Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 5WY5
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A VAL* 4.2 3.4 - - - -
140A LYS* 4.5 19.1 - - + +
141A MET* 1.3 80.5 - - - +
143A LYS* 1.3 67.8 + - - +
144A LYS* 3.2 42.5 - - + +
145A GLU* 2.9 13.2 + - + +
146A ALA* 2.8 23.1 + - - +
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Residues in contact with LYS 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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127A THR* 6.2 0.2 - - - +
130A LEU* 3.5 50.2 + - + +
131A ASN* 3.9 20.6 + - - +
133A VAL* 4.3 8.9 - - + +
134A ASP* 5.4 5.1 + - - -
142A ARG* 1.3 72.5 - - - +
144A LYS* 1.3 56.6 + - + +
146A ALA* 2.9 10.0 + - - +
147A GLU* 2.7 49.2 + - + +
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Residues in contact with LYS 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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142A ARG* 3.1 40.7 + - + +
143A LYS* 1.3 79.4 - - + +
145A GLU* 1.3 64.4 + - - +
147A GLU* 3.1 26.1 + - - +
148A GLN* 3.3 17.9 + - - +
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Residues in contact with GLU 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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104A ASN* 4.0 11.6 + - - -
105A GLU* 5.9 1.4 - - - +
139A LYS* 5.5 4.2 - - - -
140A LYS 4.5 3.0 - - - +
141A MET* 3.3 37.8 - - + +
142A ARG* 2.9 16.8 + - + +
144A LYS* 1.3 74.7 - - - +
146A ALA* 1.3 62.3 + - - +
148A GLN* 3.3 20.8 + - - +
149A VAL* 3.1 30.1 + - + +
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Residues in contact with ALA 146 (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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108A LEU* 4.2 7.1 - - + +
130A LEU* 3.9 11.4 - - + -
133A VAL* 3.6 22.7 - - + -
141A MET* 3.6 21.7 - - - -
142A ARG 2.8 11.7 + - - +
143A LYS* 3.2 10.3 - - - +
145A GLU* 1.3 75.4 - - - +
147A GLU* 1.3 65.9 + - - +
149A VAL* 3.3 5.5 + - - +
150A LEU* 3.0 27.0 + - - +
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Residues in contact with GLU 147 (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 LEU* 4.1 23.9 - - + +
143A LYS* 2.7 37.0 + - - +
144A LYS* 3.1 19.6 + - - +
146A ALA* 1.3 72.5 - - - +
148A GLN* 1.3 62.7 + - + +
150A LEU* 3.5 5.4 + - - +
151A GLN* 3.1 30.3 + - - +
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Residues in contact with GLN 148 (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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144A LYS* 3.3 10.6 + - - +
145A GLU* 3.3 23.1 + - - +
146A ALA 3.2 0.4 - - - -
147A GLU* 1.3 75.5 - - + +
149A VAL* 1.3 58.1 + - + +
151A GLN* 2.6 33.0 + - - +
152A LYS* 2.8 10.4 + - - +
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Residues in contact with VAL 149 (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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105A GLU* 3.8 36.8 - - + +
108A LEU* 3.7 10.3 - - + -
141A MET* 4.3 10.3 - - + -
145A GLU* 3.2 23.8 - - + +
146A ALA* 3.3 8.5 + - - +
148A GLN* 1.3 75.2 - - + +
150A LEU* 1.3 58.9 + - - +
152A LYS* 2.8 31.1 + - + +
153A PHE* 2.9 44.4 + - + -
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Residues in contact with LEU 150 (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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108A LEU* 4.2 13.7 - - + -
112A ALA* 5.0 4.9 - - + -
126A SER* 5.0 3.8 - - - -
129A ILE* 4.2 23.1 - - + -
130A LEU* 4.0 26.9 - - + -
146A ALA 3.0 13.6 + - - +
147A GLU* 3.7 10.8 - - - +
148A GLN 3.1 0.2 - - - -
149A VAL* 1.3 76.6 - - - +
151A GLN* 1.3 71.0 - - - +
153A PHE* 3.3 23.8 + - + +
154A VAL* 3.1 26.4 + - - +
159A LEU* 4.0 15.2 - - + +
166A PHE* 4.0 28.5 - - + -
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Residues in contact with GLN 151 (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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147A GLU* 3.1 16.0 + - - +
148A GLN* 2.6 20.8 + - - +
150A LEU* 1.3 79.5 - - - +
152A LYS* 1.3 57.1 + - - -
154A VAL* 3.2 16.6 + - + +
155A GLN* 2.8 33.2 + - + +
161A GLU* 3.6 17.8 + - - +
166A PHE* 4.4 7.5 - - - -
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Residues in contact with LYS 152 (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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101A PHE* 3.2 30.2 - - + -
105A GLU* 2.7 33.8 + - - +
148A GLN 2.8 6.6 + - - +
149A VAL* 2.8 24.3 + - + +
151A GLN* 1.3 77.8 - - - +
153A PHE* 1.3 55.0 + - - +
155A GLN* 2.9 7.8 + - + +
156A ASN* 2.9 42.1 + - - +
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Residues in contact with PHE 153 (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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97A MET* 3.9 20.2 - - + -
101A PHE* 3.8 35.2 - + - -
105A GLU 3.5 20.6 - - - -
108A LEU* 4.0 13.5 - - + -
109A PHE* 3.9 25.4 - + + -
149A VAL* 2.9 38.9 + - + -
150A LEU* 3.3 22.2 + - + +
152A LYS* 1.3 75.2 - - - +
154A VAL* 1.3 59.8 + - - +
156A ASN 3.8 0.4 - - - -
157A LYS 3.2 2.1 + - - -
158A TRP* 2.9 20.9 + + + -
159A LEU* 2.9 44.4 + - + +
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Residues in contact with VAL 154 (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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150A LEU 3.1 16.3 + - - +
151A GLN* 3.4 20.6 - - + +
152A LYS 3.0 0.6 - - - -
153A PHE* 1.3 75.3 - - - +
155A GLN* 1.3 70.4 - - + +
156A ASN 3.1 0.7 + - - -
157A LYS* 3.2 20.3 + - - +
159A LEU* 3.4 21.1 - - + +
160A ILE* 5.2 0.4 - - - -
161A GLU* 4.7 11.7 - - + +
166A PHE* 3.7 26.9 - - + -
169A HIS* 5.3 0.2 - - - -
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Residues in contact with GLN 155 (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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151A GLN* 2.8 19.8 + - + +
152A LYS* 2.9 8.9 + - + +
154A VAL* 1.3 79.7 - - + +
156A ASN* 1.3 62.4 + - - +
157A LYS* 3.4 22.2 + - - +
272B ASN* 2.9 42.3 + - - +
273B GLN* 3.4 30.4 - - - +
275B PRO* 5.5 0.5 - - - +
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Residues in contact with ASN 156 (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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26A GLY* 5.8 0.4 - - - -
100A ASP* 4.6 9.0 + - - -
101A PHE* 4.3 10.2 - - + -
152A LYS* 2.9 34.7 + - - +
155A GLN* 1.3 81.8 + - - +
157A LYS* 1.3 72.8 + - - +
158A TRP* 3.2 25.6 + - + +
171A ARG* 2.9 24.8 + - - +
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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