Contacts of the helix formed by residues 127 - 135 (chain D) in PDB entry 1VI9
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 GLY 127 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ALA* 3.5 20.8 - - - +
125D ALA 3.4 0.2 + - - -
126D PRO* 1.3 72.3 - - - +
128D VAL* 1.3 63.6 + - - +
129D ALA* 4.5 0.6 - - - +
130D GLU* 3.1 30.8 + - - +
131D PHE 3.1 17.3 + - - -
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Residues in contact with VAL 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.9 29.8 - - + +
86D SER* 3.6 35.0 - - - +
87D ALA* 3.7 5.2 - - - +
114D VAL 3.7 22.9 - - - +
124D VAL* 3.5 17.5 - - + -
125D ALA* 3.3 15.4 + - + +
126D PRO 3.3 0.4 - - - +
127D GLY* 1.3 75.8 - - - +
129D ALA* 1.3 64.1 + - - +
131D PHE* 3.2 12.9 + - - +
132D HIS* 3.3 25.0 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D MSE 3.8 37.4 - - + +
124D VAL* 5.3 1.4 - - - +
125D ALA 4.8 0.8 + - - -
127D GLY 3.2 0.6 - - - +
128D VAL* 1.3 78.2 - - - +
130D GLU* 1.3 71.9 + - - +
132D HIS* 3.2 13.2 + - - +
133D VAL* 3.3 18.6 + - - +
152D ILE* 4.8 9.4 - - + -
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLY* 3.1 34.8 + - - +
128D VAL 3.3 0.2 - - - -
129D ALA* 1.3 84.1 + - - +
131D PHE* 1.3 61.1 + - - +
133D VAL* 3.5 7.7 + - - +
134D ARG* 3.1 62.8 + - - +
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Residues in contact with PHE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 4.0 7.9 - - + -
87D ALA* 4.3 16.2 - - + -
90D GLY* 3.4 47.3 - - - -
91D GLU* 3.7 13.5 - - - +
93D ILE* 5.4 1.8 - - + -
94D LEU* 3.9 16.4 - - + -
109D TYR* 4.8 6.7 - - - -
127D GLY 3.1 12.4 + - - +
128D VAL* 3.2 8.0 + - + +
130D GLU* 1.3 77.3 - - - +
132D HIS* 1.3 87.4 + + - +
135D HIS* 2.8 55.8 + - + +
136D GLY* 2.9 23.3 + - - -
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Residues in contact with HIS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D SER* 4.9 3.6 - - - -
82D GLY 4.6 2.1 + - - -
84D LEU* 4.1 13.8 - - + +
111D CYS* 3.7 19.0 - - - -
112D ASP 4.4 3.4 - - - -
113D PRO* 3.7 40.3 - - + +
114D VAL 3.7 12.9 + - - -
115D MSE 3.9 16.4 - - + -
128D VAL* 3.3 30.6 + - + +
129D ALA 3.2 7.0 + - - +
131D PHE* 1.3 102.2 - + - +
133D VAL* 1.3 61.3 + - - +
136D GLY* 3.3 3.7 + - - +
137D LEU* 2.6 33.2 + - - +
153D LEU* 3.8 3.5 - - + +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D MSE 4.3 0.2 - - + -
129D ALA 3.3 14.3 + - - +
130D GLU* 3.7 9.4 - - - +
132D HIS* 1.3 79.8 - - - +
134D ARG* 1.3 75.5 + - + +
137D LEU* 3.9 16.6 - - - +
138D PRO* 4.0 2.6 - - - +
152D ILE* 3.6 39.9 - - + +
153D LEU* 3.6 21.7 - - + +
155D GLU* 4.3 19.5 - - - +
174D GLN* 5.5 0.7 - - - +
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU* 3.1 46.5 + - - +
133D VAL* 1.3 92.3 - - + +
135D HIS* 1.3 81.6 + - + +
138D PRO* 3.3 14.7 - - - +
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Residues in contact with HIS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLU* 5.3 5.2 + - - +
94D LEU* 3.6 25.4 - - + +
131D PHE* 2.8 32.2 + + + +
134D ARG* 1.3 94.3 - - + +
136D GLY* 1.3 66.7 + - - +
137D LEU 3.4 1.1 - - - -
138D PRO* 3.4 6.2 - - - +
139D ALA* 3.3 23.0 + - - +
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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