Contacts of the helix formed by residues 149 - 160 (chain B) in PDB entry 2W4G
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 ASP 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B SER* 3.9 0.2 - - - -
142B PRO 4.4 0.2 - - - +
143B ASP* 2.8 41.2 + - + +
146B GLY* 4.0 2.4 - - - -
147B ASN* 2.9 43.9 + - - +
148B VAL* 1.3 71.2 - - - +
150B TYR* 1.3 57.9 + - - +
151B LYS* 3.2 3.4 - - + -
152B ASN* 2.8 34.7 + - - +
153B ILE* 2.8 27.7 + - - +
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Residues in contact with TYR 150 (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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98B MET* 4.2 4.3 - - + -
101B PHE* 3.3 50.7 - + + -
105B ASP* 4.1 3.6 - - - +
111B SER* 3.2 23.6 + - - -
112B ILE* 3.3 43.7 - - + +
117B LEU* 3.0 37.9 - - + +
148B VAL* 2.5 47.8 + - + +
149B ASP* 1.3 71.0 - - - +
151B LYS* 1.3 62.7 + - + +
153B ILE* 3.4 16.8 - - + +
154B CYS* 2.9 29.6 + - - -
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Residues in contact with LYS 151 (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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98B MET* 3.8 26.9 - - + -
109B LYS* 3.8 26.1 + - - +
111B SER* 5.3 7.4 - - - +
147B ASN* 5.5 7.6 - - - +
149B ASP* 4.9 1.1 - - - -
150B TYR* 1.3 79.5 - - + +
152B ASN* 1.3 68.1 + - - +
154B CYS* 3.3 2.9 + - - +
155B TYR* 3.0 43.8 + - + +
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Residues in contact with ASN 152 (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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143B ASP* 4.3 11.0 - - + +
149B ASP* 2.8 46.7 + - + +
151B LYS* 1.3 75.6 - - - +
153B ILE* 1.3 62.6 + - - +
155B TYR* 3.0 17.0 + - - +
156B VAL* 2.9 30.4 + - + +
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Residues in contact with ILE 153 (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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101B PHE* 4.1 21.1 - - + -
136B MET* 5.7 4.9 - - + -
140B PHE* 3.7 30.9 - - + -
143B ASP* 3.2 27.5 + - - +
144B VAL* 4.2 6.3 - - + -
148B VAL* 4.0 14.8 - - + +
149B ASP 2.8 12.0 + - - +
150B TYR* 3.4 36.1 - - + +
152B ASN* 1.3 70.7 - - - +
154B CYS* 1.3 61.5 + - - +
156B VAL* 3.4 1.4 + - - -
157B ILE* 3.1 34.1 + - + +
820M VAL* 5.5 7.0 - - + -
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Residues in contact with CYS 154 (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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94B GLU* 4.5 9.4 - - + +
97B ILE* 3.6 15.0 - - + -
98B MET* 3.0 45.8 - - + -
101B PHE* 3.2 31.9 - - - -
150B TYR 2.9 10.1 + - - -
151B LYS 3.5 2.5 - - - +
153B ILE* 1.3 71.6 - - - +
155B TYR* 1.3 64.4 + - + +
157B ILE* 3.1 12.2 - - - +
158B THR* 3.1 28.0 + - - +
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Residues in contact with TYR 155 (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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94B GLU* 3.7 22.9 - - + -
98B MET* 5.3 10.2 - - + +
151B LYS* 3.0 40.5 + - + +
152B ASN* 3.0 15.5 + - - +
154B CYS* 1.3 79.2 - - + +
156B VAL* 1.3 54.9 + - + +
158B THR* 3.8 3.6 - - - -
159B HIS* 2.8 48.8 + + + +
160B GLY 4.3 0.2 - - - +
163B LYS 5.4 4.3 - - - +
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Residues in contact with VAL 156 (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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139B ALA 4.9 5.8 - - - +
140B PHE* 4.0 20.9 - - + -
143B ASP* 5.8 3.6 - - - +
152B ASN* 2.9 24.1 + - + +
153B ILE* 3.8 3.6 - - - +
155B TYR* 1.3 68.6 - - + +
157B ILE* 1.3 66.2 + - - +
160B GLY* 3.0 34.9 + - - +
161B GLU* 4.1 14.8 - - + +
163B LYS 3.2 25.6 - - - +
823M PHE* 3.6 19.7 - - + -
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Residues in contact with ILE 157 (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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97B ILE* 3.7 42.2 - - + -
101B PHE* 5.6 0.2 - - + -
140B PHE* 3.3 32.5 - - + -
153B ILE* 3.1 18.5 + - + +
154B CYS* 3.1 20.9 - - - +
156B VAL* 1.3 78.2 - - - +
158B THR* 1.3 60.5 + - - +
819M ASN* 4.8 13.5 - - + +
820M VAL* 5.5 7.2 - - + +
823M PHE* 3.6 31.4 - - + +
832M MET* 5.5 1.7 - - - +
836M PHE* 3.8 14.0 - - - -
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Residues in contact with THR 158 (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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92B ASP 4.3 4.7 - - - +
93B PRO* 4.3 2.5 - - + -
94B GLU* 3.2 63.5 + - + +
97B ILE* 4.1 12.8 - - + -
154B CYS 3.1 14.7 + - - +
155B TYR 3.5 0.2 + - - -
157B ILE* 1.3 77.1 - - - +
159B HIS* 1.3 65.2 + - - +
160B GLY 3.8 0.4 - - - -
832M MET* 5.4 1.3 - - - +
835M PHE* 5.3 0.7 - - - -
836M PHE* 3.3 15.6 - - - -
839M LYS* 3.3 19.8 + - - +
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Residues in contact with HIS 159 (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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94B GLU* 2.9 36.9 + - - -
155B TYR* 2.8 33.4 + + + +
158B THR* 1.3 79.2 + - - +
160B GLY* 1.3 60.8 + - - +
163B LYS* 5.3 6.4 + - - -
836M PHE* 4.1 10.1 - - - +
839M LYS* 3.5 35.5 + - + -
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Residues in contact with GLY 160 (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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156B VAL* 3.0 34.9 + - - +
159B HIS* 1.3 77.3 - - - +
161B GLU* 1.3 61.4 + - - -
162B ASP 3.7 1.9 + - - -
163B LYS* 4.2 5.6 + - - +
836M PHE* 3.7 35.5 - - - -
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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