Contacts of the helix formed by residues 133 - 143 (chain A) in PDB entry 5V6Y
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PRO* 3.5 29.3 - - + +
129A LYS* 3.6 4.7 + - - +
130A THR* 2.7 44.3 + - - +
132A GLU* 1.3 76.5 - - - +
134A ILE* 1.3 61.6 + - - +
135A PRO 3.6 0.7 - - - -
136A ALA* 3.9 9.6 + - + +
137A LEU* 3.3 22.3 + - - +
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Residues in contact with ILE 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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128A PRO* 3.7 20.0 - - + -
130A THR 4.1 5.2 - - - +
131A TRP* 3.1 37.5 - - + +
133A GLU* 1.3 76.9 - - - +
135A PRO* 1.3 66.2 - - + +
137A LEU* 3.0 5.3 + - + +
138A ASP* 2.8 29.4 + - + +
148A ALA* 4.3 15.0 - - + -
149A LEU* 4.4 18.6 - - + -
196A PHE* 5.2 0.4 - - + -
200A LEU* 4.6 15.9 - - + -
205A HIS* 5.8 2.7 - - + -
206A MET* 6.5 0.7 - - + -
226A MET* 3.6 26.7 - - + -
250A PRO* 5.4 5.6 - - + -
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Residues in contact with PRO 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 TRP 4.0 2.2 - - - +
132A GLU 3.3 17.7 - - - +
133A GLU 3.8 0.2 - - - -
134A ILE* 1.3 94.3 - - + +
136A ALA* 1.3 60.6 + - - +
139A LYS* 3.2 20.8 + - - +
196A PHE* 4.4 7.4 - - + -
200A LEU* 3.8 21.5 - - + -
203A ASN* 5.9 1.6 - - - +
205A HIS* 3.3 36.7 - - + +
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Residues in contact with ALA 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 GLU 5.2 0.6 + - - +
133A GLU* 3.9 10.5 + - + +
134A ILE 3.3 0.8 - - - -
135A PRO* 1.3 80.7 - - - +
137A LEU* 1.3 60.5 + - - +
139A LYS* 3.6 7.5 + - - +
140A GLU* 3.3 19.8 + - - +
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Residues in contact with LEU 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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124A LEU* 3.6 39.3 - - + -
128A PRO* 4.1 23.1 - - + -
133A GLU 3.3 15.4 + - - +
134A ILE* 3.0 7.0 + - + +
136A ALA* 1.3 77.2 - - - +
138A ASP* 1.3 64.5 + - - +
140A GLU* 3.2 25.7 + - - +
141A LEU* 3.2 35.4 + - + +
148A ALA* 4.3 3.1 - - + -
225A ALA* 6.1 0.2 - - + -
226A MET* 4.4 12.6 - - + -
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Residues in contact with ASP 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 ILE* 2.8 15.9 + - + +
135A PRO 3.9 0.2 - - - +
137A LEU* 1.3 74.3 - - - +
139A LYS* 1.3 55.0 + - - +
141A LEU* 3.1 2.2 + - - +
142A LYS* 2.5 84.2 + - - +
147A SER* 3.4 2.3 - - - -
148A ALA* 2.9 37.3 + - + +
204A LYS 4.3 0.2 - - - +
205A HIS* 2.9 44.1 + - + +
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Residues in contact with LYS 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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135A PRO 3.2 16.5 + - - +
136A ALA* 3.8 8.1 - - - +
137A LEU 3.3 0.2 - - - -
138A ASP* 1.3 78.5 + - - +
140A GLU* 1.3 60.2 + - - +
142A LYS* 3.6 8.8 + - + +
143A ALA* 3.6 18.4 + - - +
205A HIS* 4.5 6.5 - - + -
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Residues in contact with GLU 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 ALA 3.3 10.4 + - - +
137A LEU* 3.2 29.3 + - - +
138A ASP 3.1 0.8 - - - -
139A LYS* 1.3 79.2 - - - +
141A LEU* 1.3 65.4 + - + +
143A ALA* 3.9 9.9 + - - +
144A LYS* 3.8 20.7 - - + +
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Residues in contact with LEU 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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123A LEU* 4.6 23.3 - - + +
124A LEU* 6.0 2.0 - - + -
137A LEU* 3.2 23.8 + - + +
138A ASP 3.1 5.9 + - - +
140A GLU* 1.3 81.0 - - + +
142A LYS* 1.3 62.5 + - - +
143A ALA 3.2 2.2 - - - -
144A LYS* 3.0 26.5 + - + +
146A LYS* 2.8 50.1 + - + +
147A SER 3.5 22.9 - - - +
148A ALA* 3.8 11.7 - - + -
225A ALA* 3.7 18.4 - - + -
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Residues in contact with LYS 142 (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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138A ASP* 2.5 67.6 + - - +
139A LYS* 3.9 9.4 - - + +
140A GLU 3.4 0.2 - - - -
141A LEU* 1.3 73.1 - - - +
143A ALA* 1.3 61.0 + - - +
145A GLY* 3.3 12.0 + - - -
146A LYS 3.3 11.4 - - - +
147A SER* 3.8 13.9 - - - -
204A LYS 3.8 20.1 + - - -
205A HIS* 3.9 5.8 + - + -
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Residues in contact with ALA 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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139A LYS 3.6 9.9 + - - +
140A GLU* 4.0 10.5 - - - +
141A LEU 3.2 0.8 - - - -
142A LYS* 1.3 78.9 - - - +
144A LYS* 1.3 60.5 + - + +
145A GLY 3.3 2.2 + - - -
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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