Contacts of the helix formed by residues 107 - 115 (chain A) in PDB entry 5Y7G
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 GLU 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR 4.1 0.8 + - - -
106A LEU* 1.3 76.2 - - - +
108A LEU* 1.3 76.2 + - - +
109A ALA* 3.2 10.3 - - - +
110A GLN* 3.1 31.2 + - + +
111A LEU* 3.2 10.0 + - - +
143A GLN* 3.1 24.8 + - - +
147A PRO 4.0 16.3 - - - +
149A ALA* 3.5 18.6 - - + +
155A TRP* 4.3 0.4 - - - -
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Residues in contact with LEU 108 (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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107A GLU* 1.3 76.9 - - - +
109A ALA* 1.3 63.7 + - - +
111A LEU* 3.2 14.5 + - + +
112A PHE* 3.2 25.1 + - + -
124A PHE* 3.5 33.7 - - + -
139A LEU* 3.5 14.1 - - + -
142A LEU* 3.4 34.1 - - + +
143A GLN* 3.1 29.2 - - - +
146A PHE* 3.5 19.3 - - + +
148A GLU 4.2 1.6 + - - -
155A TRP* 4.0 17.0 - - + -
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Residues in contact with ALA 109 (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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107A GLU* 3.2 9.6 - - - +
108A LEU* 1.3 79.2 - - - +
110A GLN* 1.3 64.1 + - + +
112A PHE* 3.1 18.0 + - - +
113A GLY* 3.6 3.5 + - - -
139A LEU* 3.7 28.5 - - + +
143A GLN* 4.1 10.6 + - - +
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Residues in contact with GLN 110 (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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72A THR* 5.7 4.8 - - - +
73A LEU* 4.0 22.7 - - + +
105A THR 3.9 6.2 - - - +
106A LEU* 3.6 17.1 - - + -
107A GLU* 3.1 33.9 + - + +
109A ALA* 1.3 77.0 - - + +
111A LEU* 1.3 61.2 + - - +
113A GLY* 2.9 19.0 + - - +
114A LEU* 3.3 16.2 + - - +
165A GLU* 6.0 0.4 + - - -
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Residues in contact with LEU 111 (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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106A LEU* 4.4 10.2 - - + +
107A GLU 3.2 10.7 + - - +
108A LEU* 3.2 9.6 + - + +
110A GLN* 1.3 75.3 - - - +
112A PHE* 1.3 64.0 + - - +
113A GLY 3.1 1.2 + - - -
114A LEU* 3.1 8.3 + - + +
115A LEU* 3.1 61.1 + - + +
120A LEU* 4.5 2.5 - - + -
123A LEU* 4.5 2.9 - - + -
124A PHE* 4.3 18.4 - - + -
152A LEU* 3.6 28.7 - - + -
155A TRP* 3.6 47.8 - - + +
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Residues in contact with PHE 112 (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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108A LEU* 3.2 23.5 + - + -
109A ALA 3.1 14.0 + - - +
110A GLN 3.0 1.0 - - - -
111A LEU* 1.3 77.2 - - - +
113A GLY* 1.3 57.1 + - - +
115A LEU 3.4 2.8 - - - +
120A LEU* 3.3 41.5 - - + -
124A PHE* 4.2 6.1 - + - -
135A LYS* 3.0 66.4 + - + -
138A LEU* 3.6 20.0 - - + -
139A LEU* 3.5 41.1 - - + -
142A LEU* 3.8 13.0 - - + -
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Residues in contact with GLY 113 (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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109A ALA 3.6 4.6 + - - -
110A GLN* 2.9 9.0 + - - -
112A PHE* 1.3 80.9 - - - +
114A LEU* 1.3 63.5 + - - +
115A LEU 3.5 3.3 + - - +
135A LYS* 4.9 1.9 + - - -
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Residues in contact with LEU 114 (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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73A LEU* 4.1 14.8 - - + +
74A PHE* 3.9 16.4 - - - +
75A ARG* 3.0 59.5 + - + +
78A LYS* 5.5 2.6 - - - -
106A LEU* 3.5 37.7 - - + -
110A GLN 3.3 10.9 + - - +
111A LEU* 3.1 7.7 + - + +
113A GLY* 1.3 80.3 - - - +
115A LEU* 1.3 69.1 + - + +
163A VAL* 3.9 15.3 - - + -
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Residues in contact with LEU 115 (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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75A ARG* 3.4 20.9 - - + +
111A LEU* 3.1 47.4 + - + +
112A PHE 3.4 5.7 - - - +
113A GLY 3.9 1.9 - - - +
114A LEU* 1.3 86.4 - - + +
116A LYS* 1.3 64.6 + - - +
119A GLU* 3.8 18.6 - - + +
120A LEU* 3.8 24.4 - - + +
123A LEU* 5.1 9.4 - - + -
135A LYS* 3.2 18.0 + - - -
152A LEU* 5.2 1.6 - - + -
156A GLN* 5.7 6.3 - - - +
159A PHE* 4.3 19.5 - - + -
163A VAL* 5.8 0.7 - - + -
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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