Contacts of the helix formed by residues 111 - 119 (chain B) in PDB entry 3VPO
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 LYS 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ASP* 4.8 10.4 + - - +
109B LEU 2.9 1.6 + - - -
110B SER* 1.3 101.5 + - - +
112B ASP* 1.3 63.5 + - - +
113B ILE* 3.5 2.4 + - - -
114B GLN* 4.1 6.7 + - - +
115B HIS* 3.1 28.9 + - + +
253B PRO* 4.4 17.5 - - + -
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Residues in contact with ASP 112 (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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108B ASP 4.3 2.9 - - - +
109B LEU* 3.0 19.6 + - - +
111B LYS* 1.3 79.0 + - - +
113B ILE* 1.3 56.3 + - + +
115B HIS* 3.1 6.8 + - - +
116B TRP* 2.8 35.5 + - - +
183B TYR* 2.5 40.0 + - + -
252B MET* 3.7 14.4 - - + +
253B PRO* 3.6 10.4 - - - +
254B GLY* 2.8 25.8 + - - -
255B LEU 3.0 17.0 + - - -
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Residues in contact with ILE 113 (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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109B LEU 3.5 21.1 - - - +
110B SER* 4.2 13.5 - - - +
112B ASP* 1.3 76.6 - - - +
114B GLN* 1.3 64.7 + - - +
116B TRP* 3.0 13.2 + - + +
117B GLU* 2.9 47.8 + - + +
182B THR* 4.3 31.4 - - + +
183B TYR* 5.3 3.1 - - + -
185B LYS* 6.2 1.6 - - - -
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Residues in contact with GLN 114 (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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111B LYS* 4.1 7.9 + - - +
112B ASP 3.4 0.6 - - - -
113B ILE* 1.3 77.0 - - - +
115B HIS* 1.3 71.0 + - + +
117B GLU* 3.5 10.8 + - - +
118B SER* 3.3 21.9 + - - -
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Residues in contact with HIS 115 (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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111B LYS* 3.1 24.9 + - + -
112B ASP 3.1 9.0 + - - +
114B GLN* 1.3 81.7 - - + +
116B TRP* 1.3 65.0 + - - +
118B SER* 3.1 22.3 + - - -
119B LEU* 3.3 13.9 - - - +
250B GLY 3.7 23.1 + - - -
251B LEU* 3.9 12.9 - - + +
252B MET* 3.8 30.7 - - + +
253B PRO* 4.4 12.5 - - + +
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Residues in contact with TRP 116 (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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112B ASP 2.8 16.6 + - - +
113B ILE* 3.0 15.5 + - + +
115B HIS* 1.3 74.0 - - - +
117B GLU* 1.3 70.5 + - + +
119B LEU* 3.2 21.8 + - + +
124B ARG* 3.2 72.9 + - + +
127B ILE* 3.8 27.6 - - + -
128B SER* 4.2 11.2 - - - -
183B TYR* 3.1 59.3 + + + -
184B ILE* 3.9 17.6 - - + +
252B MET* 3.6 25.5 - - + -
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Residues in contact with GLU 117 (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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113B ILE* 2.9 38.6 + - + +
114B GLN* 4.0 9.1 - - - +
116B TRP* 1.3 82.1 - - + +
118B SER* 1.3 59.6 + - - +
119B LEU 3.8 1.0 - - - +
124B ARG* 3.3 15.1 + - - +
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Residues in contact with SER 118 (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 GLN* 3.3 16.0 + - - -
115B HIS* 3.1 16.0 + - - -
116B TRP 3.2 0.6 - - - -
117B GLU* 1.3 72.7 - - - +
119B LEU* 1.3 69.6 + - - +
120B LYS* 3.8 0.9 + - - +
251B LEU* 4.9 7.4 - - - +
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Residues in contact with LEU 119 (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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115B HIS 3.3 16.4 - - - +
116B TRP* 3.2 37.8 + - + +
117B GLU 3.8 1.2 - - - +
118B SER* 1.3 83.6 + - - +
120B LYS* 1.3 65.2 + - - +
121B PRO* 3.9 0.9 - - - +
123B GLU* 3.8 15.7 - - + +
124B ARG* 2.7 33.2 + - + +
127B ILE* 3.8 24.9 - - + -
246B LEU* 5.6 0.4 - - + -
249B ARG* 5.1 0.4 - - - +
251B LEU* 3.9 39.0 - - + -
252B MET* 3.9 6.7 - - + -
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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