3 0.4 - - - -
138B GLU* 1.3 80.8 - - - +
140B ARG* 1.3 61.4 + - - +
142B ARG* 3.3 9.9 + - - +
143B GLY 3.5 0.2 + - - -
144B PHE* 3.1 48.2 + - + +
145B LYS 3.7 1.6 - - - -
146B PRO* 3.5 39.0 - - + -
168B ASN* 5.1 0.2 - - + -
188B PRO* 4.6 3.4 - - + -
189B PHE 3.7 17.5 - - - +
190B ALA* 4.1 13.9 - - + -
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLU* 2.7 55.4 + - - +
137B ASN* 4.4 4.0 - - - +
139B ILE* 1.3 72.7 - - - +
141B LYS* 1.3 59.1 + - - +
142B ARG 3.0 5.2 - - - -
143B GLY* 3.0 19.6 + - - -
144B PHE 3.4 14.3 + - - +
145B LYS* 5.2 10.0 - - - +
146B PRO* 3.1 36.5 + - + +
148B VAL* 5.8 4.9 - - - +
169B ILE* 4.2 5.7 - - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ASN* 3.0 25.2 + - + +
138B GLU* 3.4 39.8 + - - +
140B ARG* 1.3 77.2 - - - +
142B ARG* 1.3 77.8 + - + +
143B 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