Contacts of the helix formed by residues 133 - 144 (chain B) in PDB entry 3VPP
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 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B SER* 1.3 74.0 - - - +
134B TRP* 1.3 65.1 + - - +
135B HIS* 4.2 9.4 - - + +
136B THR* 3.4 29.1 + - - +
137B SER* 2.8 24.8 + - - -
174B TRP* 3.6 0.7 - - - -
224B CYS 3.6 8.3 - - - +
225B ASP* 3.5 28.0 - - - +
226B THR* 3.2 20.6 - - - +
227B TRP* 3.6 19.3 - - + +
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Residues in contact with TRP 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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133B ILE* 1.3 74.4 - - - +
135B HIS* 1.3 80.8 + + + +
137B SER* 3.2 3.8 + - - -
138B GLN* 3.0 21.1 + - + +
148B LEU* 3.5 10.7 - - + +
174B TRP* 3.5 42.4 - + + +
175B VAL 2.8 22.7 + - - -
176B GLY 4.1 4.5 - - - -
177B LEU 3.7 14.6 + - - -
178B SER* 4.0 17.0 - - - -
189B GLN* 3.2 47.3 - - + -
209B GLN* 5.1 6.1 - - - -
211B CYS* 3.4 31.4 - - + -
212B GLY 4.4 0.2 - - - -
224B CYS* 3.1 20.1 + - + +
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Residues in contact with HIS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 3.4 11.0 - - + +
134B TRP* 1.3 94.3 - + + +
136B THR* 1.3 63.0 + - - +
138B GLN* 3.2 9.5 + - + +
139B GLU* 3.0 58.4 + - - +
224B CYS* 4.9 0.8 + - - +
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Residues in contact with THR 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 SER* 3.8 15.9 - - - -
133B ILE* 3.4 29.7 + - - +
134B TRP 3.3 0.4 - - - -
135B HIS* 1.3 77.5 + - - +
137B SER* 1.3 55.6 + - - +
139B GLU* 3.1 11.5 + - + +
140B ASN* 2.8 43.1 + - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 2.7 24.6 + - - -
133B ILE 2.8 19.9 + - - -
134B TRP 3.4 5.8 - - - -
136B THR* 1.3 73.8 - - - +
138B GLN* 1.3 65.1 + - - +
140B ASN* 3.1 8.5 + - - +
141B CYS* 3.0 25.1 + - - -
148B LEU* 4.1 7.9 - - - -
174B TRP* 3.4 15.4 - - - -
230B PHE* 3.3 29.6 - - - -
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Residues in contact with GLN 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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134B TRP* 3.0 14.9 + - + +
135B HIS* 3.2 14.6 + - + +
137B SER* 1.3 77.2 - - - +
139B GLU* 1.3 57.4 + - - +
141B CYS* 3.1 3.2 + - - +
142B LEU* 2.9 58.9 + - + +
147B THR* 3.0 19.7 + - - -
148B LEU* 2.9 33.4 + - + +
189B GLN* 2.8 38.7 + - - +
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Residues in contact with GLU 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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135B HIS* 3.0 48.4 + - + +
136B THR* 3.4 12.1 - - + +
138B GLN* 1.3 76.3 - - + +
140B ASN* 1.3 64.7 + - - +
142B LEU* 3.2 24.8 + - - +
143B LYS* 3.1 37.7 + - - +
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Residues in contact with ASN 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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130B ILE* 4.1 12.1 - - - +
132B SER* 3.6 24.2 + - - -
136B THR* 2.8 27.3 + - - +
137B SER 3.1 7.6 + - - +
139B GLU* 1.3 77.1 - - - +
141B CYS* 1.3 63.2 + - - +
143B LYS* 3.3 27.3 + - - +
144B GLU* 3.5 17.2 - - - +
230B PHE* 3.6 25.1 - - + -
232B CYS* 4.7 1.1 - - - -
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Residues in contact with CYS 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 SER 3.0 18.4 + - - -
138B GLN 3.5 6.7 - - - +
140B ASN* 1.3 74.9 - - - +
142B LEU* 1.3 63.8 + - - +
144B GLU* 2.9 9.6 + - - -
146B SER* 2.8 33.1 + - - +
147B THR* 3.6 18.8 - - - -
148B LEU* 3.8 21.1 - - - +
230B PHE* 4.0 1.6 - - - -
232B CYS* 2.1 50.9 - - - -
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Residues in contact with LEU 142 (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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138B GLN* 2.9 41.9 + - + +
139B GLU* 3.2 31.2 + - - +
141B CYS* 1.3 77.2 - - - +
143B LYS* 1.3 61.3 + - - +
145B GLY* 3.0 13.9 + - - -
146B SER 3.4 15.5 - - - +
147B THR* 5.2 1.3 - - - +
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Residues in contact with LYS 143 (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 GLU* 3.1 27.6 + - - +
140B ASN* 3.5 23.6 - - - +
141B CYS 3.1 0.6 - - - -
142B LEU* 1.3 77.2 - - + +
144B GLU* 1.3 73.2 + - - +
145B GLY 3.3 1.4 + - - -
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Residues in contact with GLU 144 (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 TRP* 4.1 23.1 - - + -
140B ASN 3.5 14.2 - - - +
141B CYS* 2.9 6.8 + - - +
143B LYS* 1.3 96.6 - - - +
145B GLY* 1.3 63.6 + - - +
146B SER* 3.2 2.5 + - - +
232B CYS* 5.9 1.8 - - - -
234B LYS* 3.2 24.1 + - - +
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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