Contacts of the helix formed by residues 135 - 142 (chain A) in PDB entry 1VDV
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 THR 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU 5.2 2.7 - - - +
134A PRO* 1.3 76.7 - - - +
136A VAL* 1.3 64.2 + - - +
137A GLU* 3.6 8.4 + - - +
138A GLU* 2.9 41.5 + - - +
139A ILE* 3.1 23.2 + - - +
164A ALA* 4.7 1.8 - - - -
165A LYS 5.5 0.7 - - - +
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Residues in contact with VAL 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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135A THR* 1.3 72.8 - - - +
137A GLU* 1.3 63.6 + - - +
139A ILE* 3.2 12.7 + - + +
140A GLU* 3.1 22.5 + - + +
161A ARG* 4.1 40.4 - - + +
164A ALA* 4.2 12.4 - - + +
554A PRO* 4.2 22.9 - - + -
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Residues in contact with GLU 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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135A THR* 3.1 9.0 + - - +
136A VAL* 1.3 81.0 - - - +
138A GLU* 1.3 58.2 + - + +
140A GLU* 3.3 6.3 + - - +
141A ASP* 2.9 40.2 + - - +
550A GLN* 5.5 4.8 + - - -
551A LYS* 3.6 46.5 + - + +
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Residues in contact with GLU 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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127A LEU* 3.5 21.4 - - + +
131A GLN* 4.0 14.4 - - - +
133A GLU 4.7 0.2 - - - +
134A PRO* 3.2 17.2 - - + +
135A THR* 2.9 45.3 + - - +
137A GLU* 1.3 76.1 - - + +
139A ILE* 1.3 61.8 + - - +
141A ASP* 3.9 7.8 - - - +
142A ALA* 3.1 17.0 + - - +
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Residues in contact with ILE 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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124A MET* 4.2 6.7 - - + -
127A LEU* 3.7 10.5 - - + -
134A PRO* 3.8 25.8 - - + -
135A THR 3.1 15.1 + - - +
136A VAL* 3.5 11.4 - - + +
138A GLU* 1.3 74.9 - - - +
140A GLU* 1.3 66.1 + - - +
142A ALA* 3.2 7.8 + - - +
143A PHE* 3.1 36.3 - - + -
157A LEU* 4.6 9.6 - - + +
160A PHE* 3.5 41.7 - - + +
161A ARG* 4.2 9.9 - - - +
164A ALA* 4.2 15.3 - - + +
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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 VAL* 3.1 15.6 + - + +
137A GLU* 3.3 9.3 + - - +
139A ILE* 1.3 76.4 - - - +
141A ASP* 1.3 67.0 + - - +
143A PHE* 3.1 21.5 + - - +
144A GLN* 4.2 1.0 + - - +
157A LEU* 4.1 29.7 - - + +
428A GLU* 4.8 2.8 - - - +
551A LYS* 4.5 25.5 - - - +
552A HIS 5.8 0.5 - - - +
554A PRO* 6.0 3.5 - - - +
1232A PHE* 4.9 12.2 - - + +
1233A GLY* 4.2 19.4 - - - +
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Residues in contact with ASP 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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137A GLU* 2.9 27.7 + - - +
138A GLU* 3.9 8.4 - - - +
139A ILE 3.3 0.2 - - - -
140A GLU* 1.3 80.3 - - - +
142A ALA* 1.3 61.0 + - - +
143A PHE 3.0 1.8 + - - -
144A GLN* 3.2 36.9 + - + +
340A LYS* 3.4 28.6 + - - +
551A LYS* 3.4 30.8 + - - -
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Residues in contact with ALA 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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123A SER* 3.7 32.1 + - - +
124A MET 5.1 0.2 - - - +
127A LEU* 4.0 19.3 - - + -
138A GLU 3.1 13.9 + - - +
139A ILE 3.3 13.2 - - - +
140A GLU 3.1 1.0 - - - -
141A ASP* 1.3 76.6 - - - +
143A PHE* 1.3 67.8 + - + +
144A GLN 3.6 1.2 + - - -
145A GLY 4.9 0.9 + - - -
146A ASN* 3.8 2.6 - - - +
340A LYS* 4.1 21.5 - - - +
341A GLN* 4.9 1.0 - - - +
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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