Contacts of the helix formed by residues 110 - 117 (chain D) in PDB entry 1V8O
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 ASP 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ARG* 3.0 34.3 + - - +
49B LEU* 3.9 15.0 - - + +
8D ASP* 4.8 0.9 - - - +
10D SER* 3.8 3.6 + - - +
92D ASP* 4.0 11.0 - - - +
108D THR* 3.0 14.0 + - - +
109D GLN* 1.3 75.8 - - - +
111D ARG* 1.3 59.5 + - - +
112D GLU* 2.7 40.9 + - - +
113D LEU* 3.1 15.1 + - + +
114D LEU* 2.8 30.5 + - - +
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Residues in contact with ARG 111 (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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47B ALA 4.5 4.5 - - - +
48B ARG* 2.8 16.7 + - - +
49B LEU 3.5 3.6 + - - -
50B GLY* 3.0 39.0 + - - +
109D GLN* 2.6 36.8 + - - +
110D ASP* 1.3 71.0 - - - +
112D GLU* 1.3 64.5 + - - +
114D LEU* 3.4 17.3 + - - +
115D ALA* 3.0 25.1 + - - +
122D ASP* 3.6 28.7 + - - +
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Residues in contact with GLU 112 (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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84A VAL 4.8 5.0 - - - +
87A GLY* 4.1 21.7 - - - -
48B ARG* 3.4 37.5 + - - +
87D GLY 5.5 0.2 - - - +
88D LEU* 4.5 6.3 - - + -
92D ASP* 5.6 0.4 - - - +
110D ASP* 2.7 19.7 + - - +
111D ARG* 1.3 74.5 - - - +
113D LEU* 1.3 55.4 + - - +
115D ALA* 3.2 6.8 + - - +
116D LYS* 2.9 75.1 + - + +
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Residues in contact with LEU 113 (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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8D ASP* 3.9 20.9 - - - +
88D LEU* 4.3 11.9 - - + +
92D ASP* 3.4 58.1 - - + +
95D TYR* 4.3 11.9 - - + -
96D ALA* 3.9 10.3 - - + -
106D LEU* 3.9 10.1 - - + -
108D THR* 4.0 10.8 - - + +
110D ASP* 3.1 14.2 + - + +
112D GLU* 1.3 76.0 - - - +
114D LEU* 1.3 65.1 + - - +
116D LYS* 4.4 0.4 - - - +
117D THR* 2.7 53.0 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D THR* 3.8 29.8 - - + +
110D ASP 2.8 16.6 + - - +
111D ARG* 3.6 24.9 - - - +
113D LEU* 1.3 77.6 - - - +
115D ALA* 1.3 61.8 + - - +
117D THR 3.6 13.9 - - - +
120D ALA* 3.3 37.4 + - + +
121D ILE* 3.8 4.3 - - - +
122D ASP* 3.8 19.7 - - + +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D ARG 3.0 18.4 + - - +
112D GLU* 3.5 8.5 - - - +
114D LEU* 1.3 78.9 - - - +
116D LYS* 1.3 63.9 + - + +
117D THR 3.6 1.7 + - - +
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Residues in contact with LYS 116 (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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87A GLY 5.5 2.2 + - - -
116A LYS* 5.4 6.5 - - - +
86D ARG* 2.7 73.0 + - + +
87D GLY* 3.3 18.8 + - - -
88D LEU* 3.6 23.9 - - + +
96D ALA* 4.8 0.7 - - - +
112D GLU* 2.9 49.2 + - - +
113D LEU 3.3 1.5 + - - +
115D ALA* 1.3 80.1 - - + +
117D THR* 1.3 54.3 + - - +
118D LYS* 5.4 0.9 - - - -
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Residues in contact with THR 117 (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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96D ALA* 3.5 19.7 - - - +
99D ALA* 4.5 2.7 - - + -
100D GLU* 3.7 13.2 - - + +
106D LEU* 3.8 27.6 - - + -
113D LEU* 2.7 41.5 + - - +
114D LEU 3.6 8.8 - - - +
115D ALA 3.4 2.4 - - - +
116D LYS* 1.3 79.7 - - - +
118D LYS* 1.3 65.0 + - - +
119D GLY 3.0 9.9 + - - -
120D ALA* 3.3 15.3 + - + +
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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