Contacts of the helix formed by residues 116 - 124 (chain A) in PDB entry 6HVD
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 VAL 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ALA* 1.3 73.3 - - - +
117A ASP* 1.3 64.6 + - - +
119A VAL* 3.1 3.8 + - - +
120A MET* 3.1 24.5 + - + +
127A LEU* 4.0 15.5 - - + -
135A VAL* 4.9 4.3 - - + -
158A ALA* 3.4 12.9 + - + +
161A ILE* 2.9 41.5 + - + +
163A PHE* 3.7 36.1 - - + -
169A ILE* 4.9 0.2 - - + -
228A MET* 3.9 32.1 - - + -
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Residues in contact with ASP 117 (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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115A ALA* 3.4 10.4 - - - +
116A VAL* 1.3 78.9 - - - +
118A ALA* 1.3 77.7 + - - +
120A MET* 3.3 15.5 + - + +
121A LEU* 3.0 38.4 + - + +
158A ALA* 3.5 9.9 + - + -
159A GLY* 3.3 33.7 + - - +
227A GLU* 4.1 9.9 - - - +
231A ILE 5.8 0.9 - - - +
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Residues in contact with ALA 118 (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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114A GLY* 5.8 0.4 - - - -
115A ALA* 3.2 19.2 + - + +
117A ASP* 1.3 86.5 + - - +
119A VAL* 1.3 58.9 + - + +
121A LEU* 3.3 11.2 + - - +
122A GLU* 2.8 30.6 + - - +
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Residues in contact with VAL 119 (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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113A GLY 3.9 13.2 - - - +
114A GLY 5.0 0.2 - - - -
115A ALA 3.1 14.3 + - - +
116A VAL 3.1 7.4 + - - +
118A ALA* 1.3 76.6 - - + +
120A MET* 1.3 64.0 + - - +
122A GLU* 3.2 6.3 + - - +
123A LEU* 2.9 44.8 + - + +
127A LEU* 5.2 4.9 - - + -
163A PHE* 3.8 31.0 - - + -
303A LEU* 4.6 13.7 - - + -
304A ILE* 6.2 2.2 - - + -
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Residues in contact with MET 120 (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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116A VAL* 3.1 9.5 + - + +
117A ASP* 3.8 23.8 - - + +
119A VAL* 1.3 74.6 - - - +
121A LEU* 1.3 59.0 + - - +
123A LEU* 5.0 1.3 - - - -
124A GLU* 2.7 25.3 + - - -
125A ARG 3.1 24.4 + - - +
126A PRO* 3.9 8.5 - - - -
127A LEU* 3.5 25.8 - - + -
158A ALA* 4.3 11.7 - - + -
227A GLU* 3.7 18.8 - - + +
228A MET* 3.6 34.5 - - - +
231A ILE* 3.9 26.2 - - + +
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Residues in contact with LEU 121 (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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117A ASP* 3.0 30.9 + - + +
118A ALA* 3.8 7.6 - - - +
119A VAL 3.2 0.2 - - - -
120A MET* 1.3 74.8 - - - +
122A GLU* 1.3 65.2 + - - +
124A GLU* 3.2 20.9 + - - +
231A ILE* 4.1 22.2 - - + -
232A GLU* 5.4 6.3 - - - +
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Residues in contact with GLU 122 (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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118A ALA 2.8 18.9 + - - +
119A VAL* 3.2 6.7 + - - +
121A LEU* 1.3 78.5 - - - +
123A LEU* 1.3 71.0 + - + +
124A GLU* 3.6 2.8 + - - +
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Residues in contact with LEU 123 (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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119A VAL* 2.9 28.8 + - + +
120A MET* 4.4 1.6 - - - +
122A GLU* 1.3 87.1 - - + +
124A GLU* 1.3 70.6 + - - +
125A ARG* 3.3 28.5 + - + +
127A LEU* 6.6 0.2 - - + -
303A LEU* 3.9 28.7 - - + +
307A ALA* 5.0 21.3 - - + -
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Residues in contact with GLU 124 (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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120A MET 2.7 13.2 + - - -
121A LEU* 3.2 15.7 + - - +
122A GLU 4.8 2.0 - - - +
123A LEU* 1.3 79.1 - - - +
125A ARG* 1.3 58.4 + - - +
231A ILE* 4.2 9.3 - - - +
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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